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Sample records for biased muca mutagenesis

  1. Simple sequence repeats and mucoid conversion: biased mucA mutagenesis in mismatch repair-deficient Pseudomonas aeruginosa.

    Directory of Open Access Journals (Sweden)

    Alejandro J Moyano

    Full Text Available In Pseudomonas aeruginosa, conversion to the mucoid phenotype marks the onset of an irreversible state of the infection in Cystic Fibrosis (CF patients. The main pathway for mucoid conversion is mutagenesis of the mucA gene, frequently due to -1 bp deletions in a simple sequence repeat (SSR of 5 Gs (G(5-SSR(426. We have recently observed that this mucA mutation is particularly accentuated in Mismatch Repair System (MRS-deficient cells grown in vitro. Interestingly, previous reports have shown a high prevalence of hypermutable MRS-deficient strains occurring naturally in CF chronic lung infections. Here, we used mucA as a forward mutation model to systematically evaluate the role of G(5-SSR(426 in conversion to mucoidy in a MRS-deficient background, with this being the first analysis combining SSR-dependent localized hypermutability and the acquisition of a particular virulence/persistence trait in P. aeruginosa. In this study, mucA alleles were engineered with different contents of G:C SSRs, and tested for their effect on the mucoid conversion frequency and mucA mutational spectra in a mutS-deficient strain of P. aeruginosa. Importantly, deletion of G(5-SSR(426 severely reduced the emergence frequency of mucoid variants, with no preferential site of mutagenesis within mucA. Moreover, although mutagenesis in mucA was not totally removed, this was no longer the main pathway for mucoid conversion, suggesting that G(5-SSR(426 biased mutations towards mucA. Mutagenesis in mucA was restored by the addition of a new SSR (C(6-SSR(431, and even synergistically increased when G(5-SSR(426 and C(6-SSR(431 were present simultaneously, with the mucA mutations being restricted to -1 bp deletions within any of both G:C SSRs. These results confirm a critical role for G(5-SSR(426 enhancing the mutagenic process of mucA in MRS-deficient cells, and shed light on another mechanism, the SSR- localized hypermutability, contributing to mucoid conversion in P

  2. 2004 Mutagenesis Gordon Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Sue Jinks-Robertson

    2005-09-16

    Mutations are genetic alterations that drive biological evolution and cause many, if not all, human diseases. Mutation originates via two distinct mechanisms: ''vertical'' variation is de novo change of one or few bases, whereas ''horizontal'' variation occurs by genetic recombination, which creates new mosaics of pre-existing sequences. The Mutagenesis Conference has traditionally focused on the generation of mutagenic intermediates during normal DNA synthesis or in response to environmental insults, as well as the diverse repair mechanisms that prevent the fixation of such intermediates as permanent mutations. While the 2004 Conference will continue to focus on the molecular mechanisms of mutagenesis, there will be increased emphasis on the biological consequences of mutations, both in terms of evolutionary processes and in terms of human disease. The meeting will open with two historical accounts of mutation research that recapitulate the intellectual framework of this field and thereby place the current research paradigms into perspective. The two introductory keynote lectures will be followed by sessions on: (1) mutagenic systems, (2) hypermutable sequences, (3) mechanisms of mutation, (4) mutation avoidance systems, (5) mutation in human hereditary and infectious diseases, (6) mutation rates in evolution and genotype-phenotype relationships, (7) ecology, mutagenesis and the modeling of evolution and (8) genetic diversity of the human population and models for human mutagenesis. The Conference will end with a synthesis of the meeting as the keynote closing lecture.

  3. Mutagenesis and Teratogenesis Section

    International Nuclear Information System (INIS)

    Progress is reported on research with mice in the areas of radioinduced and chemical mutagenesis, cytologic studies, radiation effects on DNA synthesis, radiation effects on germ cells, mutagenicity of coal-conversion products, and others. Research on Drosophila was concerned with mutagenesis and genetics of nucleases. Studies were conducted on hamster cells with regard to cytotoxicity and mutagenicity of alkylating agents, modification of the microtubule system, protein kinase activity, and others. Research on bacteria was concerned with effects of x radiation on bacteriophage of Haemophilus influenzae, x-ray induced DNA polymerase I-directed repair synthesis in Escherichia coli, transformation by DNA polymerase II in Bacillus subtilis, and others. Research on xenopus laevis was conducted in the areas of calcium-induced cleavage of oocytes, yolk degradation in explants, and others

  4. Lethal Mutagenesis of Bacteria

    OpenAIRE

    Bull, James J; Wilke, Claus O.

    2008-01-01

    Lethal mutagenesis, the killing of a microbial pathogen with a chemical mutagen, is a potential broad-spectrum antiviral treatment. It operates by raising the genomic mutation rate to the point that the deleterious load causes the population to decline. Its use has been limited to RNA viruses because of their high intrinsic mutation rates. Microbes with DNA genomes, which include many viruses and bacteria, have not been considered for this type of treatment because their low intrinsic mutatio...

  5. Genetic adaptation of Pseudomonas aeruginosa during chronic lung infection of patients with cystic fibrosis: strong and weak mutators with heterogeneous genetic backgrounds emerge in mucA and/or lasR mutants.

    Science.gov (United States)

    Ciofu, Oana; Mandsberg, Lotte F; Bjarnsholt, Thomas; Wassermann, Tina; Høiby, Niels

    2010-04-01

    During the chronic lung infection of patients with cystic fibrosis (CF), Pseudomonas aeruginosa can survive for long periods due to adaptive evolution mediated by genetic variation. Hypermutability is considered to play an important role in this adaptive evolution and it has been demonstrated that mutator populations are amplified in the CF lung by hitchhiking with adaptive mutations. Two of the genes that are frequently mutated in isolates from chronic infection are mucA and lasR. Loss-of-function mutations in these genes determine the phenotypic switch to mucoidy and loss of quorum sensing, which are considered hallmarks of chronic virulence. The aims of our study were to investigate (1) the genetic background of the P. aeruginosa subpopulations with non-mutator, weak or strong mutator phenotype and their dynamics during the chronic lung infection, and (2) the time sequence in which the hypermutable, mucoid and quorum-sensing-negative phenotypes emerge during chronic lung infection. For these purposes the sequences of mutS, mutL, uvrD, mutT, mutY and mutM anti-mutator genes as well as of mucA and lasR were analysed in 70 sequential P. aeruginosa isolates obtained from the respiratory secretions of 10 CF patients (one to three isolates per time point). Analysis of the genetic background of the mutator phenotype showed that mutS was the most commonly affected gene followed by mutL in isolates with strong mutator phenotype. The mutT, mutY, mutM genes were affected in isolates with low fold-changes in the mutation frequencies compared to the reference strain PAO1. Isolates with non-mutator, weak or strong mutator phenotype were represented at all time points showing co-existence of these subpopulations, which suggests parallel evolution of the various mutators in the different focal niches of infection in the CF lung. Mutations in mucA and lasR occurred earlier than mutations in the anti-mutator genes, showing that hypermutability is not a prerequisite for the

  6. Optimization of Combinatorial Mutagenesis

    Science.gov (United States)

    Parker, Andrew S.; Griswold, Karl E.; Bailey-Kellogg, Chris

    Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (stability, activity, immunogenicity, etc.). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries - a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 107 variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and

  7. Optimization of combinatorial mutagenesis.

    Science.gov (United States)

    Parker, Andrew S; Griswold, Karl E; Bailey-Kellogg, Chris

    2011-11-01

    Protein engineering by combinatorial site-directed mutagenesis evaluates a portion of the sequence space near a target protein, seeking variants with improved properties (e.g., stability, activity, immunogenicity). In order to improve the hit-rate of beneficial variants in such mutagenesis libraries, we develop methods to select optimal positions and corresponding sets of the mutations that will be used, in all combinations, in constructing a library for experimental evaluation. Our approach, OCoM (Optimization of Combinatorial Mutagenesis), encompasses both degenerate oligonucleotides and specified point mutations, and can be directed accordingly by requirements of experimental cost and library size. It evaluates the quality of the resulting library by one- and two-body sequence potentials, averaged over the variants. To ensure that it is not simply recapitulating extant sequences, it balances the quality of a library with an explicit evaluation of the novelty of its members. We show that, despite dealing with a combinatorial set of variants, in our approach the resulting library optimization problem is actually isomorphic to single-variant optimization. By the same token, this means that the two-body sequence potential results in an NP-hard optimization problem. We present an efficient dynamic programming algorithm for the one-body case and a practically-efficient integer programming approach for the general two-body case. We demonstrate the effectiveness of our approach in designing libraries for three different case study proteins targeted by previous combinatorial libraries--a green fluorescent protein, a cytochrome P450, and a beta lactamase. We found that OCoM worked quite efficiently in practice, requiring only 1 hour even for the massive design problem of selecting 18 mutations to generate 10⁷ variants of a 443-residue P450. We demonstrate the general ability of OCoM in enabling the protein engineer to explore and evaluate trade-offs between quality and

  8. Cell transformation and mutagenesis

    International Nuclear Information System (INIS)

    This chapter summarizes the studies of the dose-effect relationships of cell transformation and of mutation for heavy ions with various charges, velocities and LET values. In cell transformation studies, carbon particles consistently gave a higher frequency of transformation per viable cell than x rays. For the same cell line, the RBE is about the same for both cell killings and oncogenic transformation for a given quality of ionizing radiation. In cocarcinogenesis studies, neon irradiation showed an enhancement effect on the viral transformation of cells. To explain the enhanced transformation, it has been suggested that radiation produces strand breaks in cellular DNA that promote the attachment of viral genomes during DNA repair synthesis. In mutagenesis studies, high-LET heavy ions could not effectively induce ouabain resistant mutations

  9. Antimicrobials, stress and mutagenesis.

    Directory of Open Access Journals (Sweden)

    Alexandro Rodríguez-Rojas

    2014-10-01

    Full Text Available Cationic antimicrobial peptides are ancient and ubiquitous immune effectors that multicellular organisms use to kill and police microbes whereas antibiotics are mostly employed by microorganisms. As antimicrobial peptides (AMPs mostly target the cell wall, a microbial 'Achilles heel', it has been proposed that bacterial resistance evolution is very unlikely and hence AMPs are ancient 'weapons' of multicellular organisms. Here we provide a new hypothesis to explain the widespread distribution of AMPs amongst multicellular organism. Studying five antimicrobial peptides from vertebrates and insects, we show, using a classic Luria-Delbrück fluctuation assay, that cationic antimicrobial peptides (AMPs do not increase bacterial mutation rates. Moreover, using rtPCR and disc diffusion assays we find that AMPs do not elicit SOS or rpoS bacterial stress pathways. This is in contrast to the main classes of antibiotics that elevate mutagenesis via eliciting the SOS and rpoS pathways. The notion of the 'Achilles heel' has been challenged by experimental selection for AMP-resistance, but our findings offer a new perspective on the evolutionary success of AMPs. Employing AMPs seems advantageous for multicellular organisms, as it does not fuel the adaptation of bacteria to their immune defenses. This has important consequences for our understanding of host-microbe interactions, the evolution of innate immune defenses, and also sheds new light on antimicrobial resistance evolution and the use of AMPs as drugs.

  10. Shuttle mutagenesis: a method of transposon mutagenesis for Saccharomyces cerevisiae.

    OpenAIRE

    Seifert, H S; Chen, E Y; So, M; Heffron, F

    1986-01-01

    We have extended the method of transposon mutagenesis to the eukaryote, Saccharomyces cerevisiae. A bacterial transposon containing a selectable yeast gene can be transposed into a cloned fragment of yeast DNA in Escherichia coli, and the transposon insertion can be returned to the yeast genome by homologous recombination. Initially, the cloned yeast DNA fragment to be mutagenized was transformed into an E. coli strain containing an F factor derivative carrying the transposable element. The c...

  11. Comments on mutagenesis risk estimation

    International Nuclear Information System (INIS)

    Several hypotheses and concepts have tended to oversimplify the problem of mutagenesis and can be misleading when used for genetic risk estimation. These include: the hypothesis that radiation-induced mutation frequency depends primarily on the DNA content per haploid genome, the extension of this concept to chemical mutagenesis, the view that, since DNA is DNA, mutational effects can be expected to be qualitatively similar in all organisms, the REC unit, and the view that mutation rates from chronic irradiation can be theoretically and accurately predicted from acute irradiation data. Therefore, direct determination of frequencies of transmitted mutations in mammals continues to be important for risk estimation, and the specific-locus method in mice is shown to be not as expensive as is commonly supposed for many of the chemical testing requirements

  12. Molecular fundamentals of chromosomal mutagenesis

    International Nuclear Information System (INIS)

    Precise quantitative correlation between the yield of chromosome structure damages and the yield of DNA damages is shown when comparing data on molecular and cytogenetic investigations carried out in cultural Mammalia cells. As the chromosome structure damage is to be connected with the damage of its carcass structure, then it is natural that DNA damage in loop regions is not to affect considerably the structure, while DNA damage lying on the loop base and connected with the chromosome carcass is to play a determining role in chromosomal mutagenesis. This DNA constitutes 1-2% from the total quantity of nuclear DNA. If one accepts that damages of these regions of DNA are ''hot'' points of chromosomal mutagenesis, then it becomes clear why 1-2% of preparation damages in a cell are realized in chromosome structural damages

  13. Intergroup bias.

    Science.gov (United States)

    Hewstone, Miles; Rubin, Mark; Willis, Hazel

    2002-01-01

    This chapter reviews the extensive literature on bias in favor of in-groups at the expense of out-groups. We focus on five issues and identify areas for future research: (a) measurement and conceptual issues (especially in-group favoritism vs. out-group derogation, and explicit vs. implicit measures of bias); (b) modern theories of bias highlighting motivational explanations (social identity, optimal distinctiveness, uncertainty reduction, social dominance, terror management); (c) key moderators of bias, especially those that exacerbate bias (identification, group size, status and power, threat, positive-negative asymmetry, personality and individual differences); (d) reduction of bias (individual vs. intergroup approaches, especially models of social categorization); and (e) the link between intergroup bias and more corrosive forms of social hostility. PMID:11752497

  14. Hindsight Bias.

    Science.gov (United States)

    Roese, Neal J; Vohs, Kathleen D

    2012-09-01

    Hindsight bias occurs when people feel that they "knew it all along," that is, when they believe that an event is more predictable after it becomes known than it was before it became known. Hindsight bias embodies any combination of three aspects: memory distortion, beliefs about events' objective likelihoods, or subjective beliefs about one's own prediction abilities. Hindsight bias stems from (a) cognitive inputs (people selectively recall information consistent with what they now know to be true and engage in sensemaking to impose meaning on their own knowledge), (b) metacognitive inputs (the ease with which a past outcome is understood may be misattributed to its assumed prior likelihood), and (c) motivational inputs (people have a need to see the world as orderly and predictable and to avoid being blamed for problems). Consequences of hindsight bias include myopic attention to a single causal understanding of the past (to the neglect of other reasonable explanations) as well as general overconfidence in the certainty of one's judgments. New technologies for visualizing and understanding data sets may have the unintended consequence of heightening hindsight bias, but an intervention that encourages people to consider alternative causal explanations for a given outcome can reduce hindsight bias. PMID:26168501

  15. Photodynamic action of the methylene blue: mutagenesis and sinergism

    International Nuclear Information System (INIS)

    Two aspects of photodynamic therapy were studied: the associated mutagenesis and the interactions with physical agents, in order to increase its biological effects. The photodynamic action with methylene blue in the mutagenesis and sinergism is studied. (L.M.J.)

  16. Chicken models of retroviral insertional mutagenesis

    Czech Academy of Sciences Publication Activity Database

    Pečenka, Vladimír; Karafiát, Vít; Dvořák, Michal

    New York: Springer, 2011 - (Dupuy, A.; Largaespada, D.), s. 77-112 ISBN 978-1-4419-7655-0 R&D Projects: GA ČR GA301/09/1727 Institutional research plan: CEZ:AV0Z50520514 Keywords : insertional mutagenesis * chicken model * MAV retroviruses Subject RIV: EB - Genetics ; Molecular Biology

  17. Seed mutagenesis in Portulaca grandiflora (Hook)

    International Nuclear Information System (INIS)

    Betalain pigments have been used as natural additives. Despite their importance, the biochemistry and genetics of betalain synthesis remain relatively undetermined. Portulaca grandiflora represents an ideal material for genetic analysis. In the present work, seed mutagenesis was examined with a view to enhance the chance of detection of new genetic markers in this species

  18. Mechanisms of mutagenesis for lambda phage

    International Nuclear Information System (INIS)

    The principal experimental results are determination of the changes in DNA base sequence resulting from forward mutations in the cI (repressor) gene of lambda phage induced by various agents. For phage irradiated with ultraviolet light and assayed in lightly irradiated host cells to induce Weigle mutagenesis (targeted mutagenesis), two-thirds of the mutations are transitions. Most transitions seem to arise at the sites of Py(6-4)Pyo photoproducts, not at the more widely studied cyclobutane pyrimidine dimers. The other mutations induced by ultraviolet are equally divided among transversions, frameshifts and double mutation events. The latter, two closely spaced base changes or a base change plus a frameshift, should rarely revert and may be the deletions induced by ultraviolet which have been previously reported. Unirradiated phage assayed in host cells heavily irradiated with ultraviolet light (nontargeted mutagenesis) show mainly frameshift mutations. These frameshifts may arise from low intracellular activity of DNA polymerase I when the enzyme binds to host DNA damaged by irradiation of the cells. Mismatch repair greatly reduced the numbers of mutations from bromouracil (which induces transitions by base mispairing) and acridines which induce frameshifts at runs of G.C base pairs). Only when mismatch repair activity is saturated by the number of improperly stacked bases in the DNA does a high level of mutagenesis occur

  19. Chicken models of retroviral insertional mutagenesis

    Czech Academy of Sciences Publication Activity Database

    Pečenka, Vladimír; Karafiát, Vít; Dvořák, Michal

    New York : Springer, 2011 - (Dupuy, A.; Largaespada, D.), s. 77-112 ISBN 978-1-4419-7655-0 R&D Projects: GA ČR GA301/09/1727 Institutional research plan: CEZ:AV0Z50520514 Keywords : insertional mutagenesis * chicken model * MAV retroviruses Subject RIV: EB - Genetics ; Molecular Biology

  20. In vitro mutagenesis of chrysanthemum for breeding

    International Nuclear Information System (INIS)

    A protocol of in vitro mutagenesis for chrysanthemum was established. The 50% lethal dose (LD50) is about 5.0 kR for calli irradiation. Various growth, developmental, morphological, colour and abnormal shape mutations were identified in M1V4 generation. (author)

  1. Hormonal Factors of Anti-Mutagenesis Regulation

    OpenAIRE

    RZA, Mekhtizadeh Emin

    2009-01-01

    The genetic activity of phytohormones (Phs) was studied. The investigation was conducted with 4 plants (Allium fistulosum, Lycopersicon esculentum, Triticum aestivum, and Gossypium hirsutum). The action of Phs on plant genetic processes was evaluated by chromosome aberration testing. It was observed that the exogenic Phs exerted a stabilizing effect on spontaneous plant mutagenesis. The use of Phs before and after the action of mutagenic factors contributed to an increase in the anti-mutation...

  2. Mutagenesis and DNA repair in mammalian cells

    International Nuclear Information System (INIS)

    Two aspects of DNA damage and repair in mammalian cells were investigated. Using a lambda phage shuttle vector, a system was developed to study mutations arising in the DNA of mammalian cells. This system was used to determine the spectrum of mutations induced in cellular DNA by ultraviolet light. Also, the repair of base pair mismatches in DNA was studied by the development of a method to detect a DNA mismatch repair activity in extracts made from cultured human cells. In order to study mutations arising in mammalian cells, stable mouse L cell lines were established with multiple copies of lambda phage vector which contains the supF gene of E. coli as a target for mutagenesis. Rescue of viable phage from high molecular weight mouse cell DNA using lambda in vitro packaging extracts was efficient and yielded a negligible background of phage with mutations in the supF gene. From mouse cells exposed to 12 J/m2 of 254 nm ultraviolet (UV) light, 78,510 phage were rescued of which eight were found to have mutant supF genes. DNA sequence analysis of the mutants suggests that the primary site of UV mutagenesis in mammalian cells is at pyrimidine-cytosine (Py-C) sequences, and that the most frequent mutation at this site is a C to T transition

  3. Efficient multi-site-directed mutagenesis directly from genomic template

    Indian Academy of Sciences (India)

    Fengtao Luo; Xiaolan Du; Tujun Weng; Xuan Wen; Junlan Huang; Lin Chen

    2012-12-01

    In this article, the traditional multi-site-directed mutagenesis method based on overlap extension PCR was improved specifically for complicated templates, such as genomic sequence or complementary DNA. This method was effectively applied for multi-site-directed mutagenesis directly from mouse genomic DNA, as well as for combination, deletion or insertion of DNA fragments.

  4. Awareness Reduces Racial Bias

    OpenAIRE

    Pope, Devin G.; Price, Joseph; Wolfers, Justin

    2014-01-01

    Can raising awareness of racial bias subsequently reduce that bias? We address this question by exploiting the widespread media attention highlighting racial bias among professional basketball referees that occurred in May 2007 following the release of an academic study. Using new data, we confirm that racial bias persisted in the years after the study's original sample, but prior to the media coverage. Subsequent to the media coverage though, the bias completely disappeared. We examine poten...

  5. Homemade Site Directed Mutagenesis of Whole Plasmids

    Science.gov (United States)

    Laible, Mark; Boonrod, Kajohn

    2009-01-01

    Site directed mutagenesis of whole plasmids is a simple way to create slightly different variations of an original plasmid. With this method the cloned target gene can be altered by substitution, deletion or insertion of a few bases directly into a plasmid. It works by simply amplifying the whole plasmid, in a non PCR-based thermocycling reaction. During the reaction mutagenic primers, carrying the desired mutation, are integrated into the newly synthesized plasmid. In this video tutorial we demonstrate an easy and cost effective way to introduce base substitutions into a plasmid. The protocol works with standard reagents and is independent from commercial kits, which often are very expensive. Applying this protocol can reduce the total cost of a reaction to an eighth of what it costs using some of the commercial kits. In this video we also comment on critical steps during the process and give detailed instructions on how to design the mutagenic primers. PMID:19488024

  6. Radiation mutagenesis in selection of apple trees

    International Nuclear Information System (INIS)

    After X-radiation of grafts of antonovka apple trees, three groups of morphological mutants, namely, weak-, average- and violently-growing, have been revealed. Although the mutation spectrum has some indefinite character a dose of 6 kR causes, more frequently and in a greater number, the weak-growing mutants, and a dose of 2 kR, the violently-growing ones. Mutants of each group differ in the precociousness (precocious and latefruiting), type of fruiting (nospur and spur) and yield (high- and low-yielding). Using the method of radiation mutagenesis it is possible to rise the frequency and spectrum of somatic mutability of antonovka apple trees and to induce forms having valuable features

  7. Maximizing mutagenesis with solubilized CRISPR-Cas9 ribonucleoprotein complexes.

    Science.gov (United States)

    Burger, Alexa; Lindsay, Helen; Felker, Anastasia; Hess, Christopher; Anders, Carolin; Chiavacci, Elena; Zaugg, Jonas; Weber, Lukas M; Catena, Raul; Jinek, Martin; Robinson, Mark D; Mosimann, Christian

    2016-06-01

    CRISPR-Cas9 enables efficient sequence-specific mutagenesis for creating somatic or germline mutants of model organisms. Key constraints in vivo remain the expression and delivery of active Cas9-sgRNA ribonucleoprotein complexes (RNPs) with minimal toxicity, variable mutagenesis efficiencies depending on targeting sequence, and high mutation mosaicism. Here, we apply in vitro assembled, fluorescent Cas9-sgRNA RNPs in solubilizing salt solution to achieve maximal mutagenesis efficiency in zebrafish embryos. MiSeq-based sequence analysis of targeted loci in individual embryos using CrispRVariants, a customized software tool for mutagenesis quantification and visualization, reveals efficient bi-allelic mutagenesis that reaches saturation at several tested gene loci. Such virtually complete mutagenesis exposes loss-of-function phenotypes for candidate genes in somatic mutant embryos for subsequent generation of stable germline mutants. We further show that targeting of non-coding elements in gene regulatory regions using saturating mutagenesis uncovers functional control elements in transgenic reporters and endogenous genes in injected embryos. Our results establish that optimally solubilized, in vitro assembled fluorescent Cas9-sgRNA RNPs provide a reproducible reagent for direct and scalable loss-of-function studies and applications beyond zebrafish experiments that require maximal DNA cutting efficiency in vivo. PMID:27130213

  8. Protein engineering: single or multiple site-directed mutagenesis.

    Science.gov (United States)

    Hsieh, Pei-Chung; Vaisvila, Romualdas

    2013-01-01

    Site-directed mutagenesis techniques are invaluable tools in molecular biology to study the structural and functional properties of a protein. To expedite the time required and simplify methods for mutagenesis, we recommend two protocols in this chapter. The first method for single site-directed mutagenesis, which includes point mutations, insertions, or deletions, can be achieved by an inverse PCR strategy with mutagenic primers and the high-fidelity Phusion(®) DNA Polymerase to introduce a site-directed mutation with exceptional efficiency. The second method is for engineering multiple mutations into a gene of interest. This can be completed in one step by PCR with mutagenic primers and by assembling all mutagenized PCR products using the Gibson Assembly™ Master Mix. This method allows multiple nucleotides to be changed simultaneously, which not only saves time but also reagents compared to traditional methods of mutagenesis. PMID:23423897

  9. Symposium on molecular and cellular mechanisms of mutagenesis

    International Nuclear Information System (INIS)

    These proceedings contain abstracts only of the 21 papers presented at the Sympsoium. The papers dealt with molecular mechanisms of mutagenesis and cellular responses to chemical and physical mutagenic agents

  10. Effective mutagenesis of Arabidopsis by heavy ion beam-irradiation

    International Nuclear Information System (INIS)

    Full text: Arabidopsis researches frequently include the genetic approach, so efficient, convenient, and safe methods for mutagenesis are required. Currently, the most popular method for in house mutagenesis is application of EMS. Although this method is very effective, its base substitution-type mutations often gives leaky mutants with residual gene functions, leading some difficulty in understanding the corresponding gene functions. Heavy ion beam generated by accelerators gives highest energy transfer rates among known radiation-based mutagenesis methods including X ray, gamma ray, fast neutron, electron and proton irradiation. This feature is thought to give high frequency of the double strand break of genomic DNA and resultant short deletions, resulting frame shift-type mutations. At RIKEN Accelerator Research Facility (RARF, http://www.rarf.riken.go.jp/index-e.html), we have optimized conditions for effective mutagenesis of Arabidopsis regarding to ion species and irradiation dose, and achieved comparable mutation rates to the method with EMS. (author)

  11. Induced Mutagenesis for Crop Improvement in Bulgaria

    International Nuclear Information System (INIS)

    Experimental mutagenesis has been investigated and applied in crop breeding in various Bulgarian agricultural research institutes during the last half century. In this paper some major accomplishments achieved in Bulgaria are highlighted. Both, physical mutagens (mainly gamma rays) and chemical mutagens (mainly EMS, NMU, NEU), have been used and their proper doses have been established. According to the information available to the author, there are more than 76 new cultivars developed using induced mutants in Bulgaria, namely: barley (5), wheat (5), durum wheat (9), maize (26), sunflower (3), lentil (4), bean (2), pea (1), chickpea and vetch (2), soybean (5), tomato (6), pepper (4), cotton (2), tobacco (2). Some of the mutant cultivars such as maize hybrid Kneja 509 and durum wheat cultivar Gergana have become leading cultivars occupying up to 50% of the growing area of the crop concerned. In durum wheat, mutant cultivars have not only covered almost all the growing areas but also doubled the yield in the past 30 years. The achievements in mutation breeding programmes have also had a significant impact on the progress of genetic research by elucidating the underlying mechanisms of induced mutations and the training of many young researchers and university students through their involvement in various research projects. A number of mutant lines with novel characteristics and mutant cultivars of economical importance together with relevant techniques used in the development and characterization of those mutant lines/cultivars are described in this paper. (author)

  12. Mutagenesis for the domestication of Cuphea

    International Nuclear Information System (INIS)

    Cuphea is a herbaceous summer annual plant native to Central America. Its seed oil contains high amounts of medium chain fatty acids, depending on the species with C8, C10 and C12, respectively, amounting to sometimes more than 80% of the total fatty acids. The report summarizes over 10 years' research on the domestication of this genus. From extensive tests on the production potentials, some of these on a worldwide scale, a few most promising genotypes of the section Heterodon have been selected from among 45 species and 180 accessions for further genetic improvements. Chemical mutagenesis was effective in promoting the domestication programme and mutants have been obtained with, e.g. non-sticky hairiness, monoculm stem, and determinate growth by stem fasciation. However, the most desired mutation to indehiscent fruits has not yet been discovered within the selected productive Cuphea species. This problem of early seed dispersal in Cuphea may alternatively necessitate technical solutions, which also have been developed with a vacuum picking machine for multiple harvests. From the findings presented, some general considerations are deduced regarding the mutability of traits characterizing interspecific variation as well as regarding the need for improving the genetic background of mutants by recurrent selection procedures. (author). 17 refs, 2 figs, 9 tabs

  13. Generating Novel Allelic Variation Through Activator Insertional Mutagenesis in Maize

    OpenAIRE

    Bai, Ling; Singh, Manjit; Pitt, Lauren; Sweeney, Meredith; Brutnell, Thomas P.

    2007-01-01

    The maize transposable element Activator (Ac) has been exploited as an insertional mutagen to disrupt, clone, and characterize genes in a number of plant species. To develop an Ac-based mutagenesis platform for maize, a large-scale mutagenesis was conducted targeting the pink scutellum1 locus. We selected 1092 Ac transposition events from a closely linked donor Ac, resulting in the recovery of 17 novel ps1 alleles. Multiple phenotypic classes were identified corresponding to Ac insertions in ...

  14. Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice

    OpenAIRE

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2016-01-01

    Recent reports of CRISPR- (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) mediated heritable mutagenesis in plants highlight the need for accuracy of the mutagenesis directed by this system. Off-target mutations are an important issue when considering functional gene analysis, as well as the molecular breeding of crop plants with large genome size, i.e. with many duplicated genes, and where the whole-genome sequence is still lacking. In mammals, ...

  15. Fluorescent protein engineering by in vivo site-directed mutagenesis

    OpenAIRE

    Ceballos, Melvys Valledor; Hu, Qinghua; Schiller, Paul,; Myers, Richard S.

    2012-01-01

    In vivo site-directed mutagenesis by ssDNA recombineering is a facile method to change the color of fluorescent proteins without cloning. Two different starting alleles of GFP were targeted for mutagenesis: gfpmut3* residing in the E. coli genome and egfp carried by a bacterial/mammalian dual expression lentiviral plasmid vector. Fluorescent protein spectra were shifted by subtle modification of the chromophore region and residues interacting with the chromophore of the fluorescent protein. E...

  16. Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria.

    OpenAIRE

    Alexandro Rodríguez-Rojas; Olga Makarova; Uta Müller; Jens Rolff

    2015-01-01

    Pseudomonas aeruginosa is the causative agent of chronic respiratory infections and is an important pathogen of cystic fibrosis patients. Adaptive mutations play an essential role for antimicrobial resistance and persistence. The factors that contribute to bacterial mutagenesis in this environment are not clear. Recently it has been proposed that cationic antimicrobial peptides such as LL-37 could act as mutagens in P. aeruginosa. Here we provide experimental evidence that mutagenesis is the ...

  17. Involvement of a joker mutation in a polymerase-independent lethal mutagenesis escape mechanism.

    Science.gov (United States)

    Agudo, Rubén; de la Higuera, Ignacio; Arias, Armando; Grande-Pérez, Ana; Domingo, Esteban

    2016-07-01

    We previously characterized a foot-and-mouth disease virus (FMDV) with three amino acid replacements in its polymerase (3D) that conferred resistance to the mutagenic nucleoside analogue ribavirin. Here we show that passage of this mutant in the presence of high ribavirin concentrations resulted in selection of viruses with the additional replacement I248T in 2C. This 2C substitution alone (even in the absence of replacements in 3D) increased FMDV fitness mainly in the presence of ribavirin, prevented an incorporation bias in favor of A and U associated with ribavirin mutagenesis, and conferred the ATPase activity of 2C decreased sensitivity to ribavirin-triphosphate. Since in previous studies we described that 2C with I248T was selected under different selective pressures, this replacement qualifies as a joker substitution in FMDV evolution. The results have identified a role of 2C in nucleotide incorporation, and have unveiled a new polymerase-independent mechanism of virus escape to lethal mutagenesis. PMID:27136067

  18. The disparity mutagenesis model predicts rescue of living things from catastrophic errors

    Directory of Open Access Journals (Sweden)

    Mitsuru eFurusawa

    2014-12-01

    Full Text Available In animals including humans, mutation rates per generation will exceed a perceived threshold, which should result in an excessive genetic load. Despite this, they have survived without extinction. This is a perplexing problem for human genetics, arising at the end of the last century, and to date still does not have a fully satisfactory explanation. Shortly after we proposed the disparity theory of evolution in 1992, the disparity mutagenesis model was proposed, which forms the basis for an explanation for an acceleration of evolution and species survival. This model predicts a significant increase of the mutation threshold values if there is a high enough fidelity difference in replication between the lagging and leading strands. When applied to biological evolution, the model predicts that living things, including humans, might overcome the lethal effect of accumulated deleterious mutations and be able to survive. Artificially-prepared mutator strains of microorganisms, in which an enhanced lagging-strand-biased mutagenesis was introduced, showed unexpectedly high adaptability to severe environments. The implications of the striking behaviors shown by these disparity mutators will be discussed in relation to how living things with high mutation rates can avoid the self-defeating risk of excess mutations.

  19. [Rapid site-directed mutagenesis on full-length plasmid DNA by using designed restriction enzyme assisted mutagenesis].

    Science.gov (United States)

    Zhang, Baozhong; Ran, Duoliang; Zhang, Xin; An, Xiaoping; Shan, Yunzhu; Zhou, Yusen; Tong, Yigang

    2009-02-01

    To use the designed restriction enzyme assisted mutagenesis technique to perform rapid site-directed mutagenesis on double-stranded plasmid DNA. The target amino acid sequence was reversely translated into DNA sequences with degenerate codons, resulting in large amount of silently mutated sequences containing various restriction endonucleases (REs). Certain mutated sequence with an appropriate RE was selected as the target DNA sequence for designing mutation primers. The full-length plasmid DNA was amplified with high-fidelity Phusion DNA polymerase and the amplified product was 5' phosphorylated by T4 polynucleotide kinase and then self-ligated. After transformation into an E. coli host the transformants were rapidly screened by cutting with the designed RE. With this strategy we successfully performed the site-directed mutagenesis on an 8 kb plasmid pcDNA3.1-pIgR and recovered the wild-type amino acid sequence of human polymeric immunoglobulin receptor (pIgR). A novel site-directed mutagenesis strategy based on DREAM was developed which exploited RE as a rapid screening measure. The highly efficient, high-fidelity Phusion DNA polymerase was applied to ensure the efficient and faithful amplification of the full-length sequence of a plasmid of up to 8 kb. This rapid mutagenesis strategy avoids using any commercial site-directed mutagenesis kits, special host strains or isotopes. PMID:19459340

  20. Improvement of soybean variety 'Bragg' through mutagenesis

    International Nuclear Information System (INIS)

    Full text: Variety 'Bragg' (Jackson x D49-2491) of soybean (Glycine max. (L.) Merrill) was found to be high yielding and widely adaptable throughout India. Its yield stability, however, is unsatisfactory, probably due to low germinability necessitating use of higher seed rate. With the main objective to rectify this defect, mutagenesis involving chemical as well as physical mutagens was used. Dry seeds were treated with EMS or MMS (0.2, 0.4 and 0.6%), or gamma rays (15, 20 and 25 kR) with and without additional exposure to UV (2 hrs at 260 nm) in 1982. In M2, a mutation frequency ranging from 2.24 to 22.85% was observed. Screening of M2 and of subsequent generations yielded a broad spectrum of mutations. Some of the mutants are agronomically useful. Among them, mutant 'T214' resulting from 25 kR gamma rays + UV, was found to possess better germinability (+15%), earliness (5 days) and high yield during both rainy and post-rainy seasons in 1986 and 1987, when compared with the parent variety 'Bragg'. The mutant has smaller seed-size (TGW 125 g) than the parent (145 g). In soybean, large-seeded varieties were reported to have poorer seed germinability. Thus, the better germinability of the mutant might be related to its reduced seed size. Seeds of the mutant show a light brown colour of the hilum in contrast to the black hilum of 'Bragg'. In other characters the mutant is similar to 'Bragg'. The mutant should have potential for commercial cultivation in India. For confirmation of its agronomically superior performance, it is undergoing national evaluation in multilocational trials under 'All India Co-ordinated Research Project on Soybean (ICAR)'. The strain has been named 'NRC-2'. (author)

  1. Mutagenesis as a breeding method in lentil

    International Nuclear Information System (INIS)

    Full text: Mutagenesis was used to develop cultivars with good adaptability to exogenous factors and with increased productivity. By means of this alternative breeding procedure, increases in biological and nutritive value of the seeds were studied. To increase genetic variability in lentil (Lens culinaris Medic.) breeding material, experimental mutagenesis was applied parallel to conventional breeding methods. The aim was to characterize the mutant lines as well as determine whether some of them could be directly registered as cultivars or as gene donors in breeding programme. Within the period 1993-1996, eight mutant lentil lines were studied under field conditions. They were obtained as a result of gamma rays (60Co) and ethyl methanesulfonate (EMS) treatment of the small seeded cultivar 'Tadjikskaya 95'. Air-dried seeds were treated. During the vegetative stage, phenological observation was made. The structural elements of productivity were established by biometrical analysis of 25-30 plants from each of the variants. Phytopathological evaluations were made using the scoring procedure established by ICARDA. Protein content was determined by the Kiejdhal method. The technological qualities of the seeds were determined using the method of Tretyakova and Ustinova. The mutant lines differed considerably in their biological traits from the parent cultivar. The vegetative period ranged from 84 to 89 days. The mutant lines were latermaturing than parent variety Tadjikskaya 95 by 1-5 days. As a result of mutagen treatment, the range in plant height was expanded from 1 to 8.3 cm. Line 96-8, obtained after irradiation with gamma rays, was the tallest (40.3 cm). Lodging of the mutant lines was greater than that of the initial cultivar and ranged from 20.0 to 66.7%. The trait varied to a great extent depending on environmental conditions. Mutagenic treatments also caused changes in seed size and seed coat colour. Development of resistance to important diseases of lentil in

  2. Effective Expression-Independent Gene Trapping and Mutagenesis Mediated by Sleeping Beauty Transposon

    Institute of Scientific and Technical Information of China (English)

    Guili Song; Qing Li; Yong Long; Perry B. Hackett; Zongbin Cui

    2012-01-01

    Expression-independent gene or polyadenylation [poly(A)] trapping is a powerful tool for genome-wide mutagenesis regardless of whether a targeted gene is expressed.Although a number of poly(A)-trap vectors have been developed for the capture and mutation of genes across a vertebrate genome,further efforts are needed to avoid the 3′-terminal insertion bias and the splice donor (SD)read-through,and to improve the mutagenicity.Here,we present a Sleeping Beauty (SB) transposon-based vector that can overcome these limitations through the inclusion of three functional cassettes required for gene-finding,gene-breaking and large-scale mutagenesis,respectively.The functional cassette contained a reporter/selective marker gene driven by a constitutive promoter in front of a strong SD signal and an AU-rich RNA-destabilizing element (ARE),which greatly reduced the SD read-through events,except that the internal ribosomal entry site (IRES) element was introduced in front of the SD signal to overcome the phenomenon of 3′-bias gene trapping.The breaking cassette consisting of an enhanced splicing acceptor (SA),a poly(A) signal coupled with a transcriptional terminator (TT) effectively disrupted the transcription of trapped genes.Moreover,the Hsp70 promoter from tilapia genome was employed to drive the inducible expression of SB11,which allows the conditional remobilization of a trap insert from a non-coding region.The combination of three cassettes led to effective capture and disruption of endogenous genes in HeLa cells.In addition,the Cre/LoxP system was introduced to delete the Hsp70-SB11 cassette for stabilization of trapped gene interruption and biosafety.Thus,this poly(A)-trap vector is an alternative and effective tool for identification and mutation of endogenous genes in cells and animals.

  3. Lagrangian bias in the local bias model

    International Nuclear Information System (INIS)

    It is often assumed that the halo-patch fluctuation field can be written as a Taylor series in the initial Lagrangian dark matter density fluctuation field. We show that if this Lagrangian bias is local, and the initial conditions are Gaussian, then the two-point cross-correlation between halos and mass should be linearly proportional to the mass-mass auto-correlation function. This statement is exact and valid on all scales; there are no higher order contributions, e.g., from terms proportional to products or convolutions of two-point functions, which one might have thought would appear upon truncating the Taylor series of the halo bias function. In addition, the auto-correlation function of locally biased tracers can be written as a Taylor series in the auto-correlation function of the mass; there are no terms involving, e.g., derivatives or convolutions. Moreover, although the leading order coefficient, the linear bias factor of the auto-correlation function is just the square of that for the cross-correlation, it is the same as that obtained from expanding the mean number of halos as a function of the local density only in the large-scale limit. In principle, these relations allow simple tests of whether or not halo bias is indeed local in Lagrangian space. We discuss why things are more complicated in practice. We also discuss our results in light of recent work on the renormalizability of halo bias, demonstrating that it is better to renormalize than not. We use the Lognormal model to illustrate many of our findings

  4. On commercial media bias

    OpenAIRE

    Germano, Fabrizio

    2008-01-01

    Within the spokes model of Chen and Riordan (2007) that allows for non-localized competition among arbitrary numbers of media outlets, we quantify the effect of concentration of ownership on quality and bias of media content. A main result shows that too few commercial outlets, or better, too few separate owners of commercial outlets can lead to substantial bias in equilibrium. Increasing the number of outlets (commercial and non-commercial) tends to bring down this bias; but the strong...

  5. Bias aware Kalman filters

    DEFF Research Database (Denmark)

    Drecourt, J.-P.; Madsen, H.; Rosbjerg, Dan

    2006-01-01

    This paper reviews two different approaches that have been proposed to tackle the problems of model bias with the Kalman filter: the use of a colored noise model and the implementation of a separate bias filter. Both filters are implemented with and without feedback of the bias into the model state...... illustrated on a simple one-dimensional groundwater problem. The results show that the presented filters outperform the standard Kalman filter and that the implementations with bias feedback work in more general conditions than the implementations without feedback. 2005 Elsevier Ltd. All rights reserved....

  6. 2012 MUTAGENESIS GORDON RESEARCH CONFERENCE, AUGUST 19-23, 2012

    Energy Technology Data Exchange (ETDEWEB)

    Demple, Bruce

    2012-08-23

    The delicate balance among cellular pathways that control mutagenic changes in DNA will be the focus of the 2012 Mutagenesis Gordon Research Conference. Mutagenesis is essential for evolution, while genetic stability maintains cellular functions in all organisms from microbes to metazoans. Different systems handle DNA lesions at various times of the cell cycle and in different places within the nucleus, and inappropriate actions can lead to mutations. While mutation in humans is closely linked to disease, notably cancers, mutational systems can also be beneficial. The conference will highlight topics of beneficial mutagenesis, including full establishment of the immune system, cell survival mechanisms, and evolution and adaptation in microbial systems. Equal prominence will be given to detrimental mutation processes, especially those involved in driving cancer, neurological diseases, premature aging, and other threats to human health. Provisional session titles include Branching Pathways in Mutagenesis; Oxidative Stress and Endogenous DNA Damage; DNA Maintenance Pathways; Recombination, Good and Bad; Problematic DNA Structures; Localized Mutagenesis; Hypermutation in the Microbial World; and Mutation and Disease.

  7. Sampler bias -- Phase 1

    International Nuclear Information System (INIS)

    This documents Phase 1 determinations on sampler induced bias for four sampler types used in tank characterization. Each sampler, grab sampler or bottle-on-a-string, auger sampler, sludge sampler and universal sampler, is briefly discussed and their physical limits noted. Phase 2 of this document will define additional testing and analysis to further define Sampler Bias

  8. Mutagenesis of Trichoderma Viride by Ultraviolet and Plasma

    Institute of Scientific and Technical Information of China (English)

    姚日生; 李曼曼; 邓胜松; 胡华佳; 王淮; 李凤和

    2012-01-01

    Considering the importance of a microbial strain capable of increased cellulase production, a mutant strain UP4 of Trichoderma viride was developed by ultraviolet (UV) and plasma mutation. The mutant produced a 21.0 IU/mL FPase which was 98.1% higher than that of the parent strain Trichoderma viride ZY-1. In addition, the effect of ultraviolet and plasma mutagenesis was not merely simple superimposition of single ultraviolet mutation and single plasma mutation. Meanwhile, there appeared a capsule around some of the spores after the ultraviolet and plasma treatment, namely, the spore surface of the strain became fuzzy after ultraviolet or ultraviolet and plasma mutagenesis.

  9. Genetic and physiological factors affecting repair and mutagenesis in yeast

    International Nuclear Information System (INIS)

    Current views of DNA repair and mutagenesis in the yeast Saccharomyces cerevisiae are discussed in the light of recent data and with emphasis on the isolation and characterization of genetically well-defined mutations that affect DNA metabolism in general (including replication and recombination). Various pathways of repair are described, particularly in relation to their imvolvement in mutagenic mechanisms. In addition to genetic control, certain physiological factors such as cell age, DNA replication, and the regulatory state of the mating-type locus are shown to also play a role in repair and mutagenesis

  10. Tissue culture regeneration and radiation induced mutagenesis in banana

    International Nuclear Information System (INIS)

    Radiation induced mutagenesis is an important tool for banana genetic improvement. At BARC, protocols for shoo-tip multiplication of commercial banana varieties have been developed and transferred to user agencies for commercial production. Excellent embryogenic cell suspensions were established in banana cvs. Rasthali and Rajeli, and were maintained at low temperatures for long-term storage. Normal plantlets were successfully regenerated from these cell suspensions. The cell suspensions and shoot-tip cultures were gamma-irradiated for mutagenesis. The mutagenized populations were field screened and a few interesting mutants have been isolated. The existence of genetic variation was confirmed using DNA markers. Further evaluation of these mutants is in progress. (author)

  11. Genetic and physiological factors affecting repair and mutagenesis in yeast

    International Nuclear Information System (INIS)

    Current views of DNA repair and mutagenesis in the yeast Saccharomyces cerevisiae are discussed in the light of recent data, and with emphasis on the isolation and characterization of genetically well-defined mutations that affect DNA metabolism in general (including replication and recombination). Various pathways of repair are described particularly in relation to their involvement in mutagenic mechanisms. In addition to genetic control, certain physiological factors such as cell age, DNA replication, and the regulatory state of the mating-type locus, are shown to also play a role in repair and mutagenesis

  12. A mariner transposon vector adapted for mutagenesis in oral streptococci

    DEFF Research Database (Denmark)

    Nilsson, Martin; Christiansen, Natalia; Høiby, Niels;

    2014-01-01

    ATs-pWV01, a selectable kanamycin resistance gene, a Himar1 transposase gene regulated by a xylose-inducible promoter, and an erythromycin resistance gene flanked by himar inverted repeats. The pMN100 plasmid was transformed into Streptococcus mutans UA159 and transposon mutagenesis was performed via a...... protocol established to perform high numbers of separate transpositions despite a low frequency of transposition. The distribution of transposon inserts in 30 randomly picked mutants suggested that mariner transposon mutagenesis is unbiased in S. mutans. A generated transposon mutant library containing...

  13. Heterologous overexpression and mutagenesis of the human bile salt export pump (ABCB11 using DREAM (Directed REcombination-Assisted Mutagenesis.

    Directory of Open Access Journals (Sweden)

    Jan Stindt

    Full Text Available Homologous recombination in Saccharomyces cerevisiae is a well-studied process. Here, we describe a yeast-recombination-based approach to construct and mutate plasmids containing the cDNA of the human bile salt export pump (BSEP that has been shown to be unstable in E. coli. Using this approach, we constructed the necessary plasmids for a heterologous overexpression of BSEP in the yeast Pichia pastoris. We then applied a new site-directed mutagenesis method, DREAM (Directed REcombination-Assisted Mutagenesis that completely bypasses E. coli by using S. cerevisiae as the plasmid host with high mutagenesis efficiency. Finally, we show how to apply this strategy to unstable non-yeast plasmids by rapidly turning an existing mammalian BSEP expression construct into a S. cerevisiae-compatible plasmid and analyzing the impact of a BSEP mutation in several mammalian cell lines.

  14. Harassment, Bias, and Discrimination.

    Science.gov (United States)

    Welliver, Paul W.

    1995-01-01

    Discusses a new principle which has been added to the AECT (Association for Educational Communications and Technology) Code of Professional Ethics regarding discrimination, harassment, and bias. An example is presented which illustrates a violation of a professional colleague's rights. (LRW)

  15. Simulating publication bias

    DEFF Research Database (Denmark)

    Paldam, Martin

    censoring: selection by the size of estimate; SR3 selects the optimal combination of fit and size; and SR4 selects the first satisficing result. The last four SRs are steered by priors and result in bias. The MST and the FAT-PET have been developed for detection and correction of such bias. The simulations...... are made by data variation, while the model is the same. It appears that SR0 generates narrow funnels much at odds with observed funnels, while the other four funnels look more realistic. SR1 to SR4 give the mean a substantial bias that confirms the prior causing the bias. The FAT-PET MRA works well...

  16. Introduction to Unconscious Bias

    Science.gov (United States)

    Schmelz, Joan T.

    2010-05-01

    We all have biases, and we are (for the most part) unaware of them. In general, men and women BOTH unconsciously devalue the contributions of women. This can have a detrimental effect on grant proposals, job applications, and performance reviews. Sociology is way ahead of astronomy in these studies. When evaluating identical application packages, male and female University psychology professors preferred 2:1 to hire "Brian” over "Karen” as an assistant professor. When evaluating a more experienced record (at the point of promotion to tenure), reservations were expressed four times more often when the name was female. This unconscious bias has a repeated negative effect on Karen's career. This talk will introduce the concept of unconscious bias and also give recommendations on how to address it using an example for a faculty search committee. The process of eliminating unconscious bias begins with awareness, then moves to policy and practice, and ends with accountability.

  17. Australia's Bond Home Bias

    OpenAIRE

    Mishra, Anil V; Umaru B. Conteh

    2014-01-01

    This paper constructs the float adjusted measure of home bias and explores the determinants of bond home bias by employing the International Monetary Fund's high quality dataset (2001 to 2009) on cross-border bond investment. The paper finds that Australian investors' prefer investing in countries with higher economic development and more developed bond markets. Exchange rate volatility appears to be an impediment for cross-border bond investment. Investors prefer investing in countries with ...

  18. Measuring agricultural policy bias

    DEFF Research Database (Denmark)

    Jensen, Henning Tarp; Robinson, Sherman; Tarp, Finn

    2010-01-01

    that the agricultural price incentive bias generally perceived to exist during the 1980s was largely eliminated during the 1990s. Results also demonstrate that general equilibrium effects and country-specific characteristics are crucial for determining the sign and magnitude of agricultural bias. Our comprehensive...... protection measure is therefore uniquely suited to capture the full impact of trade policies on relative agricultural price incentives....

  19. Publication bias in situ

    Directory of Open Access Journals (Sweden)

    Phillips Carl V

    2004-08-01

    Full Text Available Abstract Background Publication bias, as typically defined, refers to the decreased likelihood of studies' results being published when they are near the null, not statistically significant, or otherwise "less interesting." But choices about how to analyze the data and which results to report create a publication bias within the published results, a bias I label "publication bias in situ" (PBIS. Discussion PBIS may create much greater bias in the literature than traditionally defined publication bias (the failure to publish any result from a study. The causes of PBIS are well known, consisting of various decisions about reporting that are influenced by the data. But its impact is not generally appreciated, and very little attention is devoted to it. What attention there is consists largely of rules for statistical analysis that are impractical and do not actually reduce the bias in reported estimates. PBIS cannot be reduced by statistical tools because it is not fundamentally a problem of statistics, but rather of non-statistical choices and plain language interpretations. PBIS should be recognized as a phenomenon worthy of study – it is extremely common and probably has a huge impact on results reported in the literature – and there should be greater systematic efforts to identify and reduce it. The paper presents examples, including results of a recent HIV vaccine trial, that show how easily PBIS can have a large impact on reported results, as well as how there can be no simple answer to it. Summary PBIS is a major problem, worthy of substantially more attention than it receives. There are ways to reduce the bias, but they are very seldom employed because they are largely unrecognized.

  20. Information-aggregation bias

    OpenAIRE

    Goodfriend, Marvin

    1991-01-01

    Aggregation in the presence of data-processing lags distorts the information content of data, violating orthogonality restrictions that hold at the individual level. Though the phenomenon is general, it is illustrated here for the life-cycle-permanent-income model. Cross-section and pooled-panel data induce information-aggregation bias akin to that in aggregate time series. Calculations show that information aggregation can seriously bias tests of the life-cycle model on aggregate time series...

  1. Biased causal inseparable game

    CERN Document Server

    Bhattacharya, Some Sankar

    2015-01-01

    Here we study the \\emph{causal inseparable} game introduced in [\\href{http://www.nature.com/ncomms/journal/v3/n10/full/ncomms2076.html}{Nat. Commun. {\\bf3}, 1092 (2012)}], but it's biased version. Two separated parties, Alice and Bob, generate biased bits (say input bit) in their respective local laboratories. Bob generates another biased bit (say decision bit) which determines their goal: whether Alice has to guess Bob's bit or vice-verse. Under the assumption that events are ordered with respect to some global causal relation, we show that the success probability of this biased causal game is upper bounded, giving rise to \\emph{biased causal inequality} (BCI). In the \\emph{process matrix} formalism, which is locally in agreement with quantum physics but assume no global causal order, we show that there exist \\emph{inseparable} process matrices that violate the BCI for arbitrary bias in the decision bit. In such scenario we also derive the maximal violation of the BCI under local operations involving tracele...

  2. Gender Bias in Tax Systems

    OpenAIRE

    Janet Gale Stotsky

    1996-01-01

    This paper examines the nature of gender bias in tax systems. Gender bias takes both explicit and implicit forms. Explicit gender bias is found in many personal income tax systems. Several countries, especially those in Western Europe, have undertaken to eliminate explicit gender bias in recent years. It is more difficult to identify implicit gender bias, since this depends in large part on value judgments as to desirable social and economic behavior. Implicit gender bias has also been a targ...

  3. Methods for targetted mutagenesis in gram-positive bacteria

    Science.gov (United States)

    Yang, Yunfeng

    2014-05-27

    The present invention provides a method of targeted mutagenesis in Gram-positive bacteria. In particular, the present invention provides a method that effectively integrates a suicide integrative vector into a target gene in the chromosome of a Gram-positive bacterium, resulting in inactivation of the target gene.

  4. Mutagenesis and carcinogenesis caused by the oxidation of nucleic acids.

    OpenAIRE

    Nakabeppu, Yusaku; Sakumi, Kunihiko; Sakamoto, Katsumi; Tsuchimoto, Daisuke; Tsuzuki, Teruhisa; Nakatsu, Yoshimichi

    2006-01-01

    KEYWORDS CLASSIFICATION: adverse effects;Animals;chemistry;deficiency;DNA Damage;DNA Glycosylases;DNA Repair;DNA Repair Enzymes;Enzymes;genetics;Genomics;Guanine;Hydrolases;Intestinal Neoplasms;Japan;Liver Neoplasms;metabolism;mechanisms of carcinogenesis;Mice;Mutagenesis;Mutation;Neoplasms;Nucleic Acids;Oxidation-Reduction;Oxidative Stress;Phosphoric Monoester Hydrolases;Skin Neoplasms;Ultraviolet Rays.

  5. OneClick: A Program for Designing Focused Mutagenesis Experiments

    Directory of Open Access Journals (Sweden)

    Mark Warburton

    2015-07-01

    Full Text Available OneClick is a user-friendly web-based program, developed specifically for quick-and-easy design of focused mutagenesis experiments (e.g., site-directed mutagenesis and saturation mutagenesis. Written in Perl and developed into a web application using CGI programming, OneClick offers a step-by-step experimental design, from mutagenic primer design to analysis of a mutant library. Upon input of a DNA sequence encoding the protein of interest, OneClick designs the mutagenic primers according to user input, e.g., amino acid position to mutate, type of amino acid substitutions (e.g., substitution to a group of amino acids with similar chemical property and type of mutagenic primers. OneClick has incorporated an extensive range of commercially available plasmids and DNA polymerases suitable for focused mutagenesis. Therefore, OneClick also provides information on PCR mixture preparation, thermal cycling condition, expected size of PCR product and agar plate to use during bacterial transformation. Importantly, OneClick also carries out a statistical analysis of the resultant mutant library, information of which is important for selection/screening. OneClick is a unique and invaluable tool in the field of protein engineering, allowing for systematic construction of a mutant library or a protein variant and simplifying molecular biology work. The program will be constantly updated to reflect the rapid development in the fields of molecular biology and protein engineering.

  6. Investiation of viral mutagenesis in X-irradiated host cells

    International Nuclear Information System (INIS)

    The basic cellular mechanism of radiation-caused carcinogenesis is unknown. The induction by radiation of mutational changes in the genetic material (DNA) is believed to play a significant role in malignant transformation. It has been hypothesized that radiation-induced mutagenesis may occur as a result of induced mutagenic, or so-called error-prone, processes such as error-prone DNA synthesis and DNA repair. Abundant evidence indicates the presence of an inducible mutagenic repair system in the bacterium Escherichia coli. A similar inducible mutagenic repair system may exist in mammalian cells. Its apparent presence in uv-irradiated cells has been detected using an experimental system which involves utilization of herpes simplex virus (HSV) as a probe for DNA repair and mutagenesis in irradiated host monkey kidney cells. A system has been developed in which the production of HSV mutants capable of growing in the presence of 5'-iododeoxycytidine (ICdR) is used as a measure of viral mutagenicity. The purpose of this study was to use this mutagenesis system to determine whether x irradiation of host cells would lead to increased mutatgenesis of virus grown in these cells as compared with unirradiated cells. Attention is focused on mutagenesis of unirradiated virus in order to establish the existence of possible ionizing radiation-induced error-prone DNA synthesis

  7. Insertional mutagenesis using Tnt1 retrotransposon in potato

    Science.gov (United States)

    Potato is the third most important food crop in the world. However, genetics and genomics research of potato has lagged behind many major crop species due to its autotetraploidy and a highly heterogeneous genome. Insertional mutagenesis using T-DNA or transposable elements, which is available in sev...

  8. Carcinogen-specific mutations in preferred Ras-Raf pathway oncogenes directed by strand bias.

    Science.gov (United States)

    Keller, Ross R; Gestl, Shelley A; Lu, Amy Q; Hoke, Alicia; Feith, David J; Gunther, Edward J

    2016-08-01

    Carcinogen exposures inscribe mutation patterns on cancer genomes and sometimes bias the acquisition of driver mutations toward preferred oncogenes, potentially dictating sensitivity to targeted agents. Whether and how carcinogen-specific mutation patterns direct activation of preferred oncogenes remains poorly understood. Here, mouse models of breast cancer were exploited to uncover a mechanistic link between strand-biased mutagenesis and oncogene preference. When chemical carcinogens were employed during Wnt1-initiated mammary tumorigenesis, exposure to either 7,12-dimethylbenz(a)anthracene (DMBA) or N-ethyl-N-nitrosourea (ENU) dramatically accelerated tumor onset. Mammary tumors that followed DMBA exposure nearly always activated the Ras pathway via somatic Hras(CAA61CTA) mutations. Surprisingly, mammary tumors that followed ENU exposure typically lacked Hras mutations, and instead activated the Ras pathway downstream via Braf(GTG636GAG) mutations. Hras(CAA61CTA) mutations involve an A-to-T change on the sense strand, whereas Braf(GTG636GAG) mutations involve an inverse T-to-A change, suggesting that strand-biased mutagenesis may determine oncogene preference. To examine this possibility further, we turned to an alternative Wnt-driven tumor model in which carcinogen exposures augment a latent mammary tumor predisposition in Apc(min) mice. DMBA and ENU each accelerated mammary tumor onset in Apc(min) mice by introducing somatic, "second-hit" Apc mutations. Consistent with our strand bias model, DMBA and ENU generated strikingly distinct Apc mutation patterns, including stringently strand-inverse mutation signatures at A:T sites. Crucially, these contrasting signatures precisely match those proposed to confer bias toward Hras(CAA61CTA) versus Braf(GTG636GAG) mutations in the original tumor sets. Our findings highlight a novel mechanism whereby exposure history acts through strand-biased mutagenesis to specify activation of preferred oncogenes. PMID:27207659

  9. MtDNA mutagenesis impairs elimination of mitochondria during erythroid maturation leading to enhanced erythrocyte destruction

    NARCIS (Netherlands)

    Ahlqvist, K.J.; Leoncini, S.; Pecorelli, A.; Wortmann, S.B.; Ahola, S.; Forsstrom, S.; Guerranti, R.; Felice, C. De; Smeitink, J.; Ciccoli, L.; Hamalainen, R.H.; Suomalainen, A.

    2015-01-01

    Haematopoietic progenitor cells show special sensitivity to mitochondrial DNA (mtDNA) mutagenesis, which suggests that increased mtDNA mutagenesis could underlie anemias. Here we show that elevated mtDNA mutagenesis in mice with a proof-reading deficient mtDNA polymerase (PolG) leads to incomplete m

  10. Measuring Agricultural Bias

    DEFF Research Database (Denmark)

    Jensen, Henning Tarp; Robinson, Sherman; Tarp, Finn

    The measurement issue is the key issue in the literature on trade policy-induced agri-cultural price incentive bias. This paper introduces a general equilibrium effective rate of protection (GE-ERP) measure, which extends and generalizes earlier partial equilibrium nominal protection measures....... For the 15 sample countries, the results indicate that the agricultural price incentive bias, which was generally perceived to exist during the 1980s, was largely eliminated during the 1990s. The results also demonstrate that general equilibrium effects and country-specific characteristics - including trade...... shares and intersectoral linkages - are crucial for determining the sign and magnitude of trade policy bias. The GE-ERP measure is therefore uniquely suited to capture the full impact of trade policies on agricultural price incentives. A Monte Carlo procedure confirms that the results are robust...

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

    Directory of Open Access Journals (Sweden)

    Kentaro Ishida

    2015-10-01

    Full Text Available 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.

  12. Molecular techniques as complementary tools in orchid mutagenesis

    International Nuclear Information System (INIS)

    Orchid breeders have always been dependent on hybridization technology to produce new orchid hybrids and varieties. The technology has proven very reliable and easy to use and has produced wide range of successful cultivars with attractive combinations of spray length, bud number, flower colour and form, vase life, fragrance, seasonality, and compactness. By introducing mutagenesis however, wide variations of flower colours, form and size can still be obtained in addition to overcoming the problem of sexual incompatibility and sterility. In addition, complementary use of molecular techniques will allow breeders to target more specific characteristic changes and cut short breeding time. PCR-based techniques used to analyse the DNA of mutagenic clones found polymorphic fragments that can be developed as molecular markers. This paper describes how mutagenesis and molecular techniques can be used to enhance orchid breeding efforts. (author)

  13. Mouse Mutagenesis Using N-Ethyl-N-Nitrosourea (ENU)

    OpenAIRE

    sprotocols

    2014-01-01

    Authors: Andrew P. Salinger and Monica J. Justice1 Corresponding author ([]()) ### INTRODUCTION This protocol describes chemical mutagenesis of male mice using N-ethyl-N-nitrosourea (ENU), which is the most efficient method for obtaining mouse mutations in phenotype-driven screens. A fractionated dose of ENU, an alkylating agent, can produce a mutation rate as high as 1.5 × 10e−3 in male mouse spermatogonial stem cells. Treatment with ENU pr...

  14. Targeted mutagenesis using CRISPR/Cas system in medaka

    OpenAIRE

    Satoshi Ansai; Masato Kinoshita

    2014-01-01

    ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system-based RNA-guided endonuclease (RGEN) has recently emerged as a simple and efficient tool for targeted genome editing. In this study, we showed successful targeted mutagenesis using RGENs in medaka, Oryzias latipes. Somatic and heritable mutations were induced with high efficiency at the targeted genomic sequence on the DJ-1 gene in embryos that had been injected with the single guide RNA...

  15. Photodynamic action of methylene blue: mutagenesis and synergism

    International Nuclear Information System (INIS)

    The associated mutagenesis and the interactions with physical agents in order to potencialize its biological effects are studied. The induction of mutation in bacterias due to photodynamic action of methylene blue is presented as well as the induction of single breaks in bacterial DNA and the relationship between the repair systems, especially the SOS one. The interaction of the photodynamic therapy with low intensity electric current is discussed. (M.A.C.)

  16. Enhancing genetic diversity through induced mutagenesis in vegetatively propagated plants

    International Nuclear Information System (INIS)

    Conventionally, crop improvement strategies rely not only on the availability of heritable genetic variations within utilisable genetic backgrounds but also on the transferability of the traits they control through hybridizations between the parental stocks. Procedures for producing hybrids of sexually reproducing plants are routine while for vegetatively propagated plants, hybridizations are usually impractical. The improvement of crops that lack botanical seeds necessitate therefore alternative strategies for generating and utilizing genetic variations. Induced mutagenesis generates allelic variants of genes that modulate the expression of traits. Some of the major drawbacks to the widespread use of induced mutations for vegetatively propagated plants include the difficulties of heterozygosity of the genetic backgrounds; the incidence of chimeras; and the confounding effects of linkage drags in putative mutants. In general, the inherent inefficiencies of the economies of time and space associated with induced mutagenesis are further exacerbated in vegetatively propagated crops mostly on account of the need for continual propagation. We highlight the mitigating roles on these drawbacks of the judicious integration of validated biotechnologies and other high throughput forward genetics assays in induced mutagenesis pipelines. Using cassava and banana as models, we demonstrate the use of cellular and tissue biology to achieve homozygosity, minimise or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, the use of these biotechnologies to attain significantly reduced propagation footprints while evaluating putative mutants without compromising population size is also presented. We also posit that molecular biology approaches, especially reverse genetics and transcriptome assays, contributes significantly to enhancing the efficiency levels of the induced mutagenesis processes. The implications for crop improvement and

  17. Enhancing Genetic Diversity Through Induced Mutagenesis in Vegetatively Propagated Plants

    International Nuclear Information System (INIS)

    Conventionally, crop improvement strategies rely not only on the availability of heritable genetic variations within utilizable genetic backgrounds, but also on the transferability of the traits they control through hybridizations between the parental stocks. Procedures for producing hybrids of sexually reproducing plants are routine, while for vegetatively propagated plants, hybridizations are usually impractical. Therefore, the improvement of crops that lack botanical seeds necessitates alternative strategies for generating and utilizing genetic variations. Induced mutagenesis generates allelic variants of genes that modulate the expression of traits. Some of the major drawbacks to the widespread use of induced mutations for vegetatively propagated plants include the difficulties of heterozygosity of the genetic backgrounds, the incidence of chimeras and the confounding effects of linkage drags in putative mutants. In general, the inherent inefficiencies of time and space economies associated with induced mutagenesis are further exacerbated in vegetatively propagated crops mostly on account of the need for continual propagation. We highlight the mitigating roles on these drawbacks of judicious integration of validated biotechnologies and other high throughput forward genetics assays in induced mutagenesis pipelines. Using cassava and banana as models, we demonstrate the use of cell and tissue biology to achieve homozygosity, minimize or eliminate chimeras, and significantly shorten the duration of the generation of mutants. Additionally, use of these biotechnologies to attain significantly reduced propagation footprints while evaluating putative mutants without compromising population size is also presented. We also posit that molecular biology approaches, especially reverse genetics and transcriptome assays, contribute significantly to enhancing the efficiency levels of the induced mutagenesis processes. The implications for crop improvement and functional

  18. A Chemical Mutagenesis Screen Identifies Mouse Models with ERG Defects.

    Science.gov (United States)

    Charette, Jeremy R; Samuels, Ivy S; Yu, Minzhong; Stone, Lisa; Hicks, Wanda; Shi, Lan Ying; Krebs, Mark P; Naggert, Jürgen K; Nishina, Patsy M; Peachey, Neal S

    2016-01-01

    Mouse models provide important resources for many areas of vision research, pertaining to retinal development, retinal function and retinal disease. The Translational Vision Research Models (TVRM) program uses chemical mutagenesis to generate new mouse models for vision research. In this chapter, we report the identification of mouse models for Grm1, Grk1 and Lrit3. Each of these is characterized by a primary defect in the electroretinogram. All are available without restriction to the research community. PMID:26427409

  19. A role for ultraviolet A in solar mutagenesis.

    OpenAIRE

    Drobetsky, E A; Turcotte, J.; Châteauneuf, A

    1995-01-01

    It is well established that exposure to solar UVB (290-320 nm) gives rise to mutations in oncogenes and tumor suppressor genes that initiate the molecular cascade toward skin cancer. Although UVA (320-400 nm) has also been implicated in multistage photocarcinogenesis, its potential contribution to sunlight mutagenesis remains poorly characterized. We have determined the DNA sequence specificity of mutations induced by UVB (lambda > 290 nm), and by UVA (lambda > 350 nm), at the adenine phospho...

  20. Use of liver cell cultures in mutagenesis studies

    Energy Technology Data Exchange (ETDEWEB)

    Huberman, E.; Jones, C.A.

    1980-09-30

    A sensitive cell-mediated assay has been developed for testing the mutagenesis of liver carcinogens. Mutagenesis was detected in Chinese hamster V79 cells that were cocultivated with hepatocytes isolated after collagenase/hyaluronidase digestion of rat liver slices. Mutations were characterized by resistance to ouabain and 6-thioguanine. Seven of the nitrosamines, which are potent liver carcinogens, exhibited a mutagenic response. Mutagenesis with these carcinogens could be detected at ..mu..molar doses. The polyaromatic hydrocarbon benzo(a)pyrene, which is not a liver carcinogen, but can cause fibrosarcomas, was not mutagenic in this assay, but was mutagenic in a fibroblast-mediated assay. The liver carcinogen, aflatoxin B/sub 1/, which usually does not induce fibrosarcomas, exhibited an inverse situation; it was mutagenic for V79 cells in the presence of liver cells but not in the presence of fibroblasts. We suggest that the use of various cell types, including hepatocytes prepared by the slicing method for carcinogen metabolism, and mutable V79 cells offers a sensitive assay for determining the mutagenic potential of chemical carcinogens, and may also allow a study of their organ specificity.

  1. SOMA: a single oligonucleotide mutagenesis and cloning approach.

    Directory of Open Access Journals (Sweden)

    Thorsten Pfirrmann

    Full Text Available Modern biology research requires simple techniques for efficient and restriction site-independent modification of genetic material. Classical cloning and mutagenesis strategies are limited by their dependency on restriction sites and the use of complementary primer pairs. Here, we describe the Single Oligonucleotide Mutagenesis and Cloning Approach (SOMA that is independent of restriction sites and only requires a single mutagenic oligonucleotide to modify a plasmid. We demonstrate the broad application spectrum of SOMA with three examples. First, we present a novel plasmid that in a standardized and rapid fashion can be used as a template for SOMA to generate GFP-reporters. We successfully use such a reporter to assess the in vivo knock-down quality of morpholinos in Xenopus laevis embryos. In a second example, we show how to use a SOMA-based protocol for restriction-site independent cloning to generate chimeric proteins by domain swapping between the two human hRMD5a and hRMD5b isoforms. Last, we show that SOMA simplifies the generation of randomized single-site mutagenized gene libraries. As an example we random-mutagenize a single codon affecting the catalytic activity of the yeast Ssy5 endoprotease and identify a spectrum of tolerated and non-tolerated substitutions. Thus, SOMA represents a highly efficient alternative to classical cloning and mutagenesis strategies.

  2. Directed mutagenesis affects recombination in Azospirillum brasilense nif genes

    Directory of Open Access Journals (Sweden)

    C.P. Nunes

    2000-12-01

    Full Text Available In order to improve the gene transfer/mutagenesis system for Azospirillum brasilense, gene-cartridge mutagenesis was used to replace the nifD gene with the Tn5 kanamycin resistance gene. The construct was transferred to A. brasilense by electrotransformation. Of the 12 colonies isolated using the suicide plasmid pSUP202 as vector, only four did not show vector integration into the chromosome. Nevertheless, all 12 colonies were deficient in acetylene reduction, indicating an Nif- phenotype. Four Nif- mutants were analyzed by Southern blot, using six different probes spanning the nif and Km r genes and the plasmid vector. Apparently, several recombination events occurred in the mutant genomes, probably caused mainly by gene disruption owing to the mutagenesis technique used: resistance gene-cartridge mutagenesis combined with electrotransformation.Com o objetivo de melhorar os sistemas de transferência gênica e mutagênese para Azospirillum brasilense, a técnica de mutagênese através do uso de um gene marcador ("gene-cartridge mutagenesis" foi utilizada para substituir a região genômica de A. brasilense correspondente ao gene nifD por um segmento de DNA do transposon Tn5 contendo o gene que confere resistência ao antibiótico canamicina. A construção foi transferida para a linhagem de A. brasilense por eletrotransformação. Doze colônias transformantes foram isoladas com o plasmídeo suicida pSUP202 servindo como vetor. Dessas, somente quatro não possuíam o vetor integrado no cromossomo da bactéria. Independentemente da integração ou não do vetor, as 12 colônias foram deficientes na redução do gás acetileno, evidenciando o fenótipo Nif -. Quatro mutantes Nif - foram analisados através da técnica de Southern blot, utilizando-se seis diferentes fragmentos contendo genes nif, de resistência à canamicina e do vetor como sondas. Os resultados sugerem a ocorrência de eventos recombinacionais variados no genoma dos mutantes. A

  3. Heterologous Overexpression and Mutagenesis of the Human Bile Salt Export Pump (ABCB11) Using DREAM (Directed REcombination-Assisted Mutagenesis)

    OpenAIRE

    Jan Stindt; Philipp Ellinger; Claudia Stross; Verena Keitel; Dieter Häussinger; Smits, Sander H. J.; Ralf Kubitz; Lutz Schmitt

    2011-01-01

    Homologous recombination in Saccharomyces cerevisiae is a well-studied process. Here, we describe a yeast-recombination-based approach to construct and mutate plasmids containing the cDNA of the human bile salt export pump (BSEP) that has been shown to be unstable in E. coli. Using this approach, we constructed the necessary plasmids for a heterologous overexpression of BSEP in the yeast Pichia pastoris. We then applied a new site-directed mutagenesis method, DREAM (Directed REcombination-Ass...

  4. Temperature trend biases

    Science.gov (United States)

    Venema, Victor; Lindau, Ralf

    2016-04-01

    In an accompanying talk we show that well-homogenized national dataset warm more than temperatures from global collections averaged over the region of common coverage. In this poster we want to present auxiliary work about possible biases in the raw observations and on how well relative statistical homogenization can remove trend biases. There are several possible causes of cooling biases, which have not been studied much. Siting could be an important factor. Urban stations tend to move away from the centre to better locations. Many stations started inside of urban areas and are nowadays more outside. Even for villages the temperature difference between the centre and edge can be 0.5°C. When a city station moves to an airport, which often happened around WWII, this takes the station (largely) out of the urban heat island. During the 20th century the Stevenson screen was established as the dominant thermometer screen. This screen protected the thermometer much better against radiation than earlier designs. Deficits of earlier measurement methods have artificially warmed the temperatures in the 19th century. Newer studies suggest we may have underestimated the size of this bias. Currently we are in a transition to Automatic Weather Stations. The net global effect of this transition is not clear at this moment. Irrigation on average decreases the 2m-temperature by about 1 degree centigrade. At the same time, irrigation has increased significantly during the last century. People preferentially live in irrigated areas and weather stations serve agriculture. Thus it is possible that there is a higher likelihood that weather stations are erected in irrigated areas than elsewhere. In this case irrigation could lead to a spurious cooling trend. In the Parallel Observations Science Team of the International Surface Temperature Initiative (ISTI-POST) we are studying influence of the introduction of Stevenson screens and Automatic Weather Stations using parallel measurements

  5. Biased Range Trees

    CERN Document Server

    Dujmovic, Vida; Morin, Pat

    2008-01-01

    A data structure, called a biased range tree, is presented that preprocesses a set S of n points in R^2 and a query distribution D for 2-sided orthogonal range counting queries. The expected query time for this data structure, when queries are drawn according to D, matches, to within a constant factor, that of the optimal decision tree for S and D. The memory and preprocessing requirements of the data structure are O(n log n).

  6. Low Frequency Biasing

    OpenAIRE

    Kadelbach, Irmgard

    2003-01-01

    Die Elektrocochleographie (EcoG) ist eine der vielversprechendsten Methoden, cochleäre Dysfunktionen mit objektiver Diagnostik zu verifizieren. Erweitert durch das Prinzip des Biasings, also der gleichzeitigen Präsentation von Testtönen in einen niederfrequenten 52-Hz-Sinusdauerton, läßt sich die Funktion der Cochlea und eine möglicherweise pathologische Arbeitsweise aufdecken. In der Auswertung der Amplituden des Summationspotentials (SP), des cochleären Mikrophonpotentials (CM) und des Summ...

  7. Photoconductivity of biased graphene

    OpenAIRE

    Freitag, Marcus; Low, Tony; Xia, Fengnian; Avouris, Phaedon

    2012-01-01

    Graphene is a promising candidate for optoelectronic applications such as photodetectors, terahertz imagers, and plasmonic devices. The origin of photoresponse in graphene junctions has been studied extensively and is attributed to either thermoelectric or photovoltaic effects. In addition, hot carrier transport and carrier multiplication are thought to play an important role. Here we report the intrinsic photoresponse in biased but otherwise homogeneous graphene. In this classic photoconduct...

  8. Assessing Bias in Search Engines.

    Science.gov (United States)

    Mowshowitz, Abbe; Kawaguchi, Akira

    2002-01-01

    Addresses the measurement of bias in search engines on the Web, defining bias as the balance and representation of items in a collection retrieved from a database for a set of queries. Assesses bias by measuring the deviation from the ideal of the distribution produced by a particular search engine. (Author/LRW)

  9. Test Bias and the Elimination of Racism

    Science.gov (United States)

    Sedlacek, William E.

    1977-01-01

    Three types of test bias are discussed: content bias, atmosphere bias, and use bias. Use bias is considered the most important. Tests reflect the bias in society, and eliminating test bias means eliminating racism and sexism in society. A six-stage model to eliminate racism and sexism is presented. (Author)

  10. Tradescantia bioassays as monitoring systems for environmental mutagenesis: a review

    International Nuclear Information System (INIS)

    Since the early studies on the genetic effects of chemical and physical agents, species and clones of Tradescantia have been used as experimental subjects, by virtue of a series of favorable genetic characteristics. Bearing just six pairs (2n = 12) of large, easily observable chromosomes, cells from almost every part of the plant, from the root tips to the developing pollen tube, yield excellent material for cytogenetic studies. As a consequence of the intensive use of Tradescantia in genetic studies, a series of genetic characteristics have been found that offer opportunities for the detection of agents affecting the stability of the genome. At least five such characteristics have been selected as endpoints for the establishment of assays to evaluate mutagenesis. Three of these, root-tip mitosis, pollen-tube, and microspore mitosis are essentially chromosome aberration assays, wherein one observes and evaluates the visible damage in the chromosomes. A fourth, the stamen-hair mutation assay (Trad-SHM), is a point mutation mitotic assay based on the expression of a recessive gene for flower color in heterozygous plants. The fifth assay is a cytogenetic test based on the formation of micronuclei (Trad-MCN) that result from chromosome breakage in the meiotic pollen mother cells. This article examines the characteristics and fundamentals of the Trad-MCN and the Trad-SHM assays and reviews the results obtained to date with these systems in the assessment of environmental mutagenesis. (author)

  11. Tissue culture and mutagenesis of rain lily (zephyranthes)

    International Nuclear Information System (INIS)

    There are three varieties of Zephyranthes used widely in landscaping due to their robust growth and attractive flowers in pink, yellow and white. Both in vivo and in vitro mutagenesis are an effective approach to increase the flower colour variations of Zephyranthes. In vitro propagation for the three varieties was attempted by using the induction medium developed by Sachar and Kapoor in 1959. The medium contains I ma of each indole 3-acetic acid (IAA), indole 3-butyric acid (IBA) and kinetin. Following surface sterilization of bulb scales, 17.8%, 10.5% and 10.7% of pink, white and yellow varieties respectively, were able to form small bulblets on the induction media. Further development of these bulblets into plantlets was also achieved on the same medium. Work is now being carried out to improve the efficiency of bulblet regeneration. Mutagenesis of Zephyranthes was initiated from bulbs of the pink varieties to develop new varieties with attractive combinations of flower colour and forms, shelf life and growth habits. These bulbs were irradiated using a gamma cell with a 60Co source. Three variants with different flower colour and morphology have been achieved so far and are now being propagated in the nursery. (Author)

  12. In vitro mutagenesis of commercial fern, Asplenium nidus from spores

    International Nuclear Information System (INIS)

    Asplenium is a largest, most diverse fern genera. One of the common species is Asplenium nidus, well known as Bird's-nest fern, a medium to large fern with erect, stout, unbranched rhizomes. In creating variability of ferns for the benefit of the ornamental plant industry, in vitro mutagenesis is used. In this study, spores of Asplenium nidus were collected from frond bearing mature sporangia. Spores were cultured in modified 1/2 MS basal medium supplemented with various combinations of 6-Benzylaminopurine (BAP) and Naphtalene Acetic Acid (NAA). Spore cultures were incubated in incubation room at 24 degree C with 16 hours photoperiod (3500 lux). It was found that, the most effective combinations were 1 mg/1 BAP + 0. 1 mg/1 NAA and 2mg/1 BAP + 0. 1 mg/1 NAA. Prothallus was formed after 10 days of cultures and gametophytes were formed 1 month later. These gametophytes were irradiated with Gamma ray at doses of 0, 20, 90, 120, 150 and 180 Gy. From the preliminary result obtained from this study, for generating variations and desired phenotypic expression for Asplenium nidus, recommended doses for in vitro mutagenesis using spores are between 90 Gy to 150 Gy. Gametophytes were subcultured at monthly interval to ensure further development and propagation. Frequent monitoring for any changes in the morphology of the irradiated Asplenium nidus plants were carried out. (Author)

  13. Human somatic cell mutagenesis creates genetically tractable sarcomas.

    Science.gov (United States)

    Molyneux, Sam D; Waterhouse, Paul D; Shelton, Dawne; Shao, Yang W; Watling, Christopher M; Tang, Qing-Lian; Harris, Isaac S; Dickson, Brendan C; Tharmapalan, Pirashaanthy; Sandve, Geir K; Zhang, Xiaoyang; Bailey, Swneke D; Berman, Hal; Wunder, Jay S; Izsvák, Zsuzsanna; Iszvak, Zsuzsanna; Lupien, Mathieu; Mak, Tak W; Khokha, Rama

    2014-09-01

    Creating spontaneous yet genetically tractable human tumors from normal cells presents a fundamental challenge. Here we combined retroviral and transposon insertional mutagenesis to enable cancer gene discovery starting with human primary cells. We used lentiviruses to seed gain- and loss-of-function gene disruption elements, which were further deployed by Sleeping Beauty transposons throughout the genome of human bone explant mesenchymal cells. De novo tumors generated rapidly in this context were high-grade myxofibrosarcomas. Tumor insertion sites were enriched in recurrent somatic copy-number aberration regions from multiple cancer types and could be used to pinpoint new driver genes that sustain somatic alterations in patients. We identified HDLBP, which encodes the RNA-binding protein vigilin, as a candidate tumor suppressor deleted at 2q37.3 in greater than one out of ten tumors across multiple tissues of origin. Hybrid viral-transposon systems may accelerate the functional annotation of cancer genomes by enabling insertional mutagenesis screens in higher eukaryotes that are not amenable to germline transgenesis. PMID:25129143

  14. Mutagenesis of ultraviolet-irradiated lambda phage by host cell irradiation: induction of Weigle mutagenesis is not an all-or-none process

    International Nuclear Information System (INIS)

    Ultraviolet mutagenesis of lambda phage to clear plaque formers is the same in the total phage population and in subpopulations of phage which have also mutated to gam- or at an amber codon. This is true for phage assayed in host cells in which Weigle mutagenesis has been either partially induced by low levels of ultraviolet irradiation, or fully induced by higher levels. If induction of Weigle mutagenesis were all-or-none, clear plaque formers in phage subpopulations selected for another mutation elsewhere would come mainly from induced cells; then the clear plaque mutation rate would always be that for fully induced host cells. Therefore, induction requires more than one lesion in host cell DNA. Although thymine starvation of cells induces synthesis of recA protein, it does not induce Weigle mutagenesis; in fact starvation inhibits induction of this process on subsequent ultraviolet irradiation of the cells. (orig.) 891 AJ/orig. 892 BRE

  15. Exchange bias theory

    International Nuclear Information System (INIS)

    Research on the exchange bias (EB) phenomenon has witnessed a flurry of activity during recent years, which stems from its use in magnetic sensors and as stabilizers in magnetic reading heads. EB was discovered in 1956 but it attracted only limited attention until these applications, closely related to giant magnetoresistance, were developed during the last decade. In this review, I initially give a short introduction, listing the most salient experimental results and what is required from an EB theory. Next, I indicate some of the obstacles in the road towards a satisfactory understanding of the phenomenon. The main body of the text reviews and critically discusses the activity that has flourished, mainly during the last 5 years, in the theoretical front. Finally, an evaluation of the progress made, and a critical assessment as to where we stand nowadays along the road to a satisfactory theory, is presented

  16. Measuring nonlocal Lagrangian peak bias

    CERN Document Server

    Biagetti, Matteo; Desjacques, Vincent; Paranjape, Aseem

    2013-01-01

    In the Lagrangian approach to halo clustering, nonlocal bias can be generated either in the initial conditions or by the subsequent gravitational motions. Here, we investigate nonlocal Lagrangian bias contributions involving gradients of the linear density field, for which we have predictions from the excursion set peak formalism. We reformulate this approach in order to explicitly take into account the variable describing the crossing of the collapse barrier. This enables us to write down a bias expansion which includes all the bias terms, including the nonlocal ones. Having checked that the model furnishes a reasonable fit to the halo mass function, we extend the 1-point cross-correlation technique of Musso, Paranjape & Sheth (2012) to bias contributions that are chi-squared distributed. We validate the method with numerical realizations of peaks of Gaussian random fields before applying it to N-body simulations. We focus on the lowest (quadratic) order nonlocal bias factors predicted by the excursion s...

  17. A mouse chromosome 4 balancer ENU-mutagenesis screen isolates eleven lethal lines

    Science.gov (United States)

    ENU-mutagenesis is a powerful technique to identify genes regulating mammalian development. To functionally annotate the distal region of mouse chromosome 4, we performed an ENU-mutagenesis screen using a balancer chromosome targeted to this region of the genome. We isolated 11 lethal lines that map...

  18. Non-targeted mutagenesis of unirradiated lambda phage in Escherichia coli

    International Nuclear Information System (INIS)

    Non-targeted mutagenesis of lambda phage by ultraviolet light is the increase over background mutagenesis when non-irradiated phage are grown in irradiated Escherichia coli host cells. Such mutagenesis is caused by different processes from targeted mutagenesis, in which mutations in irradiated phage are correlated with photoproducts in the phage DNA. Non-irradiated phage grown in heavily irradiated uvr+ host cells showed non-targeted mutations, which were 3/4 frameshifts, whereas targeted mutations were 2/3 transitions. For non-targeted mutagenesis in heavily irradiated host cells, there were one or two mutant phage per mutant burst. From the results of a series of experiments with various mutant host cells, a major pathway of non-targeted mutagenesis by ultraviolet light was proposed which acts in addition to ''SOS induction''. This pathway involves binding of the enzyme DNA polymerase I to damaged genomic DNA, and low polymerase activity leads to frameshift mutations during semiconservative DNA replication. The data suggest that this process will play a much smaller role in ultraviolet mutagenesis of the bacterial genome than it does in the mutagenesis of lambda phage. (author)

  19. Results and perspectives of mutagenesis applied to durum wheat

    International Nuclear Information System (INIS)

    A review is made of the main aspects and problems of mutagenesis applied to the breeding of durum wheat (Triticum turgidum ssp. durum). Features and type of action of the main physical and chemical mutagens are considered: a comparison is also made between the two classes of mutagens, on the basis of results so far achieved. Mentions is then made of methods of treatment; parts of plant which can be treated; growing of treated material in segregating generations: data to be successively recorded. Methods of estimating mutation frequency and the problem of arising chimerical tissues and its possible overcoming are also discussed. Examination is made of some special effects of mutagens, namely: induction of translocations; diploidization of polyploids; induction of haploids and aneuploids; genetic analysis of specific loci; induction of male sterility. Finally, results are reviewed concerning induction and utilization, either as varieties or in cross breeding programmes, of mutants for characters of agronomic interest. (Bagnara, D.)

  20. Creating Sunflower Mutant Lines (Helianthus Annuus L.) Using Induced Mutagenesis

    International Nuclear Information System (INIS)

    Immature sunflower zygotic embryos of sunflower fertility restorer line 374 R were treated with ultrasound and gamma radiation before plating embryos to culture medium. All plants were isolated and self-pollinated for several generations. New sunflower forms with inherited morphological and biochemical changes were obtained. The genetic changes occurring during the mutation procedure included fourteen morphological and biochemical characters. In comparison to the check line 374 R, decreasing of the mean value of the indexes was registered for 33 % of the total number of characters and vise verse, significant increasing was observed for 60 %. Mutation for resistance to the local population of Orobanche cumana race A-E was obtained from the susceptible Bulgarian control line 374 R. Two investigated mutant lines possessed 100 % resistance to Orobanche and stable inheritance in the next generations. Our results showed that induced mutagenesis in sunflower can be successfully used to develop new lines useful for heterosis breeding

  1. Scientific projection paper for mutagenesis, transformation and cell killing

    International Nuclear Information System (INIS)

    Our knowledge about mutagenesis, transformation, and cell killing by ionizing radiation consists of large bodies of data, which are potentially useful in terms of application to human risk assessment and to the constructive use of radiation, as in cancer treatment. The three end-points discussed above are united by at least five significant concepts in radiation research strategy: (1) The inter-relationships among the important end-points, mutation, carcinogenesis, and cell killing. Research on one is meaningful only in the context of information about the other two. (2) The interaction of radiations with other agents in producing these end-points. (3) The mechanisms of action of other environmental mutagenic, carcinogenic, and cytotoxic agents. (4) The use of repair deficient human mutant cells. (5) The study of radiation damage mechanisms. There is no better way to extrapolate laboratory data to the clinical and public worlds than to understand the underlying biological mechanisms that produced the data

  2. Role of Nicotinamide in DNA Damage, Mutagenesis, and DNA Repair

    Directory of Open Access Journals (Sweden)

    Devita Surjana

    2010-01-01

    Full Text Available Nicotinamide is a water-soluble amide form of niacin (nicotinic acid or vitamin B3. Both niacin and nicotinamide are widely available in plant and animal foods, and niacin can also be endogenously synthesized in the liver from dietary tryptophan. Nicotinamide is also commercially available in vitamin supplements and in a range of cosmetic, hair, and skin preparations. Nicotinamide is the primary precursor of nicotinamide adenine dinucleotide (NAD+, an essential coenzyme in ATP production and the sole substrate of the nuclear enzyme poly-ADP-ribose polymerase-1 (PARP-1. Numerous in vitro and in vivo studies have clearly shown that PARP-1 and NAD+ status influence cellular responses to genotoxicity which can lead to mutagenesis and cancer formation. This paper will examine the role of nicotinamide in the protection from carcinogenesis, DNA repair, and maintenance of genomic stability.

  3. Quantitative studies of the mutagenesis of Toxoplasma gondii

    International Nuclear Information System (INIS)

    The induction of mutants resistant to 5-fluorodeoxyuridine (FUDR) was used to measure the efficiency of various physical and chemical mutagens on extracellular and intracellular Toxoplasma gondii. The frequency of resistant mutant was measured by plaque assay in human fibroblast cultures in the presence and absence of FUDR. When considered as a function of lethality, the most efficient mutagenesis was obtained with nitrosoguanidine treatment of extracellular parasites and with ethylmethane sulfonate treatment of actively growing intracellular parasites. Each of these treatments increased the frequency of FUDR-resistant mutants from less than one to more than 200 per million parasites. Ultraviolet irradiation, X-rays, and the alkylating mustard ICR-191 also induced FUDR-resistant mutants in a dose-dependent fashion

  4. Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria.

    Directory of Open Access Journals (Sweden)

    Alexandro Rodríguez-Rojas

    2015-10-01

    Full Text Available Pseudomonas aeruginosa is the causative agent of chronic respiratory infections and is an important pathogen of cystic fibrosis patients. Adaptive mutations play an essential role for antimicrobial resistance and persistence. The factors that contribute to bacterial mutagenesis in this environment are not clear. Recently it has been proposed that cationic antimicrobial peptides such as LL-37 could act as mutagens in P. aeruginosa. Here we provide experimental evidence that mutagenesis is the product of a joint action of LL-37 and free iron. By estimating mutation rate, mutant frequencies and assessing mutational spectra in P. aeruginosa treated either with LL-37, iron or a combination of both we demonstrate that mutation rate and mutant frequency were increased only when free iron and LL-37 were present simultaneously. Colistin had the same effect. The addition of an iron chelator completely abolished this mutagenic effect, suggesting that LL-37 enables iron to enter the cells resulting in DNA damage by Fenton reactions. This was also supported by the observation that the mutational spectrum of the bacteria under LL-37-iron regime showed one of the characteristic Fenton reaction fingerprints: C to T transitions. Free iron concentration in nature and within hosts is kept at a very low level, but the situation in infected lungs of cystic fibrosis patients is different. Intermittent bleeding and damage to the epithelial cells in lungs may contribute to the release of free iron that in turn leads to generation of reactive oxygen species and deterioration of the respiratory tract, making it more susceptible to the infection.

  5. Cationic Peptides Facilitate Iron-induced Mutagenesis in Bacteria.

    Science.gov (United States)

    Rodríguez-Rojas, Alexandro; Makarova, Olga; Müller, Uta; Rolff, Jens

    2015-10-01

    Pseudomonas aeruginosa is the causative agent of chronic respiratory infections and is an important pathogen of cystic fibrosis patients. Adaptive mutations play an essential role for antimicrobial resistance and persistence. The factors that contribute to bacterial mutagenesis in this environment are not clear. Recently it has been proposed that cationic antimicrobial peptides such as LL-37 could act as mutagens in P. aeruginosa. Here we provide experimental evidence that mutagenesis is the product of a joint action of LL-37 and free iron. By estimating mutation rate, mutant frequencies and assessing mutational spectra in P. aeruginosa treated either with LL-37, iron or a combination of both we demonstrate that mutation rate and mutant frequency were increased only when free iron and LL-37 were present simultaneously. Colistin had the same effect. The addition of an iron chelator completely abolished this mutagenic effect, suggesting that LL-37 enables iron to enter the cells resulting in DNA damage by Fenton reactions. This was also supported by the observation that the mutational spectrum of the bacteria under LL-37-iron regime showed one of the characteristic Fenton reaction fingerprints: C to T transitions. Free iron concentration in nature and within hosts is kept at a very low level, but the situation in infected lungs of cystic fibrosis patients is different. Intermittent bleeding and damage to the epithelial cells in lungs may contribute to the release of free iron that in turn leads to generation of reactive oxygen species and deterioration of the respiratory tract, making it more susceptible to the infection. PMID:26430769

  6. Photosensitization induced by the antibacterial fluoroquinolone Rufloxacin leads to mutagenesis in yeast.

    Science.gov (United States)

    Serrentino, Maria-Elisabetta; Catalfo, Alfio; Angelin, Anne-Reynaud; de Guidi, Guido; Sage, Evelyne

    2010-10-13

    Rufloxacin (RFX) is an antibacterial fluoroquinolone that exhibits UVA photosensitization properties. Photosensitization reactions lead to the formation of oxidative damage, mainly via singlet oxygen. Here we explore the phototoxic and photomutagenic potency of RFX using a panel of yeast (Saccharomyces cerevisiae) mutants affected in different DNA repair pathways. Yeast mutants provide a sensitive tool to identify the photodamage and the DNA repair pathways that cope with it. Cell viability test at increasing dose of UVA shows that both the DNA repair deficient and wild type cells are equally sensitive to RFX-induced photosensitization, demonstrating that phototoxic effect is not due to DNA injury. Photomutagenicity of RFX is evaluated by measuring the frequency of forward Can(R) mutations. The mutation induction is low in wild type cells. A high increase in mutation frequency is observed in strains affected in Ogg1 gene, compared to wild type and other base excision repair deficient strains. The mutation spectrum photomediated by RFX in wild type cells reveals a bias in favour of GC>TA transversions, whereas transition and frameshift mutations are less represented. Altogether data demonstrates that 8-oxo-7,8-dihydroguanine (8-oxoGua) is by far the major DNA damage produced by RFX photosensitization, leading to mutagenesis. We also explore the role played by DNA mismatch repair, translesion synthesis and post-replication repair in the prevention of mutagenic effects due to RFX exposure. In addition, we show that most of RFX photodegradation products are not mutagenic. This study defines the phototoxic and photomutagenic properties of antibacterial RFX and point out possible unwanted side effects in skin under sunlight. PMID:20696178

  7. Bias in clinical intervention research

    DEFF Research Database (Denmark)

    Gluud, Lise Lotte

    2006-01-01

    Research on bias in clinical trials may help identify some of the reasons why investigators sometimes reach the wrong conclusions about intervention effects. Several quality components for the assessment of bias control have been suggested, but although they seem intrinsically valid, empirical...

  8. Cognitive Bias in Systems Verification

    Science.gov (United States)

    Larson, Steve

    2012-01-01

    Working definition of cognitive bias: Patterns by which information is sought and interpreted that can lead to systematic errors in decisions. Cognitive bias is used in diverse fields: Economics, Politics, Intelligence, Marketing, to name a few. Attempts to ground cognitive science in physical characteristics of the cognitive apparatus exceed our knowledge. Studies based on correlations; strict cause and effect is difficult to pinpoint. Effects cited in the paper and discussed here have been replicated many times over, and appear sound. Many biases have been described, but it is still unclear whether they are all distinct. There may only be a handful of fundamental biases, which manifest in various ways. Bias can effect system verification in many ways . Overconfidence -> Questionable decisions to deploy. Availability -> Inability to conceive critical tests. Representativeness -> Overinterpretation of results. Positive Test Strategies -> Confirmation bias. Debiasing at individual level very difficult. The potential effect of bias on the verification process can be managed, but not eliminated. Worth considering at key points in the process.

  9. Administrative bias in South Africa

    Directory of Open Access Journals (Sweden)

    E S Nwauche

    2005-01-01

    Full Text Available This article reviews the interpretation of section 6(2(aii of the Promotion of Administrative Justice Act which makes an administrator “biased or reasonably suspected of bias” a ground of judicial review. In this regard, the paper reviews the determination of administrative bias in South Africa especially highlighting the concept of institutional bias. The paper notes that inspite of the formulation of the bias ground of review the test for administrative bias is the reasonable apprehension test laid down in the case of President of South Africa v South African Rugby Football Union(2 which on close examination is not the same thing. Accordingly the paper urges an alternative interpretation that is based on the reasonable suspicion test enunciated in BTR Industries South Africa (Pty Ltd v Metal and Allied Workers Union and R v Roberts. Within this context, the paper constructs a model for interpreting the bias ground of review that combines the reasonable suspicion test as interpreted in BTR Industries and R v Roberts, the possibility of the waiver of administrative bias, the curative mechanism of administrative appeal as well as some level of judicial review exemplified by the jurisprudence of article 6(1 of the European Convention of Human Rights, especially in the light of the contemplation of the South African Magistrate Court as a jurisdictional route of judicial review.

  10. Comparison of CRISPR/Cas9 expression constructs for efficient targeted mutagenesis in rice

    OpenAIRE

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2015-01-01

    The CRISPR/Cas9 system is an efficient tool used for genome editing in a variety of organisms. Despite several recent reports of successful targeted mutagenesis using the CRISPR/Cas9 system in plants, in each case the target gene of interest, the Cas9 expression system and guide-RNA (gRNA) used, and the tissues used for transformation and subsequent mutagenesis differed, hence the reported frequencies of targeted mutagenesis cannot be compared directly. Here, we evaluated mutation frequency i...

  11. Role of the RecF gene product in UV mutagenesis of lambda phage

    International Nuclear Information System (INIS)

    E. coli recF mutants have a greatly reduced capacity for Weigle mutagenesis of ultraviolet light-irradiated lambda phage. A recF 332::Tn3 mutation was introduced into an E. coli recA441 lex A51 strain which constitutively expresses SOS functions. Weigle mutagenesis of phage lambda could occur in the resulting strain in the absence of host cell irradiation, and was increased when the recA441 (tif) allele was activated of recF strains to support Weigle mutagenesis can therefore be ascribed to a defect in expression of SOS functions after irradiation. (orig.)

  12. Stationary-State Mutagenesis in Escherichia coli: a Model

    Indian Academy of Sciences (India)

    S. K. Mahajan; A. V. S. S. Narayana Rao; S. K. Bhattacharjee

    2000-04-01

    Stationary-phase mutagenesis in nondividing E. coli cells exposed to a nonlethal stress was, a few years ago, claimed to be a likely case of a Lamarckian mechanism capable of producing exclusively useful mutations in a directed manner. After a heated debate over the last decade it now appears to involve a Darwinian mechanism that generates a transient state of hypermutagenesis, operating on a large number of sites spread over the entire genome, at least in a proportion of the resting cells. Most of the studies that clarified this position were on the reversion of a frameshift mutation present in a lacI -- lacZ fusion in E. coli strain FC40. Several groups have extensively examined both the sequence changes associated with these reversions and the underlying genetic requirements. On the basis of our studies on the genomic sequence analysis, we recently proposed a model to explain the specific changes associated with the reversion hotspots. Here we propose a more detailed version of this model that also takes into account the observed genetic requirements of stationary-state mutagenesis. Briefly, G:T/U mismatches produced at methylatable cytosines are preferentially repaired in nondividing cells by the very short patch mismatch repair (VSPMR) mechanism which is itself mutagenic and can produce mutations in very short stretches located in the immediate vicinity of these cytosine methylation sites. This mechanism requires a homologous or homeologous strand invasion step and an error-prone DNA synthesis step and is dependent on RecA, RecBCD and a DNA polymerase. The process is initiated near sequences recognized by Dcm and Vsr enzymes and further stimulated if these sequences are a part of CHI or CHI-like sequences, but a double-strand-break-dependent recombination mediated by the RecBCD pathways proposed by others seems to be nonessential. The strand transfer step is proposed to depend on RecA, RuvA, RuvB and RuvC and is opposed by RecG and MutS. The model also gives

  13. Cognitive biases and language universals

    CERN Document Server

    Baronchelli, Andrea; Puglisi, Andrea

    2013-01-01

    Language universals have been longly attributed to an innate Universal Grammar. An alternative explanation states that linguistic universals emerged independently in every language in response to shared cognitive, though non language-specific, biases. A computational model has recently shown how this could be the case, focusing on the paradigmatic example of the universal properties of color naming patterns, and producing results in accurate agreement with the experimental data. Here we investigate thoroughly the role of a cognitive bias in the framework of this model. We study how, and to what extent, the structure of the bias can influence the corresponding linguistic universal patterns. We show also that the cultural history of a group of speakers introduces population-specific constraints that act against the uniforming pressure of the cognitive bias, and we clarify the interplay between these two forces. We believe that our simulations can help to shed light on the possible mechanisms at work in the evol...

  14. Preferences, country bias, and international trade

    NARCIS (Netherlands)

    S. Roy (Santanu); J.M.A. Viaene (Jean-Marie)

    1998-01-01

    textabstractAnalyzes international trade where consumer preferences exhibit country bias. Why country biases arise; How trade can occur in the presence of country bias; Implication for the pattern of trade and specialization.

  15. Detecting and Punishing Unconscious Bias

    OpenAIRE

    Tetlock, Philip E; Gregory Mitchell; L. Jason Anastasopoulos

    2013-01-01

    We present experimental results demonstrating how ideology shapes evaluations of technology aimed at detecting unconscious biases: (1) liberals supported use of the technology to detect unconscious racism but not unconscious anti-Americanism, whereas conservatives showed the reverse pattern, (2) liberals and conservatives opposed punishing individuals for unconscious bias but supported punishing organizations failing to use the technology to root out, respectively, racism or anti-Americanism,...

  16. The intentionality bias and schizotypy

    OpenAIRE

    Moore, James W.; Pope, A.

    2014-01-01

    The “intentionality bias” refers to our automatic tendency to judge other people's actions to be intentional. In this experiment we extended research on this effect in two key ways. First, we developed a novel nonlinguistic task for assessing the intentionality bias. This task used video stimuli of ambiguous movements. Second, we investigated the relationship between the strength of this bias and schizotypy (schizophrenia-like symptoms in healthy individuals). Our results showed that the inte...

  17. Global systematic mutagenesis and-omics for inference of genetic networks

    Czech Academy of Sciences Publication Activity Database

    Vohradský, Jiří

    Munster, 2003, s. 24. [Biology of streptomycetes and related actinomycetes . Munster (DE), 27.02.2003-03.03.2003] Institutional research plan: CEZ:AV0Z5020903 Keywords : mutagenesis Subject RIV: EE - Microbiology, Virology

  18. A Report on 36 Years of Practical Work on Crop Improvement through Induced Mutagenesis

    International Nuclear Information System (INIS)

    Induced mutagenesis work was conducted from 1971 to July 2007, using both physical and chemical mutagens for improvement of a wide range of crops viz. vegetables, medicinal, pulse, oil-bearing, and ornamental crops. All classical and advanced methods were extensively used for the success of induced mutagenesis for the development of new and novel cultivars of economic importance. Being deeply engaged for the last 30 years on improvement of ornamentals through Gamma-ray induced mutagenesis, I have produced a large number of new and promising varieties in different ornamentals. A good number of ornamental mutant varieties have already been commercialized. A novel technique has been developed for management of floral chimeric sector in chrysanthemum through direct regeneration of mutated individual florets. A series of in vitro experiments were conducted and solid mutants developed through direct regeneration. In vitro mutagenesis has been successfully used for development of a salt-resistant strain in chrysanthemum, supported by biochemical analysis and field trials. (author)

  19. Targeted mutagenesis using CRISPR/Cas system in medaka

    Directory of Open Access Journals (Sweden)

    Satoshi Ansai

    2014-04-01

    Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR/CRISPR-associated (Cas system-based RNA-guided endonuclease (RGEN has recently emerged as a simple and efficient tool for targeted genome editing. In this study, we showed successful targeted mutagenesis using RGENs in medaka, Oryzias latipes. Somatic and heritable mutations were induced with high efficiency at the targeted genomic sequence on the DJ-1 gene in embryos that had been injected with the single guide RNA (sgRNA transcribed by a T7 promoter and capped RNA encoding a Cas9 nuclease. The sgRNAs that were designed for the target genomic sequences without the 5′ end of GG required by the T7 promoter induced the targeted mutations. This suggests that the RGEN can target any sequence adjacent to an NGG protospacer adjacent motif (PAM sequence, which occurs once every 8 bp. The off-target alterations at 2 genomic loci harboring double mismatches in the 18-bp targeting sequences were induced in the RGEN-injected embryos. However, we also found that the off-target effects could be reduced by lower dosages of sgRNA. Taken together, our results suggest that CRISPR/Cas-mediated RGENs may be an efficient and flexible tool for genome editing in medaka.

  20. ldentification and Mutagenesis of Lactic Acid Bacteria from Chinese Sauerkraut

    Institute of Scientific and Technical Information of China (English)

    Yajing CHAl; Hao SHl; Ri NA

    2015-01-01

    ln order to analyze the fermentation properties of lactic acid bacteria in Chinese sauerkraut and to improve acid production, 21 samples of Chinese sauerkraut from lnner Mongolia and Northeast China were col ected and isolated with a Man-Rogosa-Sharpe (MRS) culture. Sixteen strains of lactic acid bacteria were identified by combining both phenotype and genotype methods. After activation, the 16 strains were inoculated into the MRS medium with a concentration of 4%and then incubated at 37 ℃. The pH and the absorbance of the culture were mea-sured. The activated strains were then mutagenized in a field of 4 KV/cm mutation, with dosages administered within 20 minutes and 30 minutes, respectively. The variation curves of the pH and the absorbance of the culture were determined. The experimental results showed that the lactic acid bacteria isolated from the soup were identified as Lactobacil us and the acid production of the bacteria was signifi-cantly improved by the mutagenesis of the corona electric field.

  1. CRISPR/Cas-mediated targeted mutagenesis in Daphnia magna.

    Directory of Open Access Journals (Sweden)

    Takashi Nakanishi

    Full Text Available The water flea Daphnia magna has been used as an animal model in ecology, evolution, and environmental sciences. Thanks to the recent progress in Daphnia genomics, genetic information such as the draft genome sequence and expressed sequence tags (ESTs is now available. To investigate the relationship between phenotypes and the available genetic information about Daphnia, some gene manipulation methods have been developed. However, a technique to induce targeted mutagenesis into Daphnia genome remains elusive. To overcome this problem, we focused on an emerging genome editing technique mediated by the clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas system to introduce genomic mutations. In this study, we targeted a functionally conserved regulator of eye development, the eyeless gene in D. magna. When we injected Cas9 mRNAs and eyeless-targeting guide RNAs into eggs, 18-47% of the survived juveniles exhibited abnormal eye morphology. After maturation, up to 8.2% of the adults produced progenies with deformed eyes, which carried mutations in the eyeless loci. These results showed that CRISPR/Cas system could introduce heritable mutations into the endogenous eyeless gene in D. magna. This is the first report of a targeted gene knockout technique in Daphnia and will be useful in uncovering Daphnia gene functions.

  2. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

    Sauer, Noel J; Mozoruk, Jerry; Miller, Ryan B; Warburg, Zachary J; Walker, Keith A; Beetham, Peter R; Schöpke, Christian R; Gocal, Greg F W

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed. PMID:26503400

  3. In vitro mutagenesis for the improvement of Josapine pineapple

    International Nuclear Information System (INIS)

    Pineapple is the most important fruit in terms of revenue earner in Malaysia. There are about 10,000 ha cultivated with this fruit and half of this is owned by estates and planted for the canning industry. The export of canned pineapple is about 2 million standard cases annually valued at RM 60 million, while the export of fresh pineapple is about 40,000 tonnes worth about RM 10 million. The industry for canning is however, an ailing industry with production on the decline since the 70s. Somaclonal variations and induced mutation using irradiation in breeding are least invasive in changes to genetic make-up of an established variety and will be useful for improving the pineapple varieties. The use of tissue culture to generate somaclones with minute genetic changes that do not damage the overall varietal identity would be the most suitable tool to improve the variety. Protocols for the production of tissue culture plantlets of pineapple using bioreactor technology has been developed and proved to be much more efficient and productive compared to conventional method. In vitro mutagenesis using adventitious buds had produced new plants with smooth leaves, vigorous growth and ornamental-like characters. A total of 30,000 plants derived from tissue culture will be planted and screened in the field for the improvement of Josapine pineapple against bacterial heart rot disease and multiple crown. (Author)

  4. Genome-wide transposon mutagenesis in pathogenic Leptospira species.

    Science.gov (United States)

    Murray, Gerald L; Morel, Viviane; Cerqueira, Gustavo M; Croda, Julio; Srikram, Amporn; Henry, Rebekah; Ko, Albert I; Dellagostin, Odir A; Bulach, Dieter M; Sermswan, Rasana W; Adler, Ben; Picardeau, Mathieu

    2009-02-01

    Leptospira interrogans is the most common cause of leptospirosis in humans and animals. Genetic analysis of L. interrogans has been severely hindered by a lack of tools for genetic manipulation. Recently we developed the mariner-based transposon Himar1 to generate the first defined mutants in L. interrogans. In this study, a total of 929 independent transposon mutants were obtained and the location of insertion determined. Of these mutants, 721 were located in the protein coding regions of 551 different genes. While sequence analysis of transposon insertion sites indicated that transposition occurred in an essentially random fashion in the genome, 25 unique transposon mutants were found to exhibit insertions into genes encoding 16S or 23S rRNAs, suggesting these genes are insertional hot spots in the L. interrogans genome. In contrast, loci containing notionally essential genes involved in lipopolysaccharide and heme biosynthesis showed few transposon insertions. The effect of gene disruption on the virulence of a selected set of defined mutants was investigated using the hamster model of leptospirosis. Two attenuated mutants with disruptions in hypothetical genes were identified, thus validating the use of transposon mutagenesis for the identification of novel virulence factors in L. interrogans. This library provides a valuable resource for the study of gene function in L. interrogans. Combined with the genome sequences of L. interrogans, this provides an opportunity to investigate genes that contribute to pathogenesis and will provide a better understanding of the biology of L. interrogans. PMID:19047402

  5. The estimation method of GPS instrumental biases

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    A model of estimating the global positioning system (GPS) instrumental biases and the methods to calculate the relative instrumental biases of satellite and receiver are presented. The calculated results of GPS instrumental biases, the relative instrumental biases of satellite and receiver, and total electron content (TEC) are also shown. Finally, the stability of GPS instrumental biases as well as that of satellite and receiver instrumental biases are evaluated, indicating that they are very stable during a period of two months and a half.

  6. Insertional Mutagenesis by a Hybrid PiggyBac and Sleeping Beauty Transposon in the Rat

    OpenAIRE

    Furushima, Kenryo; Jang, Chuan-Wei; Chen, Diane W.; Xiao, Ningna; Overbeek, Paul A.; Behringer, Richard R.

    2012-01-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac trans...

  7. Restriction enzyme-free construction of random gene mutagenesis libraries in E. coli

    OpenAIRE

    Pai, Jen C.; Entzminger, Kevin C.; Maynard, Jennifer A.

    2011-01-01

    Directed evolution relies on both random and site-directed mutagenesis of individual genes and regulatory elements to create variants with altered activity profiles for engineering applications. Central to these experiments is the construction of large libraries of related variants. However, a number of technical hurdles continue to limit routine construction of random mutagenesis libraries in E. coli, in particular, inefficiencies during digestion and ligation steps. Here, we report a restri...

  8. Bias and design in software specifications

    Science.gov (United States)

    Straub, Pablo A.; Zelkowitz, Marvin V.

    1990-01-01

    Implementation bias in a specification is an arbitrary constraint in the solution space. Presented here is a model of bias in software specifications. Bias is defined in terms of the specification process and a classification of the attributes of the software product. Our definition of bias provides insight into both the origin and the consequences of bias. It also shows that bias is relative and essentially unavoidable. Finally, we describe current work on defining a measure of bias, formalizing our model, and relating bias to software defects.

  9. Genome-Wide Transposon Mutagenesis in Saccharomyces cerevisiae and Candida albicans

    Science.gov (United States)

    Xu, Tao; Bharucha, Nikë; Kumar, Anuj

    2016-01-01

    Transposon mutagenesis is an effective method for generating large sets of random mutations in target DNA, with applicability toward numerous types of genetic screens in prokaryotes, single-celled eukaryotes, and metazoans alike. Relative to methods of random mutagenesis by chemical/UV treatment, transposon insertions can be easily identified in mutants with phenotypes of interest. The construction of transposon insertion mutants is also less labor-intensive on a genome-wide scale than methods for targeted gene replacement, although transposon insertions are not precisely targeted to a specific residue, and thus coverage of the target DNA can be problematic. The collective advantages of transposon mutagenesis have been well demonstrated in studies of the budding yeast Saccharomyces cerevisiae and the related pathogenic yeast Candida albicans, as transposon mutagenesis has been used extensively for phenotypic screens in both yeasts. Consequently, we present here protocols for the generation and utilization of transposon-insertion DNA libraries in S. cerevisiae and C. albicans. Specifically, we present methods for the large-scale introduction of transposon insertion alleles in a desired strain of S. cerevisiae. Methods are also presented for transposon mutagenesis of C. albicans, encompassing both the construction of the plasmid-based transposon-mutagenized DNA library and its introduction into a desired strain of Candida. In total, these methods provide the necessary information to implement transposon mutagenesis in yeast, enabling the construction of large sets of identifiable gene disruption mutations, with particular utility for phenotypic screening in nonstandard genetic backgrounds. PMID:21815095

  10. Negativity Bias in Dangerous Drivers.

    Science.gov (United States)

    Chai, Jing; Qu, Weina; Sun, Xianghong; Zhang, Kan; Ge, Yan

    2016-01-01

    The behavioral and cognitive characteristics of dangerous drivers differ significantly from those of safe drivers. However, differences in emotional information processing have seldom been investigated. Previous studies have revealed that drivers with higher anger/anxiety trait scores are more likely to be involved in crashes and that individuals with higher anger traits exhibit stronger negativity biases when processing emotions compared with control groups. However, researchers have not explored the relationship between emotional information processing and driving behavior. In this study, we examined the emotional information processing differences between dangerous drivers and safe drivers. Thirty-eight non-professional drivers were divided into two groups according to the penalty points that they had accrued for traffic violations: 15 drivers with 6 or more points were included in the dangerous driver group, and 23 drivers with 3 or fewer points were included in the safe driver group. The emotional Stroop task was used to measure negativity biases, and both behavioral and electroencephalograph data were recorded. The behavioral results revealed stronger negativity biases in the dangerous drivers than in the safe drivers. The bias score was correlated with self-reported dangerous driving behavior. Drivers with strong negativity biases reported having been involved in mores crashes compared with the less-biased drivers. The event-related potentials (ERPs) revealed that the dangerous drivers exhibited reduced P3 components when responding to negative stimuli, suggesting decreased inhibitory control of information that is task-irrelevant but emotionally salient. The influence of negativity bias provides one possible explanation of the effects of individual differences on dangerous driving behavior and traffic crashes. PMID:26765225

  11. On the bias of BFS

    CERN Document Server

    Kurant, Maciej; Thiran, Patrick

    2010-01-01

    Breadth First Search (BFS) and other graph traversal techniques are widely used for measuring large unknown graphs, such as online social networks. It has been empirically observed that an incomplete BFS is biased toward high degree nodes. In contrast to more studied sampling techniques, such as random walks, the precise bias of BFS has not been characterized to date. In this paper, we quantify the degree bias of BFS sampling. In particular, we calculate the node degree distribution expected to be observed by BFS as a function of the fraction of covered nodes, in a random graph $RG(p_k)$ with a given degree distribution $p_k$. Furthermore, we also show that, for $RG(p_k)$, all commonly used graph traversal techniques (BFS, DFS, Forest Fire, and Snowball Sampling) lead to the same bias, and we show how to correct for this bias. To give a broader perspective, we compare this class of exploration techniques to random walks that are well-studied and easier to analyze. Next, we study by simulation the effect of gr...

  12. In vitro mutagenesis for the improvement of vegetatively propagated plants

    International Nuclear Information System (INIS)

    A number of important crops such as banana, plantain, cassava, potato, sweet potato and sugar cane are propagated from corms, tubers and stem cuttings. Some of these plants do not produce seed, and often the size of the propagule is too big to treat large populations with mutagens. In vitro techniques allow mutagenic treatment of large numbers and multiplication of the selected genotypes in a small space and short duration under disease free conditions. After treatment with mutagens, the chimeral tissues can be separated into mutated and non-mutated sectors without loss of plants, which may occur in conventional propagation. Somaclonal variation among plants regenerated from callus and cell suspension cultures may provide additional variation to that induced through mutagenesis. In vitro methods allow induction and expression of recessive mutations in the haploids, producing homozygous doubled haploids. The availability of simple, efficient and rapid techniques for screening large plant populations for desired traits is an essential component of plant breeding. In vitro culture techniques allow selection of the desired variants from large populations of cells and plants. This may be achieved by manipulating the medium composition, e.g. selection for tolerance to salinity and drought, and by co-culturing the plant tissues with pathogens or their toxins, as in the case of selection for disease resistance. The variants thus selected can be subjected to selection in the glasshouse or field. Even though the occurrence of desired mutations is empirical and random, the combination of in vitro and mutation techniques can speed up the breeding of vegetatively propagated plants. (author). 41 refs, 3 tabs

  13. Site-directed mutagenesis in plants via gene targeting

    International Nuclear Information System (INIS)

    Many agronomically valuable phenotypes and natural variations seem to be due to point (or only a few) mutations. Thus, site-directed mutagenesis via gene targeting (GT) should be the cleanest, and most direct gene manipulation technique for future molecular breeding in plants. We chose the acetolactate synthase (ALS) gene locus of rice as a target for the introduction of point mutations. ALS catalyzes the initial step common to the biosynthesis of the branched-chain amino acids. Several point mutations in the ALS gene that confer tolerance to several ALS-inhibiting herbicides have been discovered in several plant species. Using a T-DNA-mediated GT strategy, we were able to induce two point mutations in the ALS locus that confer tolerance to the ALS-inhibiting herbicide bispyribac sodium salt (BS). After detailed analysis of GT plants, we confirmed that precise modification of the ALS locus had occurred in several plants. In addition to herbicide tolerance, tolerance against other chemicals is also a potential selectable phenotype. In this context, we are attempting to use GT to introduce point mutations into the rice gene encoding anthranilate synthase alpha subunit 2 (ASA2) -- a key enzyme in tryptophan (Trp) biosynthesis - to produce Trp-accumulating rice. In this study, gene-modified plants can be selected against the Trp analogue 5-methyl-Trp (5MT). We hope to report the phenotype of ASA2-modified plants. On the other hand, many agronomically valuable phenotypes caused by a small number of point mutations are non-selectable at the stage of transformation using current methods. If the frequency of GT can be improved substantially, co-transformation of a selectable marker gene and a non-selectable GT construct, and subsequent identification of desirable targeting events will cope with this problem. We are currently trying to improve GT efficiency in plant. (author)

  14. Radiation mutagenesis from molecular and genetic points of view

    Energy Technology Data Exchange (ETDEWEB)

    Chen, D.J.C.; Park, M.S.; Okinaka, R.T.; Jaberaboansari, A.

    1993-01-01

    An important biological effect of ionizing radiation on living organisms is mutation induction. Mutation is also a primary event in the etiology of cancer. The chain events, from induction of DNA damage by ionizing radiation to processing of these damages by the cellular repair/replication machinery, that lead to mutation are not well understood. The development of quantitative methods for measuring mutation-induction, such as the HPRT system, in cultured mammalian cells has provided an estimate of the mutagenic effects of x- and [gamma]-rays as wen as of high LET radiation in both rodent and human cells. A major conclusion from these mutagenesis data is that high LET radiation induces mutations more efficiently than g-rays. Molecular analysis of mutations induced by sparsely ionizing radiation have detected major structural alterations at the gene level. Our molecular results based on analysis of human HPRT deficient mutants induced by [gamma]-rays, [alpha]-particles and high energy charged particles indicate that higher LET radiation induce more total and large deletion mutations than [gamma]-rays. Utilizing molecular techniques including polymerase chain reaction (PCR), Single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and Direct DNA sequencing, mutational spectra induced by ionizing radiation have been compared in different cell systems. Attempts have also been made to determine the mutagenic potential and the nature of mutation induced by low dose rate [gamma]-rays. Defective repair, in the form of either a diminished capability for repair or inaccurate repair, can lead to increased risk of heritable mutations from radiation exposure. Therefore, the effects of DNA repair deficiency on the mutation induction in mammalian cells is reviewed.

  15. Radiation mutagenesis from molecular and genetic points of view

    Energy Technology Data Exchange (ETDEWEB)

    Chen, D.J.C.; Park, M.S.; Okinaka, R.T.; Jaberaboansari, A.

    1993-02-01

    An important biological effect of ionizing radiation on living organisms is mutation induction. Mutation is also a primary event in the etiology of cancer. The chain events, from induction of DNA damage by ionizing radiation to processing of these damages by the cellular repair/replication machinery, that lead to mutation are not well understood. The development of quantitative methods for measuring mutation-induction, such as the HPRT system, in cultured mammalian cells has provided an estimate of the mutagenic effects of x- and {gamma}-rays as wen as of high LET radiation in both rodent and human cells. A major conclusion from these mutagenesis data is that high LET radiation induces mutations more efficiently than g-rays. Molecular analysis of mutations induced by sparsely ionizing radiation have detected major structural alterations at the gene level. Our molecular results based on analysis of human HPRT deficient mutants induced by {gamma}-rays, {alpha}-particles and high energy charged particles indicate that higher LET radiation induce more total and large deletion mutations than {gamma}-rays. Utilizing molecular techniques including polymerase chain reaction (PCR), Single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and Direct DNA sequencing, mutational spectra induced by ionizing radiation have been compared in different cell systems. Attempts have also been made to determine the mutagenic potential and the nature of mutation induced by low dose rate {gamma}-rays. Defective repair, in the form of either a diminished capability for repair or inaccurate repair, can lead to increased risk of heritable mutations from radiation exposure. Therefore, the effects of DNA repair deficiency on the mutation induction in mammalian cells is reviewed.

  16. Expression and site-directed mutagenesis of human dihydrofolate reductase

    International Nuclear Information System (INIS)

    A procaryotic high-level expression vector for human dihydrofolate reductase has been constructed and the protein characterized as a first step toward structure-function studies of this enzyme. A vector bearing the tac promoter, four synthetic oligodeoxynucleotides, and a restriction fragment from the dihydrofolate reductase cDNA were ligated in a manner which optimized the transcriptional and translational frequency of the enzyme mRNA. The reductase, comprising ca. 17% of the total soluble protein in the host bacteria, was purified to apparent homogeneity as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and characterized by amino acid composition, partial amino acid sequence, and steady-sate kinetic analysis. This expression vector has been used as a template for double-stranded plasmid DNA site-specific mutagenesis. Functional studies on a Cys-6 → Ser-6 mutant enzyme support the contention that Cys-6 is obligatory for organomercurial activation of human dihydrofolate reductase. The Ser-6 mutant enzyme was not activated to any extent following a 24-h incubation with p-(hydroxymercuri)benzoate and nicotinamide adenine dinucleotide phosphate (reduced) (NADPH), whereas the k/sub cat/ for Cys-6 reductase increased 2-fold under identical conditions. The specific activities of the Cys-6 and Ser-6 enzymes were virtually identical as determined by methotrexate titration as were the K/sub m/ values for both dihydrofolate and NADPH. The Ser-6 mutant showed a decreased temperature stability and was more sensitive to inactivation by α-chymotrypsin when compared to the wild-type enzyme. These results suggest that the Ser-6 mutant reductase is conformationally altered relative to the Cys-6 native enzyme

  17. Mutagenesis and haploid culture for disease resistance in Brassica napus

    International Nuclear Information System (INIS)

    Full text: Most winter oilseed rape cultivars share parentage and therefore show little genetic diversity. There is no known resistance to Alternaria spp. in oilseed rape or in any related Brassica species. Experiments with tissue culture yielded only transient, non-genetic resistance. Therefore, mutagenesis may be used to generate heritable resistance to Alternaria spp. Gamma irradiation was applied to seeds of 'Bienvenue', secondary embryoids of cvs 'Primor' and 'Rapora', and buds of cvs 'Primor' and 'Ariana'. Isolated microspores from cv 'Ariana' and rapid cycling B. napus were also treated. The doses used ranged from 0-100 Gy for isolated microspores and buds, up to 600 Gy for seeds and 960 Gy for secondary embryoids. EMS was used to treat seeds of line WRG-42 (supplied by Nickersons RPB) and microspores of cv 'Bienvenue' and rapid cycling B. napus. Seeds were treated with up to 2.0% EMS for 0.2 h. before plating them on the culture medium. Seed irradiation up to 600 Gy did not reduce germination. M1 and M2 progenies were tested both in the laboratory and in field trials, and none of these were found to be resistant to Alternaria. However, considerable variation for other characters was observed. Haploid cultures from these plants were extremely difficult to regenerate, and for this reason no regenerant plants have been tested for resistance. For irradiated secondary embryoids the regeneration capacity decreased with increasing dose. Regenerated plants have been tested for resistance to Alternaria, but stable resistance was not observed. Haploid cultures were obtained from irradiated buds, using both anther and microspore culture. Low irradiation treatment was beneficial to developing embryoids. Some regenerants have been obtained from EMS treated microspores and seeds. Four plants have repeatedly given increased levels of resistance to A. brassicicola, and progenies are being tested to determine the genetic nature of the resistance. (author)

  18. Structure-based design of combinatorial mutagenesis libraries

    Science.gov (United States)

    Verma, Deeptak; Grigoryan, Gevorg; Bailey-Kellogg, Chris

    2015-01-01

    The development of protein variants with improved properties (thermostability, binding affinity, catalytic activity, etc.) has greatly benefited from the application of high-throughput screens evaluating large, diverse combinatorial libraries. At the same time, since only a very limited portion of sequence space can be experimentally constructed and tested, an attractive possibility is to use computational protein design to focus libraries on a productive portion of the space. We present a general-purpose method, called “Structure-based Optimization of Combinatorial Mutagenesis” (SOCoM), which can optimize arbitrarily large combinatorial mutagenesis libraries directly based on structural energies of their constituents. SOCoM chooses both positions and substitutions, employing a combinatorial optimization framework based on library-averaged energy potentials in order to avoid explicitly modeling every variant in every possible library. In case study applications to green fluorescent protein, β-lactamase, and lipase A, SOCoM optimizes relatively small, focused libraries whose variants achieve energies comparable to or better than previous library design efforts, as well as larger libraries (previously not designable by structure-based methods) whose variants cover greater diversity while still maintaining substantially better energies than would be achieved by representative random library approaches. By allowing the creation of large-scale combinatorial libraries based on structural calculations, SOCoM promises to increase the scope of applicability of computational protein design and improve the hit rate of discovering beneficial variants. While designs presented here focus on variant stability (predicted by total energy), SOCoM can readily incorporate other structure-based assessments, such as the energy gap between alternative conformational or bound states. PMID:25611189

  19. Radiation mutagenesis from molecular and genetic points of view

    International Nuclear Information System (INIS)

    An important biological effect of ionizing radiation on living organisms is mutation induction. Mutation is also a primary event in the etiology of cancer. The chain events, from induction of DNA damage by ionizing radiation to processing of these damages by the cellular repair/replication machinery, that lead to mutation are not well understood. The development of quantitative methods for measuring mutation-induction, such as the HPRT system, in cultured mammalian cells has provided an estimate of the mutagenic effects of x- and γ-rays as wen as of high LET radiation in both rodent and human cells. A major conclusion from these mutagenesis data is that high LET radiation induces mutations more efficiently than g-rays. Molecular analysis of mutations induced by sparsely ionizing radiation have detected major structural alterations at the gene level. Our molecular results based on analysis of human HPRT deficient mutants induced by γ-rays, α-particles and high energy charged particles indicate that higher LET radiation induce more total and large deletion mutations than γ-rays. Utilizing molecular techniques including polymerase chain reaction (PCR), Single-strand conformation polymorphism (SSCP), denaturing gradient gel electrophoresis (DGGE) and Direct DNA sequencing, mutational spectra induced by ionizing radiation have been compared in different cell systems. Attempts have also been made to determine the mutagenic potential and the nature of mutation induced by low dose rate γ-rays. Defective repair, in the form of either a diminished capability for repair or inaccurate repair, can lead to increased risk of heritable mutations from radiation exposure. Therefore, the effects of DNA repair deficiency on the mutation induction in mammalian cells is reviewed

  20. Measurement Bias Detection through Factor Analysis

    Science.gov (United States)

    Barendse, M. T.; Oort, F. J.; Werner, C. S.; Ligtvoet, R.; Schermelleh-Engel, K.

    2012-01-01

    Measurement bias is defined as a violation of measurement invariance, which can be investigated through multigroup factor analysis (MGFA), by testing across-group differences in intercepts (uniform bias) and factor loadings (nonuniform bias). Restricted factor analysis (RFA) can also be used to detect measurement bias. To also enable nonuniform…

  1. Site-specific genomic (SSG and random domain-localized (RDL mutagenesis in yeast

    Directory of Open Access Journals (Sweden)

    Honigberg Saul M

    2004-04-01

    Full Text Available Abstract Background A valuable weapon in the arsenal available to yeast geneticists is the ability to introduce specific mutations into yeast genome. In particular, methods have been developed to introduce deletions into the yeast genome using PCR fragments. These methods are highly efficient because they do not require cloning in plasmids. Results We have modified the existing method for introducing deletions in the yeast (S. cerevisiae genome using PCR fragments in order to target point mutations to this genome. We describe two PCR-based methods for directing point mutations into the yeast genome such that the final product contains no other disruptions. In the first method, site-specific genomic (SSG mutagenesis, a specific point mutation is targeted into the genome. In the second method, random domain-localized (RDL mutagenesis, a mutation is introduced at random within a specific domain of a gene. Both methods require two sequential transformations, the first transformation integrates the URA3 marker into the targeted locus, and the second transformation replaces URA3 with a PCR fragment containing one or a few mutations. This PCR fragment is synthesized using a primer containing a mutation (SSG mutagenesis or is synthesized by error-prone PCR (RDL mutagenesis. In SSG mutagenesis, mutations that are proximal to the URA3 site are incorporated at higher frequencies than distal mutations, however mutations can be introduced efficiently at distances of at least 500 bp from the URA3 insertion. In RDL mutagenesis, to ensure that incorporation of mutations occurs at approximately equal frequencies throughout the targeted region, this region is deleted at the same time URA3 is integrated. Conclusion SSG and RDL mutagenesis allow point mutations to be easily and efficiently incorporated into the yeast genome without disrupting the native locus.

  2. On the halo velocity bias

    CERN Document Server

    Biagetti, Matteo; Kehagias, Alex; Riotto, Antonio

    2014-01-01

    It has been recently shown that any halo velocity bias present in the initial conditions does not decay to unity, in agreement with predictions from peak theory. However, this is at odds with the standard formalism based on the coupled fluids approximation for the coevolution of dark matter and halos. Starting from conservation laws in phase space, we discuss why the fluid momentum conservation equation for the biased tracers needs to be modified in accordance with the change advocated in Baldauf, Desjacques & Seljak (2014). Our findings indicate that a correct description of the halo properties should properly take into account peak constraints when starting from the Vlasov-Boltzmann equation.

  3. Bias in Dynamic Monte Carlo Alpha Calculations

    Energy Technology Data Exchange (ETDEWEB)

    Sweezy, Jeremy Ed [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Nolen, Steven Douglas [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Adams, Terry R. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States); Trahan, Travis John [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-02-06

    A 1/N bias in the estimate of the neutron time-constant (commonly denoted as α) has been seen in dynamic neutronic calculations performed with MCATK. In this paper we show that the bias is most likely caused by taking the logarithm of a stochastic quantity. We also investigate the known bias due to the particle population control method used in MCATK. We conclude that this bias due to the particle population control method is negligible compared to other sources of bias.

  4. Microturbulence measurements during divertor biasing

    International Nuclear Information System (INIS)

    The application of a bias voltage to a neutralization plate of the upper divertor with respect to the vacuum chamber in the Tokamak de Varennes (TdeV) influences the plasma well inside the separatrix. In particular, the unbiased Ohmic poloidal rotation edge velocity measured by visible spectroscopy is found to be in the electron diamagnetic drift direction (2-3 km/s) and increases by a factor of two for Vbias = 100 V. This coincides with a major reduction of the microturbulence signal at low frequencies (50 kHz -1 -1), as determined from coherent laser scattering measurements. One possible explanation is that the turbulence signal is simply Doppler shifted to frequencies outside the accessible range. This scenario is, however, difficult to reconcile with some observations. Another explanation invokes a reduction of the turbulence level. The variation of the turbulence signal as a function of the applied bias voltage can indeed be reproduced with a theoretical model based on radial and poloidal decorrelation mechanisms, the latter corresponding to poloidal velocity shear stabilization. This model also explains the observed steepening of the k-spectrum decay during biasing. Biasing also modifies the electron density profile inside the separatrix. These changes of nabla ne cannot explain the behaviour of microturbulence behaviour, when explained in terms of stabilization, would agree with the plasma maintaining a steeper electron density gradient. (author). 17 refs, 9 figs

  5. Perception bias in route choice

    NARCIS (Netherlands)

    Vreeswijk, J.D.; Thomas, T.; Berkum, van E.C.; Arem, van B.

    2014-01-01

    Travel time is probably one of the most studied attributes in route choice. Recently, perception of travel time received more attention as several studies have shown its importance in explaining route choice behavior. In particular, travel time estimates by travelers appear to be biased against non-

  6. Bias in Peripheral Depression Biomarkers

    DEFF Research Database (Denmark)

    Carvalho, André F; Köhler, Cristiano A; Brunoni, André R;

    2016-01-01

    BACKGROUND: To aid in the differentiation of individuals with major depressive disorder (MDD) from healthy controls, numerous peripheral biomarkers have been proposed. To date, no comprehensive evaluation of the existence of bias favoring the publication of significant results or inflating effect...

  7. Minimum Bias Trigger in ATLAS

    International Nuclear Information System (INIS)

    Since the restart of the LHC in November 2009, ATLAS has collected inelastic pp collisions to perform first measurements on charged particle densities. These measurements will help to constrain various models describing phenomenologically soft parton interactions. Understanding the trigger efficiencies for different event types are therefore crucial to minimize any possible bias in the event selection. ATLAS uses two main minimum bias triggers, featuring complementary detector components and trigger levels. While a hardware based first trigger level situated in the forward regions with 2.2 < |η| < 3.8 has been proven to select pp-collisions very efficiently, the Inner Detector based minimum bias trigger uses a random seed on filled bunches and central tracking detectors for the event selection. Both triggers were essential for the analysis of kinematic spectra of charged particles. Their performance and trigger efficiency measurements as well as studies on possible bias sources will be presented. We also highlight the advantage of these triggers for particle correlation analyses. (author)

  8. Observer Biases in the Classroom.

    Science.gov (United States)

    Kite, Mary E.

    1991-01-01

    Presents three student exercises that demonstrate common perceptual errors described in social psychological literature: actor-observer effect, false consensus bias, and priming effects. Describes methods to be followed and gives terms, sentences, and a story to be used in the exercises. Suggests discussion of the bases and impact of such…

  9. Stereotype Formation : Biased by Association

    NARCIS (Netherlands)

    Le Pelley, Mike E.; Reimers, Stian J.; Calvini, Guglielmo; Spears, Russell; Beesley, Tom; Murphy, Robin A.

    2010-01-01

    We propose that biases in attitude and stereotype formation might arise as a result of learned differences ill the extent its which social groups have previously been predictive elf behavioral or physical properties Experiments 1 and 2 demonstrate that differences in the experienced predictiveness o

  10. Hypoxia induces mitochondrial mutagenesis and dysfunction in inflammatory arthritis.

    LENUS (Irish Health Repository)

    Biniecka, Monika

    2012-02-01

    mitochondrial genome mutagenesis, and antioxidants significantly rescue these events.

  11. Genome-Wide Synthetic Genetic Screening by Transposon Mutagenesis in Candida albicans

    Science.gov (United States)

    Horton, Brooke N.; Kumar, Anuj

    2016-01-01

    Transposon-based mutagenesis is an effective method for genetic screening on a genome-wide scale, with particular applicability in organisms possessing compact genomes where transforming DNA tends to integrate by homologous recombination. Methods for transposon mutagenesis have been applied with great success in the budding yeast Saccharomyces cerevisiae and in the related pathogenic yeast Candida albicans. In C. albicans, we have implemented transposon mutagenesis to generate heterozygous mutations for the analysis of complex haploinsufficiency, a type of synthetic genetic interaction wherein a pair of non-complementing heterozygous mutations results in a stronger phenotype then either individual mutation in isolation. Genes exhibiting complex haploinsufficiency typically function within a regulatory pathway, in parallel pathways, or in parallel branches within a single pathway. Here, we present protocols to implement transposon mutagenesis for complex haploinsufficiency screening in C. albicans, indicating methods for transposon construction, mutagenesis, phenotypic screening, and identification of insertion sites in strains of interest. In total, the approach is a useful means to implement large-scale synthetic genetic screening in the diploid C. albicans. PMID:25636616

  12. Bromouracil mutagenesis in Escherichia coli evidence for involvement of mismatch repair

    Energy Technology Data Exchange (ETDEWEB)

    Rydberg, B.

    1977-01-01

    Bromouracil mutagenesis was studied in several strains of E. coli in combination with measurement of incorporation of bromouracil in DNA. For levels below 10% total replacement of bromouracil for thymine, mutagenesis was negligible compared with higher levels of incorporation. Such a nonlinear response occurred both when the bromouracil was evenly distributed over the genome and when a small proportion of the genome was highly substituted. Also, the mutation frequency could be drastically lowered by amino acid starvation following bromouracil incorporation. These observations suggest the involvement of repair phenomena. Studies of mutagenesis in recA/sup -/ and uvrA/sup -/ mutants, as well as studies of prophage induction, did not support an ''error prone'' repair pathway of mutagenesis. On the other hand, uvrD/sup -/ and uvrE/sup -/ mutants, which are deficient in DNA mismatch repair, had much increased mutation frequencies compared with wild type cells. The mutagenic action of bromouracil showed specificity under the conditions used, as demonstrated by the inability of bromouracil to revert an ochre codon that was easily revertable by ultraviolet light irradiation. The results are consistent with a mechanism of bromouracil mutagenesis involvng mispairing, but suggest that the final mutation frequencies depend on repair that removes mismatched bases.

  13. Information environment, behavioral biases, and home bias in analysts’ recommendations

    DEFF Research Database (Denmark)

    Farooq, Omar; Taouss, Mohammed

    2012-01-01

    show that optimism difference between the two groups is more than twice as much in firms with poor information environment than in firms with better information environment. We argue that poor information environment pose greater information asymmetries to foreign analysts regarding local firms...... relative to local analysts. As a result, we expect them to be less optimistic in their recommendations relative to local analysts. However, for firms with better information environment, foreign analysts face less information asymmetries. As a result, they are relatively more optimistic (less pessimistic......Can information environment of a firm explain home bias in analysts’ recommendations? Can the extent of agency problems explain optimism difference between foreign and local analysts? This paper answers these questions by documenting the effect of information environment on home bias in analysts...

  14. Is Weigle-mutagenesis in uv-irradiated bacteriophage lambda a myth

    International Nuclear Information System (INIS)

    It is argued that Weigle-mutagenesis, a higher mutation frequency observed when uv-irradiated are allowed to infect uv-irradiated bacteria, is often a trivial artifact rather than a manifestation of an error-prone bacterial DNA repair. It may occur due to the slower replication of irradiated phages which results in more replication taking place when a mutator polymerase activity has become induced and expressed than is the case with intact phages. The mutator polymerase activity is inducible in recA+ cells but it is not under the control of the lexA repressor. Weigle-mutagenesis under these conditions is untargeted and is not a good model for bacterial uv mutagenesis. 12 references

  15. Effect of umuC mutations on targeted and untargeted ultraviolet mutagenesis in bacteriophage lambda

    International Nuclear Information System (INIS)

    Mutagenesis of phage lambda towards clear-plaque (c+ → c) results in two classes of mutants that can be distinguished genetically and morphologically. Indirect mutagenesis, i.e. mutagenesis of unirradiated phage lambdac+ stimulated by the ultraviolet irradiation of the Escherichia coli host, results in mixed bursts (c/c+) of turbid wild-type and clear=plaque mutant phages. Pure bursts of lambdac mutants are induced by irradiation of the phage genome. Irradiation of both phages and host bacteria stimulates the production of the two classes of mutant clones. It is shown that three different mutant alleles of the E. coli umuC gene only prevent the appearance of pure bursts of clear-plaque mutants, while mixed bursts are produced at least as frequently in umuC mutants as in the umuC+ parent. (author)

  16. Targeted Mutagenesis in Rice Using TALENs and the CRISPR/Cas9 System.

    Science.gov (United States)

    Endo, Masaki; Nishizawa-Yokoi, Ayako; Toki, Seiichi

    2016-01-01

    Sequence-specific nucleases (SSNs), such as zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspersed short palindromic repeats (CRISPR)/CRISPR-associated protein 9 nuclease (Cas9) system, are powerful tools for understanding gene function and for developing novel traits in plants. In plant species for which transformation and regeneration systems using protoplasts are not yet established, direct delivery to nuclei of SSNs either in the form of RNA or protein is difficult. Thus, Agrobacterium-mediated transformation of SSN expression constructs in cultured cells is a practical means of delivering targeted mutagenesis in some plant species including rice. Because targeted mutagenesis occurs stochastically in transgenic cells and SSN-mediated targeted mutagenesis often leads to no selectable phenotype, identification of highly mutated cell lines is a critical step in obtaining regenerated plants with desired mutations. PMID:27557690

  17. The influence of glycerol on γ-induced mutagenesis in Salmonella typhimurium cells

    International Nuclear Information System (INIS)

    A study was made of the modifying effect of glycerol on the survival rate and γ-radiation-induced mutagenesis of Salmonella typhimurium cells TA98, TA100 and TA102. The DMF value, with respect to the survival rate, was 2.05-0.20. The dependence of the yield of γ-radiation-induced mutants on radiation dose was described by the curve with a maximum; the mutation frequency M(D) was well described by a gradual function M(D)=kDx. DMF values of the induced mutagenesis amounted to 2 for strains TA100 and TA102, and 1.5 for strain TA98

  18. Ultrafast solvation dynamics at internal site of staphylococcal nuclease investigated by site-directed mutagenesis

    CERN Document Server

    Guang-yu, Gao; Wei, Wang; Shu-feng, Wang; Zhong, Dongping; Qi-huang, Gong

    2014-01-01

    Solvation is essential for protein activities. To study internal solvation of protein, site-directed mutagenesis is applied. Intrinsic fluorescent probe, tryptophan, is inserted into desired position inside protein molecule for ultrafast spectroscopic study. Here we review this unique method for protein dynamics researches. We introduce the frontiers of protein solvation, site-directed mutagenesis, protein stability and characteristics, and the spectroscopic methods. Then we present time-resolved spectroscopic dynamics of solvation dynamics inside caves of active sites. The studies are carried out on a globular protein, staphylococcal nuclease. The solvation at internal sites of the caves indicate clear characteristics of local environment. These solvation behaviors correlated to the enzyme activity directly.

  19. Opinion Dynamics with Confirmation Bias

    CERN Document Server

    Allahverdyan, A E

    2014-01-01

    Background: Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings: We formulate a (non-Bayesian) model for revising subjective probabilistic opinion of a confirmationally-biased agent in the light of a persuasive opinion. The revision rule ensures that the agent does not react to persuasion that is either far from his current opinion or coincides with it. We demonstrate that the model accounts for the basic phenomenology of the social judgment theory, and allows to study various phenomena such as cognitive dissonance and boomerang effect. The model also displays the order of presentation effect|when consecutively exposed to two opinions, the preferenc...

  20. A quantum exchange bias model

    International Nuclear Information System (INIS)

    The origin of the exchange bias phenomenon is investigated on the basis of a quantum mechanical model. In particular, the mechanisms that determine the magnetic structure in the vicinity of an antiferromagnetic-ferromagnetic interface are reexamined. This way we establish how the breaking of translational invariance modifies quantum spin fluctuations. It is found that non-uniform fluctuations induce uncompensated spins in the antiferromagnet, which in turn give rise to a dipole field that couples to the magnetization of the ferromagnet. This coupling yields an exchange bias field that is of the order of magnitude of the one observed experimentally. A net surface magnetization should also be experimentally observable in a clean antiferromagnetic surface

  1. Variable-bias coin tossing

    International Nuclear Information System (INIS)

    Alice is a charismatic quantum cryptographer who believes her parties are unmissable; Bob is a (relatively) glamorous string theorist who believes he is an indispensable guest. To prevent possibly traumatic collisions of self-perception and reality, their social code requires that decisions about invitation or acceptance be made via a cryptographically secure variable-bias coin toss (VBCT). This generates a shared random bit by the toss of a coin whose bias is secretly chosen, within a stipulated range, by one of the parties; the other party learns only the random bit. Thus one party can secretly influence the outcome, while both can save face by blaming any negative decisions on bad luck. We describe here some cryptographic VBCT protocols whose security is guaranteed by quantum theory and the impossibility of superluminal signaling, setting our results in the context of a general discussion of secure two-party computation. We also briefly discuss other cryptographic applications of VBCT

  2. Cosmological Evolution of Linear Bias

    CERN Document Server

    Basilakos, S; Basilakos, Spyros; Plionis, Manolis

    2000-01-01

    Using linear perturbation theory and the Friedmann-Lemaitre solutions of the cosmological field equations, we derive analytically a second-order differential equation for the evolution of the linear bias factor, b(z), between the background matter and a mass-tracer fluctuation field. We find b(z) to be a strongly dependent function of redshift in all cosmological models. Comparing our analytical solution with the semi-analytic model of Mo & White, which utilises the Press-Schechter formalism and the gravitationally induced evolution of clustering, we find an extremely good agreement even at large redshifts, once we normalize to the same bias value at two different epochs, one of which is the present. Furthermore, our analytic b(z) function agrees well with the outcome of N-body simulations even up to large redshifts.

  3. Probability biases as Bayesian inference

    Directory of Open Access Journals (Sweden)

    Andre; C. R. Martins

    2006-11-01

    Full Text Available In this article, I will show how several observed biases in human probabilistic reasoning can be partially explained as good heuristics for making inferences in an environment where probabilities have uncertainties associated to them. Previous results show that the weight functions and the observed violations of coalescing and stochastic dominance can be understood from a Bayesian point of view. We will review those results and see that Bayesian methods should also be used as part of the explanation behind other known biases. That means that, although the observed errors are still errors under the be understood as adaptations to the solution of real life problems. Heuristics that allow fast evaluations and mimic a Bayesian inference would be an evolutionary advantage, since they would give us an efficient way of making decisions. %XX In that sense, it should be no surprise that humans reason with % probability as it has been observed.

  4. Jets in minimum bias physics

    International Nuclear Information System (INIS)

    Discussion was made on a phenomenological evidence to support the hypothesis that several new phenomena observed in low psub(t) physics are due to the presence of low-x QCD jets in minimum bias physics. The phenomena we examine are KNO scaling violations, growth of with multiplicity and rise of the non-single diffractive part of the total cross-section. We have discussed the importance of low-x hard parton scattering in minimum bias events and pointed out its connection to both KNO scaling violations as well as to the observed growth of with multiplicity in inclusive pion distributions. The contribution of these mini-jets to the total cross-section has been calculated and a model for the transverse energy distribution characterizing any event accompanied by jets has been presented. (author)

  5. Girl child and gender bias.

    Science.gov (United States)

    Chowdhry, D P

    1995-01-01

    This article identifies gender bias against female children and youth in India. Gender bias is based on centuries-old religious beliefs and sayings from ancient times. Discrimination is reflected in denial or ignorance of female children's educational, health, nutrition, and recreational needs. Female infanticide and selective abortion of female fetuses are other forms of discrimination. The task of eliminating or reducing gender bias will involve legal, developmental, political, and administrative measures. Public awareness needs to be created. There is a need to reorient the education and health systems and to advocate for gender equality. The government of India set the following goals for the 1990s: to protect the survival of the girl child and practice safe motherhood; to develop the girl child in general; and to protect vulnerable girl children in different circumstances and in special groups. The Health Authorities should monitor the laws carefully to assure marriage after the minimum age, ban sex determination of the fetus, and monitor the health and nutrition of pre-school girls and nursing and pregnant mothers. Mothers need to be encouraged to breast feed, and to breast feed equally between genders. Every village and slum area needs a mini health center. Maternal mortality must decline. Primary health centers and hospitals need more women's wards. Education must be universally accessible. Enrollments should be increased by educating rural tribal and slum parents, reducing distances between home and school, making curriculum more relevant to girls, creating more female teachers, and providing facilities and incentives for meeting the needs of girl students. Supplementary income could be provided to families for sending girls to school. Recreational activities must be free of gender bias. Dowry, sati, and devdasi systems should be banned. PMID:12158019

  6. Investigating Endogeneity Bias in Marketing

    OpenAIRE

    Qing Liu; Thomas Otter; Greg M. Allenby

    2007-01-01

    The use of adaptive designs in conjoint analysis has been shown to lead to an endogeneity bias in part-worth estimates using sampling experiments. In this paper, we re-examine the endogeneity issue in light of the likelihood principle. The likelihood principle asserts that all relevant information in the data about model parameters is contained in the likelihood function. We show that, once the data are collected, adhering to the likelihood principle leads to analysis where endogeneity become...

  7. Competition and Commercial Media Bias

    OpenAIRE

    BLASCO, A.; F. Sobbrio

    2011-01-01

    This paper reviews the empirical evidence on commercial media bias (i.e., advertisers influence over media accuracy) and then introduces a simple model to summarize the main elements of the theoretical literature. The analysis provides three main policy insights for media regulators: i) Media regulators should target their monitoring efforts towards news contents upon which advertisers are likely to share similar preferences; ii) In advertising industries characterized by high correlation in ...

  8. Opinion Dynamics with Confirmation Bias

    OpenAIRE

    Allahverdyan, Armen E.; Aram Galstyan

    2014-01-01

    Background: Confirmation bias is the tendency to acquire or evaluate new information in a way that is consistent with one's preexisting beliefs. It is omnipresent in psychology, economics, and even scientific practices. Prior theoretical research of this phenomenon has mainly focused on its economic implications possibly missing its potential connections with broader notions of cognitive science. Methodology/Principal Findings: We formulate a (non-Bayesian) model for revising subjective proba...

  9. Generalization of the FRAM's Bias

    International Nuclear Information System (INIS)

    The Fixed-Energy Response-Function Analysis with Multiple Efficiency (FRAM) code was developed at Los Alamos National Laboratory to measure the gamma-ray spectrometry of the isotopic composition of plutonium, uranium, and other actinides. Its reported uncertainties of the results come from the propagation of the statistics in the peak areas only. No systematic error components are included in the reported uncertainties. We have done several studies and found that the FRAM's statistical precision can be reasonably represented by its reported uncertainties. The FRAM's biases or systematic uncertainties can come from a variety of sources and can be difficult to determine. We carefully examined the FRAM analytical results of the archival plutonium data and of the data specifically acquired for this isotopic uncertainty analysis project and found the relationship between the bias and other parameters. We worked out the equations representing the biases of the measured isotopes from each measurement using the internal parameters in the spectrum such as peak resolution and shape, region of analysis, and burnup (for plutonium) or enrichment (for uranium)

  10. Significant biases affecting abundance determinations

    Science.gov (United States)

    Wesson, Roger

    2015-08-01

    I have developed two highly efficient codes to automate analyses of emission line nebulae. The tools place particular emphasis on the propagation of uncertainties. The first tool, ALFA, uses a genetic algorithm to rapidly optimise the parameters of gaussian fits to line profiles. It can fit emission line spectra of arbitrary resolution, wavelength range and depth, with no user input at all. It is well suited to highly multiplexed spectroscopy such as that now being carried out with instruments such as MUSE at the VLT. The second tool, NEAT, carries out a full analysis of emission line fluxes, robustly propagating uncertainties using a Monte Carlo technique.Using these tools, I have found that considerable biases can be introduced into abundance determinations if the uncertainty distribution of emission lines is not well characterised. For weak lines, normally distributed uncertainties are generally assumed, though it is incorrect to do so, and significant biases can result. I discuss observational evidence of these biases. The two new codes contain routines to correctly characterise the probability distributions, giving more reliable results in analyses of emission line nebulae.

  11. Random UV-C mutagenesis of Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 to improve anaerobic growth on lignocellulosic sugars

    Science.gov (United States)

    Yeast strains for anaerobic conversion of lignocellulosic sugars to ethanol were produced from Scheffersomyces (formerly Pichia) stipitis NRRL Y-7124 using UV-C mutagenesis. Random UV-C mutagenesis potentially produces large numbers of mutations broadly and uniformly over the whole genome to genera...

  12. The Probability Distribution for a Biased Spinner

    Science.gov (United States)

    Foster, Colin

    2012-01-01

    This article advocates biased spinners as an engaging context for statistics students. Calculating the probability of a biased spinner landing on a particular side makes valuable connections between probability and other areas of mathematics. (Contains 2 figures and 1 table.)

  13. Bias in Absolute Magnitude Determination from Parallaxes

    OpenAIRE

    Feast, Michael

    2002-01-01

    Relations are given for the correction of bias when mean absolute magnitudes are derived by the method of reduced parallaxes. The bias in the case of the derivation of the absolute magnitudes of individual objects is also considered.

  14. A Pharmacological Primer of Biased Agonism

    OpenAIRE

    Andresen1, Bradley T.

    2011-01-01

    Biased agonism is one of the fastest growing topics in G protein-coupled receptor pharmacology; moreover, biased agonists are used in the clinic today: carvedilol (Coreg®) is a biased agonist of beta-adrenergic receptors. However, there is a general lack of understanding of biased agonism when compared to traditional pharmacological terminology. Therefore, this review is designed to provide a basic introduction to classical pharmacology as well as G protein-coupled receptor signal transductio...

  15. Galaxy peculiar velocities and evolution-bias

    OpenAIRE

    Percival, Will; Schafer, B.

    2007-01-01

    Galaxy bias can be split into two components: a formation-bias based on the locations of galaxy creation, and an evolution-bias that details their subsequent evolution. In this letter we consider evolution-bias in the peaks model. In this model, galaxy formation takes place at local maxima in the density field, and we analyse the subsequent peculiar motion of these galaxies in a linear model of structure formation. The peak restriction yields differences in the velocity distribution and corre...

  16. Unlearning Implicit Social Biases During Sleep **

    OpenAIRE

    Hu, Xiaoqing; Antony, James W.; Creery, Jessica D.; Vargas, Iliana M.; Bodenhausen, Galen V.; Paller, Ken A.

    2015-01-01

    Although people may endorse egalitarianism and tolerance, social biases can remain operative and drive harmful actions in an unconscious manner. Here we investigated training to reduce implicit racial and gender bias. Forty participants processed counter-stereotype information paired with one sound for each type of bias. Biases were reduced immediately after training. During subsequent slow-wave sleep, one sound was unobtrusively presented to each participant, repeatedly, to reactivate one ty...

  17. Selection bias in rheumatic disease research

    OpenAIRE

    Choi, Hyon K.; Nguyen, Uyen-Sa; Niu, Jingbo; Danaei, Goodarz; Zhang, Yuqing

    2014-01-01

    The identification of modifiable risk factors for the development of rheumatic conditions and their sequelae is crucial for reducing the substantial worldwide burden of these diseases. However, the validity of such research can be threatened by sources of bias, including confounding, measurement and selection biases. In this Review, we discuss potentially major issues of selection bias—a type of bias frequently overshadowed by other bias and feasibility issues, despite being equally or more p...

  18. Spallation neutron source RF cavity bias system

    International Nuclear Information System (INIS)

    The Spallation Neutron Source r.f. cavity bias system is described under the topic headings: bias system, r.f. cavity, cables, d.c. bias power supply, transistor regulator and control system. Calculation of 4 core 300 mm solid aluminium cable inductance, coaxial shunt frequency response and transistor regulator computed frequency response, are discussed in appendices 1-3. (U.K.)

  19. Begging the Question: Is Critical Thinking Biased?

    Science.gov (United States)

    Alston, Kal

    1995-01-01

    Discusses whether critical thinking is biased, examining what is meant by critical thinking and bias and what the consequences are for addressing bias in different ways. The paper responds to the three previous papers in the critical thinking symposium in this issue of the journal. (SM)

  20. Outcome-Reporting Bias in Education Research

    Science.gov (United States)

    Pigott, Therese D.; Valentine, Jeffrey C.; Polanin, Joshua R.; Williams, Ryan T.; Canada, Dericka D.

    2013-01-01

    Outcome-reporting bias occurs when primary studies do not include information about all outcomes measured in a study. When studies omit findings on important measures, efforts to synthesize the research using systematic review techniques will be biased and interpretations of individual studies will be incomplete. Outcome-reporting bias has been…

  1. A Review of Studies on Media Bias at Home

    Institute of Scientific and Technical Information of China (English)

    辛一丹

    2015-01-01

    Bias is widely existed nowadays.Domestic scholars have done a lot of research on the bias,especially the media bias.They studied the media bias from different perspectives,such as the bias on China image,the bias of a certain media FOX,the bias on the venerable group,the bias on women and so on.The author plans to give a review of the studies on media bias at home in this paper.

  2. A Review of Studies on Media Bias at Home

    Institute of Scientific and Technical Information of China (English)

    辛一丹

    2015-01-01

    Bias is widely existed nowadays. Domestic scholars have done a lot of research on the bias, especially the media bias. They studied the media bias from different perspectives, such as the bias on China image,the bias of a certain media FOX, the bias on the venerable group, the bias on women and so on. The author plans to give a review of the studies on media bias at home in this paper.

  3. The hermes transposon of Musca domestica is an efficient tool for the mutagenesis of Schizosaccharomyces pombe.

    Science.gov (United States)

    Evertts, Adam G; Plymire, Christopher; Craig, Nancy L; Levin, Henry L

    2007-12-01

    Currently, no transposon-based method for the mutagenesis of Schizosaccharomyces pombe exists. We have developed such a system based on the introduction of the hermes transposon from the housefly into S. pombe. This system efficiently disrupts open reading frames and allows the insertion sites to be readily identified. PMID:17947404

  4. Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis.

    Science.gov (United States)

    Wang, Kaile; Ma, Xiaolu; Zhang, Xue; Wu, Dafei; Sun, Chenyi; Sun, Yazhou; Lu, Xuemei; Wu, Chung-I; Guo, Caixia; Ruan, Jue

    2016-01-01

    Next generation sequencing (NGS) technologies have dramatically improved studies in biology and biomedical science. However, no optimal NGS approach is available to conveniently analyze low frequency mutations caused by DNA damage treatments. Here, by developing an exquisite ultra-sensitive NGS (USNGS) platform "EasyMF" and incorporating it with a widely used supF shuttle vector-based mutagenesis system, we can conveniently dissect roles of lesion bypass polymerases in damage-induced mutagenesis. In this improved mutagenesis analysis pipeline, the initial steps are the same as in the supF mutation assay, involving damaging the pSP189 plasmid followed by its transfection into human 293T cells to allow replication to occur. Then "EasyMF" is employed to replace downstream MBM7070 bacterial transformation and other steps for analyzing damage-induced mutation frequencies and spectra. This pipeline was validated by using UV damaged plasmid after its replication in lesion bypass polymerase-deficient 293T cells. The increased throughput and reduced cost of this system will allow us to conveniently screen regulators of translesion DNA synthesis pathway and monitor environmental genotoxic substances, which can ultimately provide insight into the mechanisms of genome stability and mutagenesis. PMID:27122023

  5. Applied an Efficient Site-directed Mutagenesis Method into Escherichia coli

    Directory of Open Access Journals (Sweden)

    Muqing Qiu

    2011-03-01

    Full Text Available A new technique for conducting site-directed mutagenesis was developed. This method allows the color selection of mutants through the simultaneous activation or deactivation of the α-peptide of ß-galactosidase. The method can efficiently create mutations at multiple sites simultaneously and can be used to perform multiple rounds of mutation on the same construct. In this paper, in order to develop an efficient site-directed mutagenesis method in vivo, the tests were tested by the following methods. The methods that the fragment knock-out ompR gene was constructed through overlapping PCR, digested by Notand SalⅠⅠ, ligated to plasmid pKOV were applied. The recombination plasmid was transformed into Escherichia coli WMC-001 strain, integrated into the genomic DNA through two step homologous recombination. The Escherichia coli WMC-001/ompR- mutant was obtained due to gene replacement. The fragment of the mutant ompR gene was amplified through overlapping PCR, cloned into pKOV vector. The recombinant plasmid was introduced into Escherichia coli WMC-001/ompR- mutant. The Escherichia coli WMC-001/ompR mutant was also obtained due to gene replacement. Results: The site-directed mutagenesis has been successfully constructed in the ompR gene by sequencing. Conclusion: The method is effective for construction of gene site-directed mutagenesis in vivo.

  6. Using ultra-sensitive next generation sequencing to dissect DNA damage-induced mutagenesis

    Science.gov (United States)

    Wang, Kaile; Ma, Xiaolu; Zhang, Xue; Wu, Dafei; Sun, Chenyi; Sun, Yazhou; Lu, Xuemei; Wu, Chung-I; Guo, Caixia; Ruan, Jue

    2016-01-01

    Next generation sequencing (NGS) technologies have dramatically improved studies in biology and biomedical science. However, no optimal NGS approach is available to conveniently analyze low frequency mutations caused by DNA damage treatments. Here, by developing an exquisite ultra-sensitive NGS (USNGS) platform “EasyMF” and incorporating it with a widely used supF shuttle vector-based mutagenesis system, we can conveniently dissect roles of lesion bypass polymerases in damage-induced mutagenesis. In this improved mutagenesis analysis pipeline, the initial steps are the same as in the supF mutation assay, involving damaging the pSP189 plasmid followed by its transfection into human 293T cells to allow replication to occur. Then “EasyMF” is employed to replace downstream MBM7070 bacterial transformation and other steps for analyzing damage-induced mutation frequencies and spectra. This pipeline was validated by using UV damaged plasmid after its replication in lesion bypass polymerase-deficient 293T cells. The increased throughput and reduced cost of this system will allow us to conveniently screen regulators of translesion DNA synthesis pathway and monitor environmental genotoxic substances, which can ultimately provide insight into the mechanisms of genome stability and mutagenesis. PMID:27122023

  7. Insertion mutagenesis of the yeast Candida famata (Debaryomyces hansenii) by random integration of linear DNA fragments.

    Science.gov (United States)

    Dmytruk, Kostyantyn V; Voronovsky, Andriy Y; Sibirny, Andriy A

    2006-09-01

    The feasibility of using random insertional mutagenesis to isolate mutants of the flavinogenic yeast Candida famata was explored. Mutagenesis was performed by transformation of the yeast with an integrative plasmid containing the Saccharomyces cerevisiae LEU2 gene as a selective marker. The addition of restriction enzyme together with the plasmid (restriction enzyme-mediated integration, REMI) increased the transformation frequency only slightly. Integration of the linearized plasmid occurred randomly in the C. famata genome. To investigate the potential of insertional mutagenesis, it was used for tagging genes involved in positive regulation of riboflavin synthesis in C. famata. Partial DNA sequencing of tagged genes showed that they were homologous to the S. cerevisiae genes RIB1, MET2, and SEF1. Intact orthologs of these genes isolated from Debaryomyces hansenii restored the wild phenotype of the corresponding mutants, i.e., the ability to overproduce riboflavin under iron limitation. The Staphylococcus aureus ble gene conferring resistance to phleomycin was used successfully in the study as a dominant selection marker for C. famata. The results obtained indicate that insertional mutagenesis is a powerful tool for tagging genes in C. famata. PMID:16770625

  8. Building on the Past, Shaping the Future: The Environmental Mutagenesis and Genomics Society

    Science.gov (United States)

    In late 2012 the members of the Environmental Mutagen Society voted to change its name to the Environmental Mutagenesis and Genomics Society. Here we describe the thought process that led to adoption of the new name, which both respects the rich history of a Society founded in 19...

  9. Workshop on ENU Mutagenesis: Planning for Saturation, July 25-28, 2002

    Energy Technology Data Exchange (ETDEWEB)

    Nadeau, Joseph H

    2002-07-25

    The goal of the conference is to enhance the development of improved technologies and new approaches to the identification of genes underlying chemically-induced mutant phenotypes. The conference brings together ENU mutagenesis experts from the United States and aborad for a small, intensive workshop to consider these issues.

  10. Improvement of Biocatalysts for Industrial and Environmental Purposes by Saturation Mutagenesis

    Directory of Open Access Journals (Sweden)

    Francesca Valetti

    2013-10-01

    Full Text Available Laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. The palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. A technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturation mutagenesis. Here we will present and discuss this approach in its many facets, also tackling the issue of randomization, statistical evaluation of library completeness and throughput efficiency of screening methods. Successful recent applications covering different classes of enzymes will be presented referring to the literature and to research lines pursued in our group. The focus is put on saturation mutagenesis as a tool for designing novel biocatalysts specifically relevant to production of fine chemicals for improving bulk enzymes for industry and engineering technical enzymes involved in treatment of waste, detoxification and production of clean energy from renewable sources.

  11. Identification of a novel streptococcal gene cassette mediating SOS mutagenesis in Streptococcus uberis

    NARCIS (Netherlands)

    Varhimo, Emilia; Savijoki, Kirsi; Jalava, Jari; Kuipers, Oscar P.; Varmanen, Pekka

    2007-01-01

    Streptococci have been considered to lack the classical SOS response, defined by increased mutation after UV exposure and regulation by LexA. Here we report the identification of a potential self-regulated SOS mutagenesis gene cassette in the Streptococcaceae family. Exposure to UV light was found t

  12. Random mutagenesis strategies for construction of large and diverse clone libraries of mutated DNA fragments.

    Science.gov (United States)

    Chusacultanachai, Sudsanguan; Yuthavong, Yongyuth

    2004-01-01

    The first important step toward a successful preparation of large and diverse DNA libraries with desired complexity is to select a suitable mutagenesis strategy. This chapter describes three different methods for random mutagenesis, the use of XL1-red cells, error-prone polymerase chain reaction (PCR), and degenerate oligonucleotides-Pfu (DOP). These mutagenesis strategies possess different benefits and pitfalls; thus, they are differentially useful for production of DNA libraries with different density and complexity. The use of XL1-red, an engineered Escherichia coli with DNA repair deficiency, is one of the simplest mutagenesis and requires no subcloning step. After plasmid encoding DNA of inter-est is transformed into the cells, the mutations are simply generated during each round of DNA replication. The mutation frequency of this method is reported to be 1 base change per 2000 nucleotides; however, it can be slightly increased by extending the culture period to allow the accumulation of more mutations. This strategy is suitable for generation of random mutations with low frequency in a large target DNA. Error-prone PCR is one of the most widely used random mutagenesis. During DNA amplification, misincorporation of nucleotides can be promoted by altering the nucleotide ratio and the concentration of divalent cations in the reaction. We discovered that, by adjusting template concentration, frequency of mutation could be controlled easily and a library with desired mutation rate could be obtained. Additionally, efficiency of subsequent cloning steps to insert the PCR product into plasmid DNA is also a key factor determining size and complexity of the libraries. DOP mutagenesis is a rapid and effective method for random mutagenesis of small DNA and peptides. This strategy uses two chemically synthesized degenerate oligonucleotides as primers. By controlling the positions and ratios of degenerate nucleotides used during oligonucleotide synthesis, it is possible to

  13. Challenges in bias correcting climate change simulations

    Science.gov (United States)

    Maraun, Douglas; Shepherd, Ted; Zappa, Giuseppe; Gutierrez, Jose; Widmann, Martin; Hagemann, Stefan; Richter, Ingo; Soares, Pedro; Mearns, Linda

    2016-04-01

    Biases in climate model simulations - if these are directly used as input for impact models - will introduce further biases in subsequent impact simulations. In response to this issue, so-called bias correction methods have been developed to post-process climate model output. These methods are now widely used and a crucial component in the generation of high resolution climate change projections. Bias correction is conceptually similar to model output statistics, which has been successfully used for several decades in numerical weather prediction. Yet in climate science, some authors outrightly dismiss any form of bias correction. Starting from this seeming contradiction, we highlight differences between the two contexts and infer consequences and limitations for the applicability of bias correction to climate change projections. We first show that cross validation approaches successfully used to evaluate weather forecasts are fundamentally insufficient to evaluate climate change bias correction. We further demonstrate that different types of model mismatches with observations require different solutions, and some may not sensibly be mitigated. In particular we consider the influence of large-scale circulation biases, biases in the persistence of weather regimes, and regional biases caused by an insufficient representation of the flow-topography interaction. We conclude with a list of recommendations and suggestions for future research to reduce, to post-process, and to cope with climate model biases.

  14. Unlearning Implicit Social Biases During Sleep **

    Science.gov (United States)

    Hu, Xiaoqing; Antony, James W.; Creery, Jessica D.; Vargas, Iliana M.; Bodenhausen, Galen V.; Paller, Ken A.

    2015-01-01

    Although people may endorse egalitarianism and tolerance, social biases can remain operative and drive harmful actions in an unconscious manner. Here we investigated training to reduce implicit racial and gender bias. Forty participants processed counter-stereotype information paired with one sound for each type of bias. Biases were reduced immediately after training. During subsequent slow-wave sleep, one sound was unobtrusively presented to each participant, repeatedly, to reactivate one type of training. Corresponding bias reductions were fortified in comparison to the social bias not externally reactivated during sleep. This advantage remained one week later, the magnitude of which was associated with time in slow-wave and rapid-eye-movement sleep after training. We conclude that memory reactivation during sleep enhances counter-stereotype training, and that maintaining a bias reduction is sleep-dependent. PMID:26023137

  15. Distraction from emotional information reduces biased judgements.

    Science.gov (United States)

    Lench, Heather C; Bench, Shane W; Davis, Elizabeth L

    2016-06-01

    Biases arising from emotional processes are some of the most robust behavioural effects in the social sciences. The goal of this investigation was to examine the extent to which the emotion regulation strategy of distraction could reduce biases in judgement known to result from emotional information. Study 1 explored lay views regarding whether distraction is an effective strategy to improve decision-making and revealed that participants did not endorse this strategy. Studies 2-5 focused on several established, robust biases that result from emotional information: loss aversion, desirability bias, risk aversion and optimistic bias. Participants were prompted to divert attention away from their feelings while making judgements, and in each study this distraction strategy resulted in reduced bias in judgement relative to control conditions. The findings provide evidence that distraction can improve choice across several situations that typically elicit robustly biased responses, even though participants are not aware of the effectiveness of this strategy. PMID:25787937

  16. Selection bias in rheumatic disease research

    Science.gov (United States)

    Choi, Hyon K.; Nguyen, Uyen-Sa; Niu, Jingbo; Danaei, Goodarz; Zhang, Yuqing

    2014-01-01

    The identification of modifiable risk factors for the development of rheumatic conditions and their sequelae is crucial for reducing the substantial worldwide burden of these diseases. However, the validity of such research can be threatened by sources of bias, including confounding, measurement and selection biases. In this Review, we discuss potentially major issues of selection bias—a type of bias frequently overshadowed by other bias and feasibility issues, despite being equally or more problematic—in key areas of rheumatic disease research. We present index event bias (a type of selection bias) as one of the potentially unifying reasons behind some unexpected findings, such as the ‘risk factor paradox’—a phenomenon exemplified by the discrepant effects of certain risk factors on the development versus the progression of osteoarthritis (OA) or rheumatoid arthritis (RA). We also discuss potential selection biases owing to differential loss to follow-up in RA and OA research, as well as those due to the depletion of susceptibles (prevalent user bias) and immortal time bias. The lesson remains that selection bias can be ubiquitous and, therefore, has the potential to lead the field astray. Thus, we conclude with suggestions to help investigators avoid such issues and limit the impact on future rheumatology research. PMID:24686510

  17. Forecasts: uncertain, inaccurate and biased?

    DEFF Research Database (Denmark)

    Nicolaisen, Morten Skou; Ambrasaite, Inga; Salling, Kim Bang

    2012-01-01

    construction costs, which account for the majority of total project costs. Second are the forecasts of travel time savings, which account for the majority of total project benefits. The latter of these is, inter alia, determined by forecasts of travel demand, which we shall use as a proxy for the forecasting......Cost Benefit Analysis (CBA) is the dominating methodology for appraisal of transport infrastructure projects across the globe. In order to adequately assess the costs and benefits of such projects two types of forecasts are crucial to the validity of the appraisal. First are the forecasts of...... accuracy of project benefits. This paper presents results from an on-going research project on uncertainties in transport project evaluation (UNITE) that find forecasts of demand to be not only uncertain, but at times also highly inaccurate and often displaying a concerning degree of bias. Demand for road...

  18. Modeling confirmation bias and polarization

    CERN Document Server

    Del Vicario, Michela; Caldarelli, Guido; Stanley, H Eugene; Quattrociocchi, Walter

    2016-01-01

    Online users tend to select claims that adhere to their system of beliefs and to ignore dissenting information. Confirmation bias, indeed, plays a pivotal role in viral phenomena. Furthermore, the wide availability of content on the web fosters the aggregation of likeminded people where debates tend to enforce group polarization. Such a configuration might alter the public debate and thus the formation of the public opinion. In this paper we provide a mathematical model to study online social debates and the related polarization dynamics. We assume the basic updating rule of the Bounded Confidence Model (BCM) and we develop two variations a) the Rewire with Bounded Confidence Model (RBCM), in which discordant links are broken until convergence is reached; and b) the Unbounded Confidence Model, under which the interaction among discordant pairs of users is allowed even with a negative feedback, either with the rewiring step (RUCM) or without it (UCM). From numerical simulations we find that the new models (UCM...

  19. Social reward shapes attentional biases.

    Science.gov (United States)

    Anderson, Brian A

    2016-01-01

    Paying attention to stimuli that predict a reward outcome is important for an organism to survive and thrive. When visual stimuli are associated with tangible, extrinsic rewards such as money or food, these stimuli acquire high attentional priority and come to automatically capture attention. In humans and other primates, however, many behaviors are not motivated directly by such extrinsic rewards, but rather by the social feedback that results from performing those behaviors. In the present study, I examine whether positive social feedback can similarly influence attentional bias. The results show that stimuli previously associated with a high probability of positive social feedback elicit value-driven attentional capture, much like stimuli associated with extrinsic rewards. Unlike with extrinsic rewards, however, such stimuli also influence task-specific motivation. My findings offer a potential mechanism by which social reward shapes the information that we prioritize when perceiving the world around us. PMID:25941868

  20. Symmetry as Bias: Rediscovering Special Relativity

    Science.gov (United States)

    Lowry, Michael R.

    1992-01-01

    This paper describes a rational reconstruction of Einstein's discovery of special relativity, validated through an implementation: the Erlanger program. Einstein's discovery of special relativity revolutionized both the content of physics and the research strategy used by theoretical physicists. This research strategy entails a mutual bootstrapping process between a hypothesis space for biases, defined through different postulated symmetries of the universe, and a hypothesis space for physical theories. The invariance principle mutually constrains these two spaces. The invariance principle enables detecting when an evolving physical theory becomes inconsistent with its bias, and also when the biases for theories describing different phenomena are inconsistent. Structural properties of the invariance principle facilitate generating a new bias when an inconsistency is detected. After a new bias is generated. this principle facilitates reformulating the old, inconsistent theory by treating the latter as a limiting approximation. The structural properties of the invariance principle can be suitably generalized to other types of biases to enable primal-dual learning.

  1. Quantum Criticality in the Biased Dicke Model.

    Science.gov (United States)

    Zhu, Hanjie; Zhang, Guofeng; Fan, Heng

    2016-01-01

    The biased Dicke model describes a system of biased two-level atoms coupled to a bosonic field, and is expected to produce new phenomena that are not present in the original Dicke model. In this paper, we study the critical properties of the biased Dicke model in the classical oscillator limits. For the finite-biased case in this limit, We present analytical results demonstrating that the excitation energy does not vanish for arbitrary coupling. This indicates that the second order phase transition is avoided in the biased Dicke model, which contrasts to the original Dicke model. We also analyze the squeezing and the entanglement in the ground state, and find that a finite bias will strongly modify their behaviors in the vicinity of the critical coupling point. PMID:26786239

  2. Cognitive Biases and Nonverbal Cue Availability in Detecting Deception

    Science.gov (United States)

    Burgoon, Judee K.; Blair, J. Pete; Strom, Renee E.

    2008-01-01

    In potentially deceptive situations, people rely on mental shortcuts to help process information. These heuristic judgments are often biased and result in inaccurate assessments of sender veracity. Four such biases--truth bias, visual bias, demeanor bias, and expectancy violation bias--were examined in a judgment experiment that varied nonverbal…

  3. Publication Bias in Methodological Computational Research

    OpenAIRE

    Anne-Laure Boulesteix; Veronika Stierle; Alexander Hapfelmeier

    2015-01-01

    The problem of publication bias has long been discussed in research fields such as medicine. There is a consensus that publication bias is a reality and that solutions should be found to reduce it. In methodological computational research, including cancer informatics, publication bias may also be at work. The publication of negative research findings is certainly also a relevant issue, but has attracted very little attention to date. The present paper aims at providing a new formal framework...

  4. Investigating bias in squared regression structure coefficients

    OpenAIRE

    Nimon, Kim F.; Zientek, Linda R.; Thompson, Bruce

    2015-01-01

    The importance of structure coefficients and analogs of regression weights for analysis within the general linear model (GLM) has been well-documented. The purpose of this study was to investigate bias in squared structure coefficients in the context of multiple regression and to determine if a formula that had been shown to correct for bias in squared Pearson correlation coefficients and coefficients of determination could be used to correct for bias in squared regression structure coefficie...

  5. Exponential Growth Bias and Financial Literacy

    OpenAIRE

    Almenberg, Johan; Gerdes, Christer

    2011-01-01

    The tendency to underestimate the future value of a variable growing at a constant rate, an example of exponential growth bias, has been linked to household financial decision making. We show that exponential growth bias and standard measures of financial literacy are negatively correlated in a representative sample of Swedish adults. Since financial literacy is linked to household decision making, our results indicate that examining the relationship between exponential growth bias and househ...

  6. Voter Confirmation Bias and Electoral Accountability

    OpenAIRE

    Lockwood, Benjamin

    2015-01-01

    This paper considers the implications of an important cognitive bias in information processing, confirmation bias, in a political agency setting. In the baseline two-period case where only the politician’s actions are observable before the election, we show that when voters have this bias, it decreases pandering by the incumbent, and can raise voter welfare as a consequence. This result is robust in several directions, including to the case where the voter can also observe payoffs with some p...

  7. BUSINESS LEADERSHIP BIASES: ANDROCENTRISM, ETHNOCENTRISM AND CHRONOCENTRISM

    OpenAIRE

    SOFICA Aurelian; NEGRUTA Adina

    2012-01-01

    The aim of the paper is to explore the unconscious biases that accompany the business leadership icons. The main objectives of the paper are: to look for evidence of leadership biases on ground of gender (androcentrism), ethnicity (ethnocentrism) and age (cronocentrism); to look for potential reasons behind the biases and for potential effects at the organizational and social level. The article confirms some of the evidence from various international empirical or theoretical studies, and prop...

  8. Childhood Obesity: Issues of Weight Bias

    OpenAIRE

    Washington, Reginald L.

    2011-01-01

    Although the effects of obesity on children's physical health are well documented, the social consequences of obesity are less well described and may not be addressed in intervention programs. Weight bias may take several forms. It may result in teasing and discrimination and may affect employment and educational opportunities. Health care providers may limit care of overweight or obese children. The media promote weight bias in multiple ways. Some parents are biased against their obese child...

  9. δ-biased Josephson tunnel junctions

    International Nuclear Information System (INIS)

    The behavior of a long Josephson tunnel junction drastically depends on the distribution of the dc bias current. We investigate the case in which the bias current is fed in the central point of a one-dimensional junction. Such junction configuration has been recently used to detect the persistent currents circulating in a superconducting loop. Analytical and numerical results indicate that the presence of fractional vortices leads to remarkable differences from the conventional case of uniformly distributed dc bias current. The theoretical findings are supported by detailed measurements on a number of δ-biased samples having different electrical and geometrical parameters.

  10. Weak coin flipping with small bias

    CERN Document Server

    Kerenidis, I; Kerenidis, Iordanis; Nayak, Ashwin

    2002-01-01

    This note presents a quantum protocol that demonstrates that_weak_ coin flipping with bias approximately 0.239, less than 1/4, is possible. A bias of 1/4 was the smallest known, and followed from the strong coin flipping protocol of [Ambainis 2001]. Protocols with yet smaller bias, approximately 0.207, have independently been discovered [Ambainis 2001, Spekkens and Rudolph 2002]. We also present an alternative strong coin flipping protocol with bias 1/4 with analysis simpler than that of [Ambainis 2001].

  11. Bias-correction in vector autoregressive models

    DEFF Research Database (Denmark)

    Engsted, Tom; Pedersen, Thomas Quistgaard

    2014-01-01

    We analyze the properties of various methods for bias-correcting parameter estimates in both stationary and non-stationary vector autoregressive models. First, we show that two analytical bias formulas from the existing literature are in fact identical. Next, based on a detailed simulation study...... improvement over ordinary least squares. We pay special attention to the risk of pushing an otherwise stationary model into the non-stationary region of the parameter space when correcting for bias. Finally, we consider a recently proposed reduced-bias weighted least squares estimator, and we find that it...

  12. Transposon mutagenesis as an approach to improved understanding of Borrelia pathogenesis and biology

    Directory of Open Access Journals (Sweden)

    Tao eLin

    2014-05-01

    Full Text Available Transposon insertion provides a method for near-random mutation of bacterial genomes, and has been utilized extensively for the study of bacterial pathogenesis and biology. This approach is particularly useful for organisms that are relatively refractory to genetic manipulation, including Lyme disease Borrelia. In this review, progress to date in the application of transposon mutagenesis to the study of Borrelia burgdorferi is reported. An effective Himar1-based transposon vector has been developed and used to acquire a sequence-defined library of nearly 4,500 mutants in the infectious, moderately transformable B. burgdorferi B31 derivative 5A18NP1. Analysis of these transposon mutants using signature-tagged mutagenesis (STM and Tn-seq approaches has begun to yield valuable information regarding the genes important in the pathogenesis and biology of this organism.

  13. Mechanism of the genetic mutagenesis effects of far infrared ray laser

    Institute of Scientific and Technical Information of China (English)

    ZHOU Ling-yun; XU Lin; ZHANG Can-bang; WU Guang-min; LI Ling; WEN Chuan-jing; YANG Ji-sheng

    2005-01-01

    We have analyzed the order-disordering variance due to resonance effect and the nonlinear behavior of far infrared ray laser (FIRL)-biological system interaction.The analytic results show that the interaction between the living biological system and FIRL can produce resonance excitation effect,and so the original high ordered state of the system can be destroyed and thus the conformation variation in the system can be produced under further action of the laser.In addition,we have analyzed the nonlinear properties of the FIRL bio-molecule interaction and explained the mutagenesis effects of FIRL.The theoretic analysis is consistent with the results of FIRL mutagenesis breeding test.

  14. Molecular mechanism of mutagenesis and interaction of incident ions with organism implanted by heavy ions beam

    International Nuclear Information System (INIS)

    As a new mutagenesis technique, low energy heavy ion implantation started in China for the study of interaction effect between incident ions and organism, and great achievements have been obtained in crop breeding. The article reviewed the main biological effects induced by heavy ion implantation, including physiology, biochemistry and genetics effects, on levels of cell and chromosome, gene expression, DNA methylation, DNA damage and reparation etc. It compared the differences in mutagenesis for organism by high energy and low energy ion implantation, as well as γ ray radiation. Future investigation topics were proposed, the emphasis of researches in future was pointed out, i.e., the molecular mechanism and effects of gene differential expression of organism treated by ion implantation. (authors)

  15. Pecularities of mutagenesis of T4Br bacteriophage under the direct and indirect radiation effects

    International Nuclear Information System (INIS)

    Different lethal and mutagenic effects were shown when bacteriophage T4Br+ (470 r/min) was irradiated in broth (direct effect) and a buffer solution (direct and indirect action). The survival rate of the bacteriophage in the buffer solution was 0.1 percent for a dose rate of 60 kr; in the broth it was 10 percent. The frequency of mutation of the bacteriophage also showed the greater effect of the irradiation in the buffer solution than in the broth (25 and 5 r-mutants respectively at a dose rate of 10 kr). An analysis of the ratio of the r-groups when the bacteriophage was treated in various ways revealed differences between mutagenesis produced in the broth and the buffer, and spontaneous mutagenesis. (V.A.P.)

  16. Triplex technology in studies of DNA damage, DNA repair, and mutagenesis.

    Science.gov (United States)

    Mukherjee, Anirban; Vasquez, Karen M

    2011-08-01

    Triplex-forming oligonucleotides (TFOs) can bind to the major groove of homopurine-homopyrimidine stretches of double-stranded DNA in a sequence-specific manner through Hoogsteen hydrogen bonding to form DNA triplexes. TFOs by themselves or conjugated to reactive molecules can be used to direct sequence-specific DNA damage, which in turn results in the induction of several DNA metabolic activities. Triplex technology is highly utilized as a tool to study gene regulation, molecular mechanisms of DNA repair, recombination, and mutagenesis. In addition, TFO targeting of specific genes has been exploited in the development of therapeutic strategies to modulate DNA structure and function. In this review, we discuss advances made in studies of DNA damage, DNA repair, recombination, and mutagenesis by using triplex technology to target specific DNA sequences. PMID:21501652

  17. The mutagenesis and breeding of high productive strains of streptomyces jingyangensis '5406'

    International Nuclear Information System (INIS)

    The purpose of these experiments is to explore the mutagenesis rhythm and breed high productive strains of actinomycete '5406'. The single colony agar pieces of strain F358 were treated with fast neutron and 60Co-γ ray irradiation Two mutants have been selected from 20025 treated single colonies. The output of cytokinins from them is higher than from strain F358. The original strain 'Mu-Tan-al' rejuvenated by freezing was treated with several physical and chemical mutagens. The mutagenesis rhythm has been summed up tentatively. Eight mutants obtained from 93014 treated single colonies produced more '5406' antibiotics than that of strain 'Mu-Tan-al,. The effect of mutant 'N2-10-Ra3' was the best

  18. Back to BAC: The Use of Infectious Clone Technologies for Viral Mutagenesis

    Directory of Open Access Journals (Sweden)

    Robyn N. Hall

    2012-02-01

    Full Text Available Bacterial artificial chromosome (BAC vectors were first developed to facilitate the propagation and manipulation of large DNA fragments in molecular biology studies for uses such as genome sequencing projects and genetic disease models. To facilitate these studies, methodologies have been developed to introduce specific mutations that can be directly applied to the mutagenesis of infectious clones (icBAC using BAC technologies. This has resulted in rapid identification of gene function and expression at unprecedented rates. Here we review the major developments in BAC mutagenesis in vitro. This review summarises the technologies used to construct and introduce mutations into herpesvirus icBAC. It also explores developing technologies likely to provide the next leap in understanding these important viruses.

  19. Radiosensitivity and in vitro mutagenesis in African accessions of cassava, Manihot esculenta Crantz

    International Nuclear Information System (INIS)

    Induced mutagenesis holds promise for the subtle manipulation of traits of interest in crop plants. For a vegetatively propagated crop like cassava with severe constraints posed on its genetic improvement by inherent biological systems, the adoption of this methodology seems even the more appealing. However, there is scant information on protocols for inducing mutations in this crop. We present in this report the preliminary data on the determination of radiosensitivities for some African cassava accessions. The optimal doses of gamma ray irradiation varied from as low 12 Gy to 25 Gy. The probable implication of genotypic variation in response to gamma irradiation as was found in this study buttresses the need to carry out this larger scale study in order to avail cassava scientists intending to adopt induced mutagenesis of requisite information in this regard. A modified in vitro culture medium, half strength MS without growth hormones, was also shown to greatly enhance the growth of the plantlets without producing callus. (author)

  20. Cell-mediated mutagenesis and cell transformation of mammalian cells by chemical carcinogens

    International Nuclear Information System (INIS)

    We have developed a cell-mediated mutagenesis assay in which cells with the appropriate markers for mutagenesis are co-cultivated with either lethally irradiated rodent embryonic cells that can metabolize carcinogenic hydrocarbons or with primary rat liver cells that can metabolize chemicals carcinogenic to the liver. During co-cultivation, the reactive metabolites of the procarcinogen appear to be transmitted to the mutable cells and induce mutations in them. Assays of this type make it possible to demonstrate a relationship between carcinogenic potency of the chemicals and their ability to induce mutations in mammalian cells. In addition, by simultaneously comparing the frequencies of transformation and mutation induced in normal diploid hamster cells by benzo(a)pyrene (BP) and one of its metabolites, it is possible to estimate the genetic target size for cell transformation in vitro

  1. Study on mutagenesis of Signal grass (Brachiaria decumbens) by gamma irradiation

    International Nuclear Information System (INIS)

    Before starting experiments on induced mutation breeding of crops it is essential to carry out radiosensitivity test when determining the optimum doses of every plant genotype. Factors such as moisture content and oxsigen availability could influence mutagenesis process through ionizing radiation. Many methodologies could be used for determining the effect of radiation on seed of plants such as the 'Sandwich blotter technique' and 'Sand bed technique'. Different species have different sensitivity to mutagenic agents. Even varieties of the same species show variations in sensitivity to irradiation. Brachiaria clecumbens was found to be less sensitive to gamma radiation. At a dose of 800 Gy, the percentage reduction in growth was around 40%. Early result has shown that the optimum doses for mutagenesis was between 700 to 900 Gy

  2. Cysteine Mutagenesis and Computer Modeling of the S6 Region of an Intermediate Conductance IKCa Channel

    OpenAIRE

    Simoes, Manuel; Garneau, Line; Klein, Hélène; Banderali, Umberto; Hobeila, Fadi; Roux, Benoit; Parent, Lucie; Sauvé, Rémy

    2002-01-01

    Cysteine-scanning mutagenesis (SCAM) and computer-based modeling were used to investigate key structural features of the S6 transmembrane segment of the calcium-activated K+ channel of intermediate conductance IKCa. Our SCAM results show that the interaction of [2-(trimethylammonium)ethyl] methanethiosulfonate bromide (MTSET) with cysteines engineered at positions 275, 278, and 282 leads to current inhibition. This effect was state dependent as MTSET appeared less effective at inhibiting IKCa...

  3. Sleeping Beauty Transposon Mutagenesis of the Rat Genome in Spermatogonial Stem Cells

    OpenAIRE

    Ivics, Zoltán; Izsvák, Zsuzsanna; Chapman, Karen M.; Hamra, F. Kent

    2010-01-01

    Since several aspects of physiology in rats has evolved to be more similar to humans than that of mice, it is highly desirable to link the rat into the process of annotating the human genome with function. However, the lack of technology for generating defined mutants in the rat genome has hindered the identification of causative relationships between genes and disease phenotypes. As an important step towards this goal, an approach of establishing transposon-mediated insertional mutagenesis i...

  4. Transposon mutagenesis as an approach to improved understanding of Borrelia pathogenesis and biology

    OpenAIRE

    Lin, Tao; Troy, Erin B.; Linden T. Hu; Gao, Lihui; Norris, Steven J

    2014-01-01

    Transposon insertion provides a method for near-random mutation of bacterial genomes, and has been utilized extensively for the study of bacterial pathogenesis and biology. This approach is particularly useful for organisms that are relatively refractory to genetic manipulation, including Lyme disease Borrelia. In this review, progress to date in the application of transposon mutagenesis to the study of Borrelia burgdorferi is reported. An effective Himar1-based transposon vector has been dev...

  5. Transposon mutagenesis as an approach to improved understanding of Borrelia pathogenesis and biology

    OpenAIRE

    Tao eLin; Troy, Erin B.; Linden T. Hu; Lihui eGao; Norris, Steven J

    2014-01-01

    Transposon insertion provides a method for near-random mutation of bacterial genomes, and has been utilized extensively for the study of bacterial pathogenesis and biology. This approach is particularly useful for organisms that are relatively refractory to genetic manipulation, including Lyme disease Borrelia. In this review, progress to date in the application of transposon mutagenesis to the study of Borrelia burgdorferi is reported. An effective Himar1-based transposon vector has been ...

  6. Mutagenesis of Jatropha curcas - Exploring new traits in the breeding of a biofuel plant

    International Nuclear Information System (INIS)

    Mutagenesis in plant species is considered effective in recovering and producing useful mutants as it leads to a high degree of chimerism and produces high degree of somaclonal variations for further selection in breeding programmes. Jatropha curcas is a species with many attributes and considerable potential, especially as bio diesel. Narrow genetic background of Jatropha spp. gives less selection to growers for better quality plant materials. In this study, a new method through nuclear technology was used to increase the genetic variability of Jatropha towards novel superior potential mutant lines. The objective of the study is to generate new mutant varieties of Jatropha curcas through the mutagenesis approach in getting new sustainable mutants for high oil yield and improved plant characteristics. Seeds of a Jatropha cultivar were from selected materials from Lembaga Kenaf and Tembakau Negara, Kelantan. Radiosensitivity test was done by irradiating a total of each 60 seeds at multiple doses (0 Gy, 20 Gy, 40 Gy, 60 Gy, 80 Gy, 100 Gy, 200 Gy, 300 Gy, 400 Gy, 600 Gy and 700 Gy). After getting the LD50, three doses i.e. 250 Gy, 300 Gy and 350 Gy were selected for mutagenesis, where a total of 1000 seeds were exposed to gamma radiation. The seeds were hardened and field planted at close distance of 1 m x 1 m. Pruning was conducted three times at two months interval prior to screening for early flowering, short stature and high branching mutant lines. Radiosensitivity of seeds to acute gamma irradiation revealed that the LD50 was at 320 Gy. At nursery stage, somatic mutations related to chlorophyll changes were observed on leaves with certain shapes. Screening of Jatropha via seed mutagenesis bore 6 early flowering mutants, 7 dwarf mutants and, 17 high branching plants. In narrowing the mutant lines, cuttings from each selected trait were collected and re-planted for further evaluation. (author)

  7. A directed mutagenesis screen in Drosophila melanogaster reveals new mutants that influence hedgehog signaling.

    OpenAIRE

    Haines, N; van den Heuvel, M

    2000-01-01

    The Hedgehog signaling pathway has been recognized as essential for patterning processes in development of metazoan animal species. The signaling pathway is, however, not entirely understood. To start to address this problem, we set out to isolate new mutations that influence Hedgehog signaling. We performed a mutagenesis screen for mutations that dominantly suppress Hedgehog overexpression phenotypes in the Drosophila melanogaster wing. We isolated four mutations that influence Hedgehog sign...

  8. PiggyBac Transposon Mutagenesis: A Tool for Cancer Gene Discovery in Mice

    OpenAIRE

    Rad, Roland; Rad, Lena; Wang, Wei; Cadinanos, Juan; Vassiliou, George; Rice, Stephen; Campos, Lia S.; Yusa, Kosuke; Banerjee, Ruby; Li, Meng Amy; de la Rosa, Jorge; Strong, Alexander; Lu, Dong; Ellis, Peter; Conte, Nathalie

    2010-01-01

    Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon/transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed the unique qualities o...

  9. Repair and mutagenesis of herpes simplex virus in UV-irradiated monkey cells

    International Nuclear Information System (INIS)

    Mutagenic repair in mammalian cells was investigated by determining the mutagenesis of UV-irradiated or unirradiated herpes simplex virus in UV-irradiated CV-1 monkey kidney cells. These results were compared with the results for UV-enhanced virus reactivation (UVER) in the same experimental situation. High and low multiplicities of infection were used to determine the effects of multiplicity reactivation (MR). UVER and MR were readily demonstrable and were approximately equal in amount in an infectious center assay. For this study, a forward-mutation assay was developed to detect virus mutants resistant to iododeoxycytidine (ICdR), probably an indication of the mutant virus being defective at its thymidine kinase locus. ICdR-resistant mutants did not have a growth advantage over wild-type virus in irradiated or unirradiated cells. Thus, higher fractions of mutant virus indicated greater mutagenesis during virus repair and/or replication. The data showed that: (1) unirradiated virus was mutated in unirradiated cells, providing a background level of mutagenesis; (2) unirradiated virus was mutated about 40% more in irradiated cells, indicating that virus replication (DNA synthesis) became more mutagenic as a result of cell irradiation; (3) irradiated virus was mutated much more (about 6-fold) than unirradiated virus, even in unirradiated cells; (4) cell irradiation did not change the mutagenesis of irradiated virus except at high multiplicity of infection. High multiplicity of infection did not demonstrate UVER or MR alone to be either error-free or error-prone. When the two processes were present simultaneously, they were mutagenic. (orig.)

  10. Chemical and radiation-induced mutagenesis of the rat liver chromosomes

    International Nuclear Information System (INIS)

    It was shown that radiation and chemical mutagenesis in rat liver cells is determined chiefly by long-lived premutational potential changes. The intensification of intrachromosomal processes under the action of an inducer of gene activity - phenobarbital - does not modify the yield of chromosome aberrations, both under the action of radiation and under the action of an alkylating agent -dipin. The facts obtained support the hypothesis that the chemical nature of the premutational changes differs from the primary molecular damages to DNA. (author)

  11. Influence of duration of exposition in the Chernobyl zone on spontaneous and chemically induced mutagenesis

    International Nuclear Information System (INIS)

    The cycle of researches according to influence of an exposition of laboratory mice of line Af in a zone of Chernobyl disaster on spontaneous and chemically induced mutagenesis has been performed. The frequency of micronucleated erythrocytes in the mouse bone marrow was increase in term of an exposition in a zone of Chernobyl disaster with 1 till 4 months in comparison with the control. (authors)

  12. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion

    OpenAIRE

    Batista, Rita; Saibo, Nelson; Lourenço, Tiago; Oliveira, Maria Margarida

    2008-01-01

    Controversy regarding genetically modified (GM) plants and their potential impact on human health contrasts with the tacit acceptance of other plants that were also modified, but not considered as GM products (e.g., varieties raised through conventional breeding such as mutagenesis). What is beyond the phenotype of these improved plants? Should mutagenized plants be treated differently from transgenics? We have evaluated the extent of transcriptome modification occurring ...

  13. Characterization and site-directed mutagenesis of NifU from Azotobacter vinelandii

    OpenAIRE

    Jack, Richard F.

    1995-01-01

    In order to elucidate the function of the nifU gene product in nitrogenase maturation in Azotobacter vinelandii. the gene product has been hyperexpressed in Escherichia coli and characterized by various biophysical techniques. Following the initial characterization, site-directed mutagenesis of conserved cysteinyl residues was performed in order to gain further insight into the structure/function relationship of NifU. Both the Fe protein and the MoFe protein of nitrogena...

  14. Random Insertional Mutagenesis of Leptospira interrogans, the Agent of Leptospirosis, Using a mariner Transposon

    OpenAIRE

    Bourhy, Pascale; Louvel, Hélène; Saint Girons, Isabelle; Picardeau, Mathieu

    2005-01-01

    The recent availability of the complete genome sequences of Leptospira interrogans, the agent of leptospirosis, has allowed the identification of several putative virulence factors. However, to our knowledge, attempts to carry out gene transfer in pathogenic Leptospira spp. have failed so far. In this study, we show that the Himar1 mariner transposon permits random mutagenesis in the pathogen L. interrogans. We have identified genes that have been interrupted by Himar1 insertion in 35 L. inte...

  15. Transposon Mutagenesis To Improve the Growth of Recombinant Saccharomyces cerevisiae on d-Xylose▿

    OpenAIRE

    Ni, Haiying; Laplaza, José M.; Jeffries, Thomas W.

    2007-01-01

    Saccharomyces cerevisiae L2612 transformed with genes for xylose reductase and xylitol dehydrogenase (XYL1 and XYL2) grows well on glucose but very poorly on d-xylose. When a gene for d-xylulokinase (XYL3 or XKS1) is overexpressed, growth on glucose is unaffected, but growth on xylose is blocked. Spontaneous or chemically induced mutants of this engineered yeast that would grow on xylose could, however, be obtained. We therefore used insertional transposon mutagenesis to identify two loci tha...

  16. Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System

    OpenAIRE

    Andrew R. Bassett; Charlotte Tibbit; Chris P. Ponting; Ji-Long Liu

    2013-01-01

    Here, we present a simple and highly efficient method for generating and detecting mutations ofany gene in Drosophila melanogaster through theuse of the CRISPR/Cas9 system (clustered regularlyinterspaced palindromic repeats/CRISPR-associated). We show that injection of RNA into the Drosophila embryo can induce highly efficient mutagenesis of desired target genes in up to 88% of injected flies. These mutations can be transmitted through the germline to make stable lines. Our system provides at...

  17. Site-specific mutagenesis by triple helix-forming oligonucleotides containing a reactive nucleoside analog

    OpenAIRE

    Nagatsugi, Fumi; Sasaki, Shigeki; Miller, Paul S.; Seidman, Michael M.

    2003-01-01

    The specific recognition of homopurine–homo pyrimidine regions in duplex DNA by triplex-forming oligonucleotides (TFOs) provides an attractive strategy for genetic manipulation. Alkylation of nucleobases with functionalized TFOs would have the potential for site-directed mutagenesis. Recently, we demonstrated that a TFO bearing 2-amino-6-vinylpurine derivative, 1, achieves triplex-mediated reaction with high selectivity toward the cytosine of the G-C target site. In this report, we have inves...

  18. Transposon and Deletion Mutagenesis of Genes Involved in Perchlorate Reduction in Azospira suillum PS

    OpenAIRE

    Melnyk, Ryan A.; Clark, Iain C.; Liao, Annette; Coates, John D.

    2013-01-01

    ABSTRACT Although much work on the biochemistry of the key enzymes of bacterial perchlorate reduction, chlorite dismutase, and perchlorate reductase has been published, understanding of the molecular mechanisms of this metabolism has been somewhat hampered by the lack of a clear model system amenable to genetic manipulation. Using transposon mutagenesis and clean deletions, genes important for perchlorate reduction in Azospira suillum PS have been identified both inside and outside the previo...

  19. Oligonucleotide-directed mutagenesis by microscale 'shot-gun' gene synthesis.

    OpenAIRE

    Grundström, T; Zenke, W M; Wintzerith, M; Matthes, H W; Staub, A; Chambon, P

    1985-01-01

    We describe a rapid and efficient microscale method for in vitro site-directed mutagenesis by gene synthesis. Mutants are constructed by "shot-gun ligation" of overlapping synthetic oligonucleotides yielding double stranded synthetic DNA of more than 120 nucleotides in length. The terminal oligonucleotides of the DNA segment to be synthesized are designed to create sticky ends complementary to unique restriction sites of a polylinker present in an M13 vector. The oligonucleotides are hybridiz...

  20. Site-specific mutagenesis of histidine residues in the lac permease of Escherichia coli.

    OpenAIRE

    Padan, E; Sarkar, H K; Viitanen, P V; Poonian, M S; Kaback, H R

    1985-01-01

    The lacY gene of Escherichia coli, which encodes the lac permease, has been modified by oligonucleotide-directed, site-specific mutagenesis such that each of the four histidine residues in the molecule is replaced with an arginine residue. Replacement of histidine-35 and histidine-39 with arginine has no apparent effect on permease activity. In contrast, replacement of either histidine-205 or histidine-322 by arginine causes a dramatic loss of transport activity, although the cells contain a ...

  1. Molecular processes as basis for plasmid-mediated bacterial UV-light resistance and mutagenesis

    International Nuclear Information System (INIS)

    The increase of UV-resistance and UV-induced mutagenesis by lambda 1 pint intmid as well as molecular-genetic mechanisms of plasmid participation in reparation and DNA replication and its degradation after UV-irradiation in plasmid cells on pKM101 plasmid model have been investigated. Data testifying to the necessity of intmid integration in chromosome as obligatory stage of intmid participation in increasing UV-resistance of bacterial cells are obtained. It has been found that intmid raises UV-resistance of cells and increases respectively the UV-induced reverants efficiency. On the basis of the experiment data the conclusion is drawn that the intmid capacity to raise UV-resistance and, possibly, mutagenesis is bound not only with its integration into chromosome but also with pol A+ chromosome replication by dependendent imtmid replication complex. It is shown that pKM101 plasmid ensures functioning in E coli cells of inducible, chloroamphenicol-resistant DNA replication, highly resistant to UV-light harmful effect and that the volume of excision reparation in E. coli cells carrying pKM101 plasmid is increased as compared with the volume of reparation in plasmid legs cells. The combination of the data obtained gives grounds to the authors to assume that inducible replication, inducible reparation of DNA and inducible decrease of DNA degradation determined by pKM101 plasmid may serve as recA+lexA+ basis dependent increase of UV-resistance and mutagenesis and that these processes provide the possibility of functioning of integrative replication mechanism of plasmid participation in ensuring UV-resistance and mutagenesis of plants

  2. General Mutagenesis of F Plasmid TraI Reveals Its Role in Conjugative Regulation

    OpenAIRE

    Haft, Rembrandt J F; Palacios, Gilberto; Nguyen, Tran; Mally, Manuela; Gachelet, Eliora G.; Zechner, Ellen L.; Traxler, Beth

    2006-01-01

    Bacteria commonly exchange genetic information by the horizontal transfer of conjugative plasmids. In gram-negative conjugation, a relaxase enzyme is absolutely required to prepare plasmid DNA for transit into the recipient via a type IV secretion system. Here we report a mutagenesis of the F plasmid relaxase gene traI using in-frame, 31-codon insertions. Phenotypic analysis of our mutant library revealed that several mutant proteins are functional in conjugation, highlighting regions of TraI...

  3. Mutagenesis and mitotic recombination in Aspergillus niger, an expedition from gene to genome

    OpenAIRE

    Vondervoort, Peter Jozef Ida van de

    2007-01-01

    Aspergillus niger is a cosmopolitan fungus and its spores can be found in air and soil worldwide. This saprophyte is used in food biotechnology for the production of proteins, mainly enzymes and for the production of organic acids. In the production of proteins, several problems are encountered such as repressed gene-expression, morphologic and genetic instability and undesired metabolite accumulation. To find solutions to these problems, often mutagenesis and mitotic recombination have been ...

  4. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila

    OpenAIRE

    Häcker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A.

    2003-01-01

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniqu...

  5. A sensitized mutagenesis screen identifies Gli3 as a modifier of Sox10 neurocristopathy

    OpenAIRE

    Matera, Ivana; Watkins-Chow, Dawn E.; Loftus, Stacie K.; Hou, Ling; Incao, Arturo; Silver, Debra L.; Rivas, Cecelia; Elliott, Eugene C.; Baxter, Laura L.; Pavan, William J.

    2008-01-01

    Haploinsufficiency for the transcription factor SOX10 is associated with the pigmentary deficiencies of Waardenburg syndrome (WS) and is modeled in Sox10 haploinsufficient mice (Sox10LacZ/+). As genetic background affects WS severity in both humans and mice, we established an N-ethyl-N-nitrosourea (ENU) mutagenesis screen to identify modifiers that increase the phenotypic severity of Sox10LacZ/+ mice. Analysis of 230 pedigrees identified three modifiers, named modifier of Sox10 neurocristopat...

  6. Site-directed mutagenesis of the foot-and-mouth disease virus RNA-polymerase gene

    International Nuclear Information System (INIS)

    The foot-and-mouth disease virus RNA-polymerase gene was mutagenised in its active site. Pst I digestion of the polymerase gene (cDNA) generated a 790 bp fragment containing the critical sequence. This fragment was subcloned in M13mp8 for mutagenesis method. The polymerase gene was then reconstructed and subcloned in pUC19. These mutants will be used to study the enzyme structure and activity and to develop intracellular immunization assays in eukaryotic cells. (author)

  7. Induced mutagenesis of plasmids and chromosomal genes inserted into plasmid DNA 1. Mutagenic effects of irradiations

    International Nuclear Information System (INIS)

    Effect of two physical agents: UV- and γ-radiation has been considered in comparison. DNA of RSF2124 plasmid, determining colcine synthesis and ampicillin resistance, was used as a model. Mutagenous effect is taken into account according to the appearance of Col--mutants, which are not capable of colicine synthesis. Lethal effect is determined according to ampicillin marker inactivation. After reisolation of plasmid DNA from mutant transformant, new traits and antibiotic resistance are preserved during subsequent transformations and reseedings of transformed colonies, which proves mutational nature of the transformations. Under short-wave UV irradiation (lambda=254 nm) of RSF2124 DNA a clear mutagenous effect is detected: relative amount of Col--mutants at the optimum for mutagenesis doses increased by a factor of 10. Under conditions of W-reactivation (additional UV-irradiation of recipient cells of wild C600 type) of lethal injuries an increase in mutagenous effect was observed, which is reliable for 95%. A distinct increase in mutagenesis (approximately by a factor of 4) is observed during UV-irradiation in small doses of only one recipient cell (a so-called indirect UV-mutagenesis). Thus, according to its ability to W- and indirect UV-mutagenesis plasmid DNA behaves as DNA of moderate phages, which can testify to their evolution relationship. Treatment of plasmid DNA with acridine orange before UV-irradiation protected only from lethal injuries. γ-irradiation of 60Co at inactivation approximately 10-2 increased by an order the yield of Col--mutants. The presence of the plasmid in a cell did not affect its UV-resistance

  8. Marinomonas mediterranea MMB-1 Transposon Mutagenesis: Isolation of a Multipotent Polyphenol Oxidase Mutant

    OpenAIRE

    Solano, Francisco; Lucas-Elío, Patricia; Fernández, Eva; Sanchez-Amat, Antonio

    2000-01-01

    Marinomonas mediterranea is a melanogenic marine bacterium expressing a multifunctional polyphenol oxidase (PPO) able to oxidize substrates characteristic for laccases and tyrosinases, as well as produce a classical tyrosinase. A new and quick method has been developed for screening laccase activity in culture plates to detect mutants differentially affected in this PPO activity. Transposon mutagenesis has been applied for the first time to M. mediterranea by using different minitransposons l...

  9. CRISPR/Cas9-mediated targeted gene mutagenesis in Spodoptera litura.

    Science.gov (United States)

    Bi, Hong-Lun; Xu, Jun; Tan, An-Jiang; Huang, Yong-Ping

    2016-06-01

    Custom-designed nuclease technologies such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system provide attractive genome editing tools for insect functional genetics. The targeted gene mutagenesis mediated by the CRISPR/Cas9 system has been achieved in several insect orders including Diptera, Lepidoptera and Coleoptera. However, little success has been reported in agricultural pests due to the lack of genomic information and embryonic microinjection techniques in these insect species. Here we report that the CRISPR/Cas9 system induced efficient gene mutagenesis in an important Lepidopteran pest Spodoptera litura. We targeted the S. litura Abdominal-A (Slabd-A) gene which is an important embryonic development gene and plays a significant role in determining the identities of the abdominal segments of insects. Direct injection of Cas9 messenger RNA and Slabd-A-specific single guide RNA (sgRNA) into S. litura embryos successfully induced the typical abd-A deficient phenotype, which shows anomalous segmentation and ectopic pigmentation during the larval stage. A polymerase chain reaction-based analysis revealed that the Cas9/sgRNA complex effectively induced a targeted mutagenesis in S. litura. These results demonstrate that the CRISPR/Cas9 system is a powerful tool for genome manipulation in Lepidopteran pests such as S. litura. PMID:27061764

  10. PiggyBac transposon mutagenesis: a tool for cancer gene discovery in mice.

    Science.gov (United States)

    Rad, Roland; Rad, Lena; Wang, Wei; Cadinanos, Juan; Vassiliou, George; Rice, Stephen; Campos, Lia S; Yusa, Kosuke; Banerjee, Ruby; Li, Meng Amy; de la Rosa, Jorge; Strong, Alexander; Lu, Dong; Ellis, Peter; Conte, Nathalie; Yang, Fang Tang; Liu, Pentao; Bradley, Allan

    2010-11-19

    Transposons are mobile DNA segments that can disrupt gene function by inserting in or near genes. Here, we show that insertional mutagenesis by the PiggyBac transposon can be used for cancer gene discovery in mice. PiggyBac transposition in genetically engineered transposon-transposase mice induced cancers whose type (hematopoietic versus solid) and latency were dependent on the regulatory elements introduced into transposons. Analysis of 63 hematopoietic tumors revealed that PiggyBac is capable of genome-wide mutagenesis. The PiggyBac screen uncovered many cancer genes not identified in previous retroviral or Sleeping Beauty transposon screens, including Spic, which encodes a PU.1-related transcription factor, and Hdac7, a histone deacetylase gene. PiggyBac and Sleeping Beauty have different integration preferences. To maximize the utility of the tool, we engineered 21 mouse lines to be compatible with both transposon systems in constitutive, tissue- or temporal-specific mutagenesis. Mice with different transposon types, copy numbers, and chromosomal locations support wide applicability. PMID:20947725

  11. Yeasts acquire resistance secondary to antifungal drug treatment by adaptive mutagenesis.

    Directory of Open Access Journals (Sweden)

    David Quinto-Alemany

    Full Text Available Acquisition of resistance secondary to treatment both by microorganisms and by tumor cells is a major public health concern. Several species of bacteria acquire resistance to various antibiotics through stress-induced responses that have an adaptive mutagenesis effect. So far, adaptive mutagenesis in yeast has only been described when the stress is nutrient deprivation. Here, we hypothesized that adaptive mutagenesis in yeast (Saccharomyces cerevisiae and Candida albicans as model organisms would also take place in response to antifungal agents (5-fluorocytosine or flucytosine, 5-FC, and caspofungin, CSP, giving rise to resistance secondary to treatment with these agents. We have developed a clinically relevant model where both yeasts acquire resistance when exposed to these agents. Stressful lifestyle associated mutation (SLAM experiments show that the adaptive mutation frequencies are 20 (S. cerevisiae -5-FC, 600 (C. albicans -5-FC or 1000 (S. cerevisiae--CSP fold higher than the spontaneous mutation frequency, the experimental data for C. albicans -5-FC being in agreement with the clinical data of acquisition of resistance secondary to treatment. The spectrum of mutations in the S. cerevisiae -5-FC model differs between spontaneous and acquired, indicating that the molecular mechanisms that generate them are different. Remarkably, in the acquired mutations, an ectopic intrachromosomal recombination with an 87% homologous gene takes place with a high frequency. In conclusion, we present here a clinically relevant adaptive mutation model that fulfils the conditions reported previously.

  12. Sleeping Beauty mutagenesis in a mouse medulloblastoma model defines networks that discriminate between human molecular subgroups

    Science.gov (United States)

    Genovesi, Laura A.; Ng, Ching Ging; Davis, Melissa J.; Remke, Marc; Taylor, Michael D.; Adams, David J.; Rust, Alistair G.; Ward, Jerrold M.; Ban, Kenneth H.; Jenkins, Nancy A.; Copeland, Neal G.; Wainwright, Brandon J.

    2013-01-01

    The Sleeping Beauty (SB) transposon mutagenesis screen is a powerful tool to facilitate the discovery of cancer genes that drive tumorigenesis in mouse models. In this study, we sought to identify genes that functionally cooperate with sonic hedgehog signaling to initiate medulloblastoma (MB), a tumor of the cerebellum. By combining SB mutagenesis with Patched1 heterozygous mice (Ptch1lacZ/+), we observed an increased frequency of MB and decreased tumor-free survival compared with Ptch1lacZ/+ controls. From an analysis of 85 tumors, we identified 77 common insertion sites that map to 56 genes potentially driving increased tumorigenesis. The common insertion site genes identified in the mutagenesis screen were mapped to human orthologs, which were used to select probes and corresponding expression data from an independent set of previously described human MB samples, and surprisingly were capable of accurately clustering known molecular subgroups of MB, thereby defining common regulatory networks underlying all forms of MB irrespective of subgroup. We performed a network analysis to discover the likely mechanisms of action of subnetworks and used an in vivo model to confirm a role for a highly ranked candidate gene, Nfia, in promoting MB formation. Our analysis implicates candidate cancer genes in the deregulation of apoptosis and translational elongation, and reveals a strong signature of transcriptional regulation that will have broad impact on expression programs in MB. These networks provide functional insights into the complex biology of human MB and identify potential avenues for intervention common to all clinical subgroups. PMID:24167280

  13. UV-induced mutagenesis in Escherichia coli SOS response: a quantitative model.

    Directory of Open Access Journals (Sweden)

    Sandeep Krishna

    2007-03-01

    Full Text Available Escherichia coli bacteria respond to DNA damage by a highly orchestrated series of events known as the SOS response, regulated by transcription factors, protein-protein binding, and active protein degradation. We present a dynamical model of the UV-induced SOS response, incorporating mutagenesis by the error-prone polymerase, Pol V. In our model, mutagenesis depends on a combination of two key processes: damage counting by the replication forks and a long-term memory associated with the accumulation of UmuD'. Together, these provide a tight regulation of mutagenesis, resulting, we show, in a "digital" turn-on and turn-off of Pol V. Our model provides a compact view of the topology and design of the SOS network, pinpointing the specific functional role of each of the regulatory processes. In particular, we suggest that the recently observed second peak in the activity of promoters in the SOS regulon (Friedman et al., 2005, PLoS Biology 3(7: e238 is the result of positive feedback from Pol V to RecA filaments.

  14. DNA damage and mutagenesis of lambda phage induced by gamma-rays

    International Nuclear Information System (INIS)

    Lambda phage DNA was gamma irradiated in aqueous solution and strand breakage determined. Twice as much minor structural damage per lethal hit was found in this DNA compared with DNA from irradiated phage suspensions. The in vitro irradiated DNA was repackaged into infectious particles. Induction of mutations in the cI or cII cistron was scored using SOS-induced host cells. In vitro prepared particles were found to have second-order kinetics for mutagenesis induced by gamma rays indicating two pre-mutational events were necessary to produce a mutation, but bacteria-free phage suspensions ('lys-phage') showed single hit kinetics for mutagenesis after irradiation. Increase in the mutation rate in the phage particles was mainly due to minor lesions, i.e. ssb, als and unidentified base damage. In lys-phage, mutagenesis might be enhanced by clustered DNA damage - configuration not existing in pack-phage. Loss of infectivity was analysed in comparison with structural damage. All lesions contributed to biological inactivation. Minor lesions were tolerated by lambda phage to a limited extent. Major lesions (e.g. dsb) contributed most to infectivity loss and were considered lethal events. (U.K.)

  15. Spontaneous mutability and light-induced mutagenesis in Salmonella typhimurium: effects of an R-plasmid

    International Nuclear Information System (INIS)

    The UV-protecting plasmid R46 was transferred by conjugation to a genetically marked mouse-virulent Salmonella typhimurium strain, not derived from LT2; in this host the plasmid conferred UV protection and enhanced UV mutagenesis just as it does in LT2 lines. Tra-derivatives of R46 encountered during transduction retained UV-protecting and mutagenesis-enhancing ability. Stored strains carrying the R46-derived plasmids with strong mutator effect but not UV-protecting had lost most of their original streptomycin resistance but were slightly resistant to spectinomycin; attempts to transfer such plasmids failed. R46 enhanced the weak mutagenic effect of visible light on several his and trp mutants of strain LT2, including some whose frequency of spontaneous reversion was not increased by the plasmid. A mutagenic effect was produced by visible-light irradiation of hisG46(R46), either growing cells or nonmultiplying (histidine-deprived cells at 100C). Presence of catalase or cyanide during irradiation did not prevent mutagenesis, which excludes some hypothetical mechanisms. Visible-light irradiation of hisG46 or hisG46(R46) under strict anaerobiosis had little or no mutagenic effect (controls showed that revertants if produced would have been detected). This is as expected if visible-light irradiation in air causes photodynamic damage to DNA and mutations are produced during error-prone, plasmid-enhanced repair

  16. Transgenic Chinese hamster V79 cell lines which exhibit variable levels of gpt mutagenesis

    International Nuclear Information System (INIS)

    The Escherichia coli gpt gene coding for xanthine-guanine phosphoribosyl transferase has been stably transfected into HPRT- Chinese hamster V79 cells. Several gpt- cell lines have been established, which retain the sequence(s) even after long-term culture without selection for gpt. While spontaneous mutagenesis to gpt- occurs rather frequently for most cell lines, it cannot be correlated with either the number of plasmid integration sites or deletion of the plasmid sequence(s). One transgenic cell line (g12), which continuously maintains a low spontaneous mutation frequency was used in comparative mutagenesis studies with wild-type V79 cells (gpt vs. hprt). Alkylating agents such as N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and β-propiolactone (BPL) are shown to be equally toxic and mutagenic in both g12 and V79 cells. UV and X-rays are also equally toxic to both cell lines. The data presented here suggests that g12 cells may be useful to study mammalian mutagenesis by agents which yield limited response at the hprt locus

  17. Induction of Pectinase Hyper Production by Multistep Mutagenesis Using a Fungal Isolate--Aspergillus flavipes.

    Science.gov (United States)

    Akbar, Sabika; Prasuna, R Gyana; Khanam, Rasheeda

    2014-04-01

    Aspergillus flavipes, a slow growing pectinase producing ascomycete, was isolated from soil identified and characterised in the previously done preliminary studies. Optimisation studies revealed that Citrus peel--groundnut oil cake [CG] production media is the best media for production of high levels of pectinase up to 39 U/ml using wild strain of A. flavipes. Strain improvement of this isolated strain for enhancement of pectinase production using multistep mutagenesis procedure is the endeavour of this project. For this, the wild strain of A. flavipes was treated with both physical (UV irradiation) and chemical [Colchicine, Ethidium bromide, H2O2] mutagens to obtain Ist generation mutants. The obtained mutants were assayed and differentiated basing on pectinase productivity. The better pectinase producing strains were further subjected to multistep mutagenesis to attain stability in mutants. The goal of this project was achieved by obtaining the best pectinase secreting mutant, UV80 of 45 U/ml compared to wild strain and sister mutants. This fact was confirmed by quantitatively analysing 3rd generation mutants obtained after multistep mutagenesis. PMID:26563068

  18. Mouse ENU Mutagenesis to Understand Immunity to Infection: Methods, Selected Examples, and Perspectives

    Directory of Open Access Journals (Sweden)

    Grégory Caignard

    2014-09-01

    Full Text Available Infectious diseases are responsible for over 25% of deaths globally, but many more individuals are exposed to deadly pathogens. The outcome of infection results from a set of diverse factors including pathogen virulence factors, the environment, and the genetic make-up of the host. The completion of the human reference genome sequence in 2004 along with technological advances have tremendously accelerated and renovated the tools to study the genetic etiology of infectious diseases in humans and its best characterized mammalian model, the mouse. Advancements in mouse genomic resources have accelerated genome-wide functional approaches, such as gene-driven and phenotype-driven mutagenesis, bringing to the fore the use of mouse models that reproduce accurately many aspects of the pathogenesis of human infectious diseases. Treatment with the mutagen N-ethyl-N-nitrosourea (ENU has become the most popular phenotype-driven approach. Our team and others have employed mouse ENU mutagenesis to identify host genes that directly impact susceptibility to pathogens of global significance. In this review, we first describe the strategies and tools used in mouse genetics to understand immunity to infection with special emphasis on chemical mutagenesis of the mouse germ-line together with current strategies to efficiently identify functional mutations using next generation sequencing. Then, we highlight illustrative examples of genes, proteins, and cellular signatures that have been revealed by ENU screens and have been shown to be involved in susceptibility or resistance to infectious diseases caused by parasites, bacteria, and viruses.

  19. Optimizing glycosyltransferase specificity via ‘hot spot’ saturation mutagenesis presents a new catalyst for novobiocin glycorandomization

    OpenAIRE

    Williams, Gavin J.; Goff, Randal D.; Zhang, Changsheng; Thorson, Jon S.

    2008-01-01

    A comprehensive two phase ‘hot spot’ saturation mutagenesis strategy to rapidly evolve glycosyltransferase specificity for non-natural acceptors is described. Specifically, the application of a high throughput screen (based upon the fluorescent acceptor umbelliferone) was used to identify key amino acid ‘hot spots’ that contribute to GT proficiency and/or promiscuity. Saturation mutagenesis of the corresponding hot spots facilitated the utilization of a lower throughput screen to provide OleD...

  20. Measurement bias and multidimensionality; an illustration of bias detection in multidimensonal measurement models

    OpenAIRE

    Jak, S.; Oort, F.J.; Dolan, C. V.

    2010-01-01

    Restricted factor analysis can be used to investigate measurement bias. A prerequisite for the detection of measurement bias through factor analysis is the correct specification of the measurement model. We applied restricted factor analysis to two subtests of a Dutch cognitive ability test. These two examples serve to illustrate the relationship between multidimensionality and measurement bias. We conclude that measurement bias implies multidimensionality, whereas multidimensionality shows u...

  1. Distinctive Characteristics of Sexual Orientation Bias Crimes

    Science.gov (United States)

    Stacey, Michele

    2011-01-01

    Despite increased attention in the area of hate crime research in the past 20 years, sexual orientation bias crimes have rarely been singled out for study. When these types of crimes are looked at, the studies are typically descriptive in nature. This article seeks to increase our knowledge of sexual orientation bias by answering the question:…

  2. delta-biased Josephson tunnel junctions

    DEFF Research Database (Denmark)

    Monaco, R.; Mygind, Jesper; Koshelet, V.;

    2010-01-01

    Abstract: The behavior of a long Josephson tunnel junction drastically depends on the distribution of the dc bias current. We investigate the case in which the bias current is fed in the central point of a one-dimensional junction. Such junction configuration has been recently used to detect the...

  3. Production bias and cluster annihilation: Why necessary?

    DEFF Research Database (Denmark)

    Singh, B.N.; Trinkaus, H.; Woo, C.H.

    1994-01-01

    the primary cluster density is high. Therefore, a sustained high swelling rate driven by production bias must involve the annihilation of primary clusters at sinks. A number of experimental observations which are unexplainable in terms of the conventional dislocation bias for monointerstitials is...

  4. A simple model for biased divertors

    Energy Technology Data Exchange (ETDEWEB)

    Lachambre, J.-L.; Quirion, B.; Gunn, J.; Boucher, C.; Stansfield, B.; Gauvreau, J.-L. [Centre canadien de fusion magnetique, 1804, boulevard Lionel-Boulet, Varennes, Quebec, J3X 1S1 (Canada)

    1997-12-01

    Ionization near the target plate is shown to play an important role in biasing experiments. Our previous SOL model, which calculates the induced radial electric field, is found to be inadequate to treat the new divertor geometry of TdeV. When recycling is included via the measured D{sub {alpha}} emission near the plate, the upgraded model correctly reproduces all the observed electric currents and fields during biasing in the new divertor configuration. A simple divertor model using this calculated field has been developed to simulate the evolution of the divertor ion and neutral parameters under the action of neutralization plate biasing. Using a 1D adiabatic fluid model for the divertor ions, a 1D convective representation for the SOL neutrals and a 0D calculation for the plenum pressure, this divertor model satisfactorily simulates most of the TdeV biasing experiments at all biasing voltages and all toroidal field directions at low line-averaged densities. The weaker agreement at high densities is largely a consequence of the crudeness of the general divertor physics rather than of the deficiency of the biasing physics implemented in the model. The model is finally used to explain the polarity asymmetries observed in divertor efficiencies during biasing, and to demonstrate that no mechanism other than plate current saturation is required to interpret the saturation of toroidal rotation observed in the SOL at large biasing voltages of either polarity. (author)

  5. Understanding Implicit Bias: What Educators Should Know

    Science.gov (United States)

    Staats, Cheryl

    2016-01-01

    The desire to ensure the best for children is precisely why educators should become aware of the concept of implicit bias: the attitudes or stereotypes that affect our understanding, actions, and decisions in an unconscious manner. Operating outside of our conscious awareness, implicit biases are pervasive, and they can challenge even the most…

  6. Biases in Children's and Adults' Moral Judgments

    Science.gov (United States)

    Powell, Nina L.; Derbyshire, Stuart W. G.; Guttentag, Robert E.

    2012-01-01

    Two experiments examined biases in children's (5/6- and 7/8-year-olds) and adults' moral judgments. Participants at all ages judged that it was worse to produce harm when harm occurred (a) through action rather than inaction (omission bias), (b) when physical contact with the victim was involved (physical contact principle), and (c) when the harm…

  7. Racially Biased Policing: Determinants of Citizen Perceptions

    Science.gov (United States)

    Weitzer, Ronald; Tuch, Steven A.

    2005-01-01

    The current controversy surrounding racial profiling in America has focused renewed attention on the larger issue of racial bias by the police. Yet little is known about the extent of police racial bias and even less about public perceptions of the problem. This article analyzes recent national survey data on citizens' views of and reported…

  8. How Many Hindsight Biases Are There?

    Science.gov (United States)

    Blank, Hartmut; Nestler, Steffen; von Collani, Gernot; Fischer, Volkhard

    2008-01-01

    The answer is three: questioning a conceptual default assumption in hindsight bias research, we argue that the hindsight bias is not a unitary phenomenon but consists of three separable and partially independent subphenomena or components, namely, memory distortions, impressions of foreseeability and impressions of necessity. Following a detailed…

  9. Attention bias modification: the Emperor's new suit?

    Directory of Open Access Journals (Sweden)

    Emmelkamp Paul MG

    2012-06-01

    Full Text Available Abstract A series of primarily laboratory-based studies found attention bias modification in socially anxious participants to lead to reduced anxiety. It is argued that the failure to replicate the positive results of attention bias modification in the study of Carlbring et al. may be due to reasons other than the application through the Internet. A number of controlled studies failed to replicate the positive effects of attention bias modification in clinically rather than subclinically socially anxious subjects. Given the lack of robust evidence for attention bias modification in clinically socially anxious individuals, the author is inclined to consider attention bias modification as 'the Emperor's new suit'. Results achieved with regular Internet-based treatments for social anxiety disorder based on cognitive therapy and exposure methods are much better than those achieved with attention bias modification procedures delivered 'face to face' in clinically distressed participants. Given the lack of robust evidence for attention bias modification in clinical samples, there is no need yet to investigate the implementation of attention bias modification through the Internet. Please see related article: http://www.biomedcentral.com/1471-244X/12/66

  10. EVIDENCE OF NATIONALISTIC BIAS IN MUAYTHAI

    Directory of Open Access Journals (Sweden)

    Tony D. Myers

    2006-07-01

    Full Text Available MuayThai is a combat sport with a growing international profile but limited research conducted into judging practices and processes. Problems with judging of other subjectively judged combat sports have caused controversy at major international tournaments that have resulted in changes to scoring methods. Nationalistic bias has been central to these problems and has been identified across a range of sports. The aim of this study was to examine nationalistic bias in MuayThai. Data were collected from the International Federation of MuayThai Amateur (IFMA World Championships held in Almaty, Kazakhstan September 2003 and comprised of tournament results from 70 A-class MuayThai bouts each judged by between five and nine judges. Bouts examined featured 62 competitors from 21 countries and 25 judges from 11 countries. Results suggested that nationalistic bias was evident. The bias observed equated to approximately one round difference between opposing judges over the course of a bout (a mean of 1.09 (SE=0.50 points difference between judges with opposing affilations. The number of neutral judges used meant that this level of bias generally did not influence the outcome of bouts. Future research should explore other ingroup biases, such as nearest neighbour bias and political bias as well as investigating the feasibility adopting an electronic scoring system

  11. A report on 36 years practical work on crop improvement through induced mutagenesis

    International Nuclear Information System (INIS)

    Physical and/or chemical mutagens cause random changes in the nuclear DNA or cytoplasmic organelles, resulting in gene, chromosomal or genomic mutations. The author will share his life time experience and achievement on induced mutagenesis. The author initiated induced mutagenesis work in 1971 till July 2007 and used both physical (X-ray and Gamma rays) and chemical (EMS, MMS, Colchicine) mutagens for improvement of vegetables (Trichosanthes anguina L, T. cucumarina , Cucurbita maxima L, Cephalandra indica, Luffa acutangula Roxb., Lagenaria ciceraria), medicinal (Trigonella foenum-graecum L, Mentha citrate Ehrh), pulse (Winged Bean (Psophocarpus tetragonolobus L. D.C.), oil bearing (Jatropha curcas L, Rosa damascene, Cymbopogon flexuosus (Nees) Wats) and ornamental (Bougainvillea, Chrysanthemum, Dahlia, Gladiolus, Hibiscus, Lantana depressa Naud, Rose, Tuberose, Narcissus etc.) crops. All classical and advanced mutagenesis methods have been extensively used for the development of new and novel cultivars of economic importance. Early flowering, late flowering, dwarf, yellow fruit color, crinkled leaf, short thick fruit, increased branching, increased pod and seed number, seed size, seed color (green, brown, chocolate color) high fruit-, seed-, oil- and punicic acidyielding mutants have been developed in T. anguina, T. fornum-graecum, Winged Bean and in J.curcas containing 'curcas oil', an efficient substitute fuel for diesel engines. Induction of flower color and chlorophyll variegated mutants in L. depressa proved the efficiency of mutation technique for domestication of wild relatives. Author was deeply engaged for the last 30 years for improvement of ornamentals and has been most successful to produce quite a large number of new promising mutant varieties in different ornamentals. Colchicine has been successfully used to develop new flower color in chrysanthemum and rose and high yielding strains in T. anguina. A novel direct in vitro regeneration technique has

  12. Galaxy Bias in Quintessence Cosmological Models

    CERN Document Server

    Basilakos, S

    2003-01-01

    We derive the evolution of the linear bias factor, $b(z)$, in cosmological models driven by an exotic fluid with an equation of state: $p_{x}=w\\rho_{x}$, where $-1\\le w<0$ (quintessence). Our aim is to put constrains on different cosmological and biasing models by combining the recent observational clustering results of optical ({\\em 2dF}) galaxies (Hawkings et al.) with those predicted by the models. We find that our bias model when fitted to the {\\em 2dF} clustering results predicts different bias evolution for different values of $w$. The models that provide the weak biasing ($b_{\\circ} \\sim 1.1$) of optical galaxies found in many recent observational studies are flat, $\\Omega_{\\rm m}=0.3$ with $w\\le -0.9$. These models however, predict a weak redshift evolution of $b(z)$, not corroborated by N-body simulations.

  13. Composite biasing in Monte Carlo radiative transfer

    CERN Document Server

    Baes, Maarten; Lunttila, Tuomas; Bianchi, Simone; Camps, Peter; Juvela, Mika; Kuiper, Rolf

    2016-01-01

    Biasing or importance sampling is a powerful technique in Monte Carlo radiative transfer, and can be applied in different forms to increase the accuracy and efficiency of simulations. One of the drawbacks of the use of biasing is the potential introduction of large weight factors. We discuss a general strategy, composite biasing, to suppress the appearance of large weight factors. We use this composite biasing approach for two different problems faced by current state-of-the-art Monte Carlo radiative transfer codes: the generation of photon packages from multiple components, and the penetration of radiation through high optical depth barriers. In both cases, the implementation of the relevant algorithms is trivial and does not interfere with any other optimisation techniques. Through simple test models, we demonstrate the general applicability, accuracy and efficiency of the composite biasing approach. In particular, for the penetration of high optical depths, the gain in efficiency is spectacular for the spe...

  14. Implicit Social Biases in People With Autism.

    Science.gov (United States)

    Birmingham, Elina; Stanley, Damian; Nair, Remya; Adolphs, Ralph

    2015-11-01

    Implicit social biases are ubiquitous and are known to influence social behavior. A core diagnostic criterion of autism spectrum disorders (ASD) is abnormal social behavior. We investigated the extent to which individuals with ASD might show a specific attenuation of implicit social biases, using Implicit Association Tests (IATs) involving social (gender, race) and nonsocial (nature, shoes) categories. High-functioning adults with ASD showed intact but reduced IAT effects relative to healthy control participants. We observed no selective attenuation of implicit social (vs. nonsocial) biases in our ASD population. To extend these results, we supplemented our healthy control data with data collected from a large online sample from the general population and explored correlations between autistic traits and IAT effects. We observed no systematic relationship between autistic traits and implicit social biases in our online and control samples. Taken together, these results suggest that implicit social biases, as measured by the IAT, are largely intact in ASD. PMID:26386014

  15. Statistical framework for estimating GNSS bias

    Science.gov (United States)

    Vierinen, Juha; Coster, Anthea J.; Rideout, William C.; Erickson, Philip J.; Norberg, Johannes

    2016-03-01

    We present a statistical framework for estimating global navigation satellite system (GNSS) non-ionospheric differential time delay bias. The biases are estimated by examining differences of measured line-integrated electron densities (total electron content: TEC) that are scaled to equivalent vertical integrated densities. The spatiotemporal variability, instrumentation-dependent errors, and errors due to inaccurate ionospheric altitude profile assumptions are modeled as structure functions. These structure functions determine how the TEC differences are weighted in the linear least-squares minimization procedure, which is used to produce the bias estimates. A method for automatic detection and removal of outlier measurements that do not fit into a model of receiver bias is also described. The same statistical framework can be used for a single receiver station, but it also scales to a large global network of receivers. In addition to the Global Positioning System (GPS), the method is also applicable to other dual-frequency GNSS systems, such as GLONASS (Globalnaya Navigazionnaya Sputnikovaya Sistema). The use of the framework is demonstrated in practice through several examples. A specific implementation of the methods presented here is used to compute GPS receiver biases for measurements in the MIT Haystack Madrigal distributed database system. Results of the new algorithm are compared with the current MIT Haystack Observatory MAPGPS (MIT Automated Processing of GPS) bias determination algorithm. The new method is found to produce estimates of receiver bias that have reduced day-to-day variability and more consistent coincident vertical TEC values.

  16. Biased mutagenesis in the N-terminal region by degenerate oligonucleotide gene shuffling enhances secretory expression of barley alpha-amylase 2 in yeast

    DEFF Research Database (Denmark)

    Fukuda, Kenji; Jensen, Malene Hillerup; Aghajari, Nushin; Haser, Richard; Svensson, Birte

    2005-01-01

    Recombinant barley alpha-amylase 1 (rAMY1) and 2 (rAMY2), despite 80% sequence identity, are produced in very different amounts of 1.1 and alpha loop 2 that interacts with domain B (beta-->alpha loop 3) protruding from the catalytic (beta/alpha)(8)-barrel. Most remarkably Pichia pastoris strain GS...

  17. Forecast Bias Correction: A Second Order Method

    CERN Document Server

    Crowell, Sean

    2010-01-01

    The difference between a model forecast and actual observations is called forecast bias. This bias is due to either incomplete model assumptions and/or poorly known parameter values and initial/boundary conditions. In this paper we discuss a method for estimating corrections to parameters and initial conditions that would account for the forecast bias. A set of simple experiments with the logistic ordinary differential equation is performed using an iterative version of a first order version of our method to compare with the second order version of the method.

  18. Skill-Biased Technological Change in Denmark

    DEFF Research Database (Denmark)

    Malchow-Møller, Nikolaj; Rose Skaksen, Jan

    2003-01-01

    Skill-Biased Technological Change in Denmark:A Disaggregate Perspective@*In this paper, we provide an industry-level analysis of skill-biased technological change(SBTC) in Denmark over the last two decades. The analysis shows that SBTC has variedconsiderably across industries, and traditionally l...... information aboutfuture labour requirements, as the relative importance of these industries must be expectedto grow, thereby reinforcing the shift in demand for skilled labour.JEL Classification: J24, J31, L6Keywords: skill-biased technological change, Danish industries...

  19. Mutagenesis as a Functional Genomics Platform for Pharmaceutical Alkaloid Biosynthetic Gene Discovery in Opium Poppy

    International Nuclear Information System (INIS)

    Opium poppy (Papaver somniferum) accumulates the analgesic benzyl-isoquinoline alkaloids morphine, codeine and thebaine, and remains one of the world's most important medicinal plants. The development of varieties that accumulate valuable compounds, such as thebaine and codeine, but not morphine precludes the illicit synthesis of heroin (O,O-diacetylmorphine) and has led to the establishment of alternative cash crops. Novel cDNAs encoding a growing number of biosynthetic enzymes have been isolated, and various -omics resources including EST databases and DNA microarray chips have been established. However, the full potential of functional genomics as a tool for gene discovery in opium poppy remains limited by the relative inefficiency of genetic transformation protocols, which also restricts the application of metabolic engineering for both experimental and commercial purposes. We are establishing an effective functional genomics initiative based on induced mutagenesis and recently developed reverse genetics methodology, such as TILLING (Targeting Induced Local Lesions IN Genomes), with the aim of identifying biosynthetic genes that can be used to engineer opium poppy for the production of copious levels of high-value pharmaceutical alkaloids. Mutagenesis involves the treatment of seeds with ethyl methane sulfonate (EMS) or by fast-neutron bombardment (FNB). In preliminary experiments with EMS-treated seeds, the screening of 1,250 independent M2 plants led to the isolation of four mutants that displayed two distinctly altered alkaloid profiles. Two lines accumulated the central pathway intermediate reticuline and relatively low levels of morphine, codeine and thebaine compared to wild-type plants. Two other lines showed the unusual accumulation in the latex of the antimicrobial alkaloid sanguinarine, which is the product of a branch pathway distinct from that leading to morphine. The present status of -omics resources and functional genomics platforms available to

  20. Mutagenesis as a functional genomics platform for pharmaceutical alkaloid biosynthetic gene discovery in opium poppy

    International Nuclear Information System (INIS)

    Opium poppy (Papaver somniferum) accumulates the analgesic alkaloids morphine, codeine and thebaine, and remains one of the world's most important medicinal plants. The development of varieties that accumulate valuable compounds, such as thebaine and codeine, but not morphine precludes the illicit synthesis of heroin (O,O-diacetylmorphine) and has created opportunities to establish alternative cash crops. Novel cDNAs encoding more than a dozen biosynthetic enzymes have been isolated, and substantial EST databases and DNA microarray chips have been established. The full potential of functional genomics as a tool for gene discovery in opium poppy remains limited by the relative inefficiency of genetic transformation protocols, which also restricts the application of metabolic engineering for both experimental and commercial purposes. We are establishing an effective functional genomics initiative based on induced mutagenesis and TILLING (Targeting Induced Local Lesions IN Genomes) and with the aim of identifying biosynthetic genes that can be used to engineer opium poppy to produce copious levels of high-value pharmaceutical alkaloids. Mutagenesis involves the treatment of seeds by fast-neutron bombardment (FNB) or with ethyl methane sulfonate (EMS). Mutagenized opium poppy plants are cultivated in a secure underground growth facility in partnership with a Canadian biotechnology company. In preliminary experiments with EMS-treated seeds, the screening of 1,250 independent M2 plants led to the isolation of four mutants that displayed two distinctly altered alkaloid profiles. Two lines accumulated the central pathway intermediate (S)- reticuline and only low levels of morphine, codeine and thebaine. Two other lines showed the unusual accumulation of the antimicrobial alkaloid sanguinarine, which is the product of a branch pathway distinct from that leading to morphine, in the latex. The present status of -omics resources and functional genomics platforms available to

  1. piggyBac-based insertional mutagenesis in the presence of stably integrated P elements in Drosophila.

    Science.gov (United States)

    Hacker, Udo; Nystedt, Sverker; Barmchi, Mojgan Padash; Horn, Carsten; Wimmer, Ernst A

    2003-06-24

    P element-mediated mutagenesis has been used to disrupt an estimated 25% of genes essential for Drosophila adult viability. Mutation of all genes in the fly genome, however, poses a problem, because P elements show significant hotspots of integration. In addition, advanced screening scenarios often require the use of P element-based tools like the generation of germ-line mosaics using FLP recombinase-mediated recombination or gene misexpression using the UAS/Gal4 system. These techniques are P element-based and can therefore not be combined with the use of P elements as mutagenic agents. To circumvent these limitations, we have developed an insertional mutagenesis system using non-P element transposons. An enhanced yellow fluorescent protein-marked piggyBac-based mutator element was mobilized by a piggyBac specific transposase source expressed from a Hermes-based jump-starter transposon marked with enhanced cyan fluorescent protein. In a pilot screen, we have generated 798 piggyBac insertions on FRT bearing third chromosomes of which 9% have sustained a putatively piggyBac-related lethal hit. The FRTs present on the target chromosome remained stably integrated during the screen and could subsequently be used to generate germ-line clones associated with maternal and zygotic phenotypes. PCR-based analysis of insertion loci shows that 57% of the insertions are in genes for which no P element insertions have been reported. Our data demonstrate the potential of this technique to facilitate the quest for saturation mutagenesis of the Drosophila genome. The system is Drosophila nonspecific and potentially applicable in a broad spectrum of nonmodel organisms. PMID:12802016

  2. Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation.

    Science.gov (United States)

    Wylie, C Scott; Shakhnovich, Eugene I

    2012-01-01

    Reproduction is inherently risky, in part because genomic replication can introduce new mutations that are usually deleterious toward fitness. This risk is especially severe for organisms whose genomes replicate "semi-conservatively," e.g. viruses and bacteria, where no master copy of the genome is preserved. Lethal mutagenesis refers to extinction of populations due to an unbearably high mutation rate (U), and is important both theoretically and clinically, where drugs can extinguish pathogens by increasing their mutation rate. Previous theoretical models of lethal mutagenesis assume infinite population size (N). However, in addition to high U, small N can accelerate extinction by strengthening genetic drift and relaxing selection. Here, we examine how the time until extinction depends jointly on N and U. We first analytically compute the mean time until extinction (τ) in a simplistic model where all mutations are either lethal or neutral. The solution motivates the definition of two distinct regimes: a survival phase and an extinction phase, which differ dramatically in both how τ scales with N and in the coefficient of variation in time until extinction. Next, we perform stochastic population-genetics simulations on a realistic fitness landscape that both (i) features an epistatic distribution of fitness effects that agrees with experimental data on viruses and (ii) is based on the biophysics of protein folding. More specifically, we assume that mutations inflict fitness penalties proportional to the extent that they unfold proteins. We find that decreasing N can cause phase transition-like behavior from survival to extinction, which motivates the concept of "lethal isolation." Furthermore, we find that lethal mutagenesis and lethal isolation interact synergistically, which may have clinical implications for treating infections. Broadly, we conclude that stably folded proteins are only possible in ecological settings that support sufficiently large populations

  3. Mutation induced extinction in finite populations: lethal mutagenesis and lethal isolation.

    Directory of Open Access Journals (Sweden)

    C Scott Wylie

    Full Text Available Reproduction is inherently risky, in part because genomic replication can introduce new mutations that are usually deleterious toward fitness. This risk is especially severe for organisms whose genomes replicate "semi-conservatively," e.g. viruses and bacteria, where no master copy of the genome is preserved. Lethal mutagenesis refers to extinction of populations due to an unbearably high mutation rate (U, and is important both theoretically and clinically, where drugs can extinguish pathogens by increasing their mutation rate. Previous theoretical models of lethal mutagenesis assume infinite population size (N. However, in addition to high U, small N can accelerate extinction by strengthening genetic drift and relaxing selection. Here, we examine how the time until extinction depends jointly on N and U. We first analytically compute the mean time until extinction (τ in a simplistic model where all mutations are either lethal or neutral. The solution motivates the definition of two distinct regimes: a survival phase and an extinction phase, which differ dramatically in both how τ scales with N and in the coefficient of variation in time until extinction. Next, we perform stochastic population-genetics simulations on a realistic fitness landscape that both (i features an epistatic distribution of fitness effects that agrees with experimental data on viruses and (ii is based on the biophysics of protein folding. More specifically, we assume that mutations inflict fitness penalties proportional to the extent that they unfold proteins. We find that decreasing N can cause phase transition-like behavior from survival to extinction, which motivates the concept of "lethal isolation." Furthermore, we find that lethal mutagenesis and lethal isolation interact synergistically, which may have clinical implications for treating infections. Broadly, we conclude that stably folded proteins are only possible in ecological settings that support sufficiently

  4. A Bias in the Diagnosis of Schizophrenia

    Science.gov (United States)

    Reade, William Kent; Wertheimer, Michael

    1976-01-01

    Research shows a relationship between diagnoses of schizophrenia among twins. It was studied whether information that a twin was schizophrenic would bias diagnoses. Such information almost doubled the rater's estimates of probability of schizophrenia in a hypothetical case history. (NG)

  5. Gender bias in the force concept inventory?

    Science.gov (United States)

    Dietz, R. D.; Pearson, R. H.; Semak, M. R.; Willis, C. W.

    2012-02-01

    Could the well-established fact that males tend to score higher than females on the Force Concept Inventory (FCI) be due to gender bias in the questions? The eventual answer to the question hinges on the definition of bias. We assert that a question is biased only if a factor other than ability (in this case gender) affects the likelihood that a student will answer the question correctly. The statistical technique of differential item functioning allows us to control for ability in our analysis of student performance on each of the thirty FCI questions. This method uses the total score on the FCI as the measure of ability. We conclude that the evidence for gender bias in the FCI questions is marginal at best.

  6. Galaxy Bias and Primordial Non-Gaussianity

    CERN Document Server

    Assassi, Valentin; Schmidt, Fabian

    2015-01-01

    We present a systematic study of galaxy biasing in the presence of primordial non-Gaussianity. For a large class of non-Gaussian initial conditions, we define a general bias expansion and prove that it is closed under renormalization, thereby showing that the basis of operators in the expansion is complete. We then study the effects of primordial non-Gaussianity on the statistics of galaxies. We show that the equivalence principle enforces a relation between the scale-dependent bias in the galaxy power spectrum and that in the dipolar part of the bispectrum. This provides a powerful consistency check to confirm the primordial origin of any observed scale-dependent bias. Finally, we also discuss the imprints of anisotropic non-Gaussianity as motivated by recent studies of higher-spin fields during inflation.

  7. Galaxy bias and primordial non-Gaussianity

    Science.gov (United States)

    Assassi, Valentin; Baumann, Daniel; Schmidt, Fabian

    2015-12-01

    We present a systematic study of galaxy biasing in the presence of primordial non-Gaussianity. For a large class of non-Gaussian initial conditions, we define a general bias expansion and prove that it is closed under renormalization, thereby showing that the basis of operators in the expansion is complete. We then study the effects of primordial non-Gaussianity on the statistics of galaxies. We show that the equivalence principle enforces a relation between the scale-dependent bias in the galaxy power spectrum and that in the dipolar part of the bispectrum. This provides a powerful consistency check to confirm the primordial origin of any observed scale-dependent bias. Finally, we also discuss the imprints of anisotropic non-Gaussianity as motivated by recent studies of higher-spin fields during inflation.

  8. Statistical framework for estimating GNSS bias

    CERN Document Server

    Vierinen, Juha; Rideout, William C; Erickson, Philip J; Norberg, Johannes

    2015-01-01

    We present a statistical framework for estimating global navigation satellite system (GNSS) non-ionospheric differential time delay bias. The biases are estimated by examining differences of measured line integrated electron densities (TEC) that are scaled to equivalent vertical integrated densities. The spatio-temporal variability, instrumentation dependent errors, and errors due to inaccurate ionospheric altitude profile assumptions are modeled as structure functions. These structure functions determine how the TEC differences are weighted in the linear least-squares minimization procedure, which is used to produce the bias estimates. A method for automatic detection and removal of outlier measurements that do not fit into a model of receiver bias is also described. The same statistical framework can be used for a single receiver station, but it also scales to a large global network of receivers. In addition to the Global Positioning System (GPS), the method is also applicable to other dual frequency GNSS s...

  9. Future research in weight bias: What next?

    Science.gov (United States)

    Alberga, Angela S; Russell-Mayhew, Shelly; von Ranson, Kristin M; McLaren, Lindsay; Ramos Salas, Ximena; Sharma, Arya M

    2016-06-01

    The 2015 Canadian Weight Bias Summit disseminated the newest research advances and brought together 40 experts, stakeholders, and policy makers in various disciplines in health, education, and public policy to identify future research directions in weight bias. In this paper we aim to share the results of the Summit as well as encourage international and interdisciplinary research collaborations in weight bias reduction. Consensus emerged on six research areas that warrant further investigation in weight bias: costs, causes, measurement, qualitative research and lived experience, interventions, and learning from other models of discrimination. These discussions highlighted three key lessons that were informed by the Summit, namely: language matters, the voices of people living with obesity should be incorporated, and interdisciplinary stakeholders should be included. PMID:27129601

  10. Bootstrap bias-adjusted GMM estimators

    OpenAIRE

    Ramalho, Joaquim J.S.

    2005-01-01

    The ability of six alternative bootstrap methods to reduce the bias of GMM parameter estimates is examined in an instrumental variable framework using Monte Carlo analysis. Promising results were found for the two bootstrap estimators suggested in the paper.

  11. Accounting for Unobservable Exposure Time Bias Wh...

    Data.gov (United States)

    U.S. Department of Health & Human Services — Accounting for Unobservable Exposure Time Bias When Using Medicare Prescription Drug Data Unobservable exposure time is common among Medicare Part D beneficiaries,...

  12. Bias Modeling for Distantly Supervised Relation Extraction

    Directory of Open Access Journals (Sweden)

    Yang Xiang

    2015-01-01

    Full Text Available Distant supervision (DS automatically annotates free text with relation mentions from existing knowledge bases (KBs, providing a way to alleviate the problem of insufficient training data for relation extraction in natural language processing (NLP. However, the heuristic annotation process does not guarantee the correctness of the generated labels, promoting a hot research issue on how to efficiently make use of the noisy training data. In this paper, we model two types of biases to reduce noise: (1 bias-dist to model the relative distance between points (instances and classes (relation centers; (2 bias-reward to model the possibility of each heuristically generated label being incorrect. Based on the biases, we propose three noise tolerant models: MIML-dist, MIML-dist-classify, and MIML-reward, building on top of a state-of-the-art distantly supervised learning algorithm. Experimental evaluations compared with three landmark methods on the KBP dataset validate the effectiveness of the proposed methods.

  13. Improving Antigenicity of the Recombinant Hepatitis C Virus Core Protein via Random Mutagenesis

    OpenAIRE

    Chen-Ji Huang; Hwei-Ling Peng; Chih-Yu Cheng

    2011-01-01

    In order to enhance the sensitivity of diagnosis, a recombinant clone containing domain I of HCV core (amino acid residues 1 to 123) was subjected to random mutagenesis. Five mutants with higher sensitivity were obtained by colony screening of 616 mutants using reverse ELISA. Sequence analysis of these mutants revealed alterations focusing on W84, P95, P110, or V129. The inclusion bodies of these recombinant proteins overexpressed in E. coli BL21(DE3) were subsequently dissolved using 6 M ure...

  14. Near-Ultraviolet Mutagenesis in Superoxide Dismutase-deficient Strains of Escherichia coli.

    OpenAIRE

    Knowles, RL; Eisenstark, A.

    1994-01-01

    We compared mutagenic spectra induced by polychromatic near-ultraviolet radiation (near-UV; 300-400 nm) with superoxide anion (O2-) -dependent mutagenesis using a set of Escherichia coli tester strains. Near-UV radiation produced increased frequencies of G:C to A:T transitions, G:C to T:A and A:T to T:A transversions, and small increases in frameshift mutations in wild-type cells. Tester strains lacking superoxide dismutase (SOD) activity (sodAsodB double mutants) demonstrated high spontaneou...

  15. Suicide plasmid vehicles for insertion mutagenesis in Rhizobium meliloti and related bacteria.

    OpenAIRE

    Selvaraj, G; Iyer, V. N.

    1983-01-01

    We describe the construction and use of a set of plasmid vectors of the transposons Tn1, Tn5, and Tn9 that are suicidal in Rhizobium species and therefore suitable for mutagenesis with these three transposons. The vectors are composed of the p15A replicon which functions in Escherichia coli but not in Rhizobium species and a region encoding the N type of bacterial conjugation system which is very efficient in matings between E. coli and Rhizobium species. The usefulness of the vectors has bee...

  16. Design of Deinococcus radiodurans thioredoxin reductase with altered thioredoxin specificity using computational alanine mutagenesis

    OpenAIRE

    Obiero, Josiah; Sanders, David AR

    2011-01-01

    In this study, the X-ray crystal structure of the complex between Escherichia coli thioredoxin reductase (EC TrxR) and its substrate thioredoxin (Trx) was used as a guide to design a Deinococcus radiodurans TrxR (DR TrxR) mutant with altered Trx specificity. Previous studies have shown that TrxRs have higher affinity for cognate Trxs (same species) than that for Trxs from different species. Computational alanine scanning mutagenesis and visual inspection of the EC TrxR–Trx interface suggested...

  17. Improved inhibitor tolerance in xylose-fermenting yeast Spathaspora passalidarum by mutagenesis and protoplast fusion

    DEFF Research Database (Denmark)

    Hou, Xiaoru; Yao, Shuo

    2012-01-01

    inhibitor tolerance of this yeast, a combination of UV mutagenesis and protoplast fusion was used to construct strains with improved performance. Firstly, UVinduced mutants were screened and selected for improved tolerance towards furfural. The most promised mutant, S. passalidarum M7, produced 50% more...... from fusion of the protoplasts of S. passalidarum M7 and a robust yeast, Saccharomyces cerevisiae ATCC 96581, were able to grow in 75% WSLQ and produce around 0.4 g ethanol/g consumed xylose. Among the selected hybrid strains, the hybrid FS22 showed the best fermentation capacity in 75% WSLQ...

  18. Energy Biased Technical Change: A CGE Analysis

    OpenAIRE

    Löschel, Andreas; Otto, Vincent M.; Rob B. Dellink

    2005-01-01

    This paper studies energy bias in technical change. For this purpose, we develop a computable general equilibrium model that builds on endogenous growth models. The model explicitly captures links between energy, the rate and direction of technical change, and the economy. We derive the equilibrium determinants of biased technical change and show the importance of feedback in technical change, substitution possibilities between final goods, and general-equilibrium effects for the equilibrium ...

  19. Constraints on Assembly Bias from Galaxy Clustering

    OpenAIRE

    Zentner, Andrew R.; Hearin, Andrew; Bosch, Frank C. van den; Lange, Johannes U.; Villarreal, Antonio

    2016-01-01

    We constrain the newly-introduced decorated Halo Occupation Distribution (HOD) model using SDSS DR7 measurements of projected galaxy clustering or r-band luminosity threshold samples. The decorated HOD is a model for the galaxy-halo connection that augments the HOD by allowing for the possibility of galaxy assembly bias: galaxy luminosity may be correlated with dark matter halo properties besides mass, Mvir. We demonstrate that it is not possible to rule out galaxy assembly bias using DR7 mea...

  20. Spending Biased Legislators - Discipline Through Disagreement

    OpenAIRE

    Facundo Piguillem; Alessandro Riboni

    2013-01-01

    This paper studies politicians who have a present-bias for spending; they want to increase current spending and procrastinate spending cuts. We argue that legislators' bias is more severe in economies with low institutional quality. We show that disagreement in legislatures leads to policy persistence and that this attenuates the temptation to overspend. Depending on the environment, legislators' decisions to be fiscally responsible may either complement or substitute other legislator's decis...

  1. Bias, Misinformation and the Paradox of Neutrality

    OpenAIRE

    Bednar, Peter; Welch, Christine

    2008-01-01

    What is normally described as bias? A possible definition comprises attempts to distort or mislead to achieve a certain perspective, i.e. subjective descriptions intended to mislead. If designers were able to exclude bias from informing systems, then this would maximize their effectiveness. This implicit conjecture appears to underpin much of the research in our field. However, in our efforts to support the evolution and design of informing systems, the way we think, communicate and conceptua...

  2. Clustering coefficient without degree correlations biases

    OpenAIRE

    Soffer, Sara Nadiv; Vazquez, Alexei

    2004-01-01

    The clustering coefficient quantifies how well connected are the neighbors of a vertex in a graph. In real networks it decreases with the vertex degree, which has been taken as a signature of the network hierarchical structure. Here we show that this signature of hierarchical structure is a consequence of degree correlation biases in the clustering coefficient definition. We introduce a new definition in which the degree correlation biases are filtered out, and provide evidence that in real n...

  3. The Local Bias of Individual Investors

    OpenAIRE

    Ning Zhu

    2002-01-01

    This study investigates individual investors' bias towards nearby companies. Using data from a large U.S. discount brokerage, we find that individual investors tend to invest in companies closer to them relative to the market portfolio. Unlike Coval and Moskowitz's (1999) findings on institutional investors, however, we find that advantageous information cannot explain individual investors' local bias. Accounting numbers and information asymmetry matter less to individual investors' local bia...

  4. Biased liquid crystal photonic bandgap fiber

    DEFF Research Database (Denmark)

    Weirich, Johannes; Lægsgaard, Jesper; Alkeskjold, Thomas Tanggaard;

    2008-01-01

    We simulate the director structure of all capillaries in a biased photonic crystal fiber infiltrated with liquid crystals. Various mode simulations for different capillaries show the necessity to consider the entire structure.......We simulate the director structure of all capillaries in a biased photonic crystal fiber infiltrated with liquid crystals. Various mode simulations for different capillaries show the necessity to consider the entire structure....

  5. Resolving Bias in Laser Ablation Geochronology

    Science.gov (United States)

    Bowring, James; Horstwood, Matthew; Gehrels, George

    2013-06-01

    Increasingly, scientific investigations requiring geochronology utilize laser ablation (LA)-inductively coupled plasma mass spectrometry (ICPMS), taking advantage of the efficiency and throughput possible for uranium-thorium-lead (U-Th-Pb) dating. A number of biases exist when comparing data among laboratories and an ongoing community-based effort is working to resolve and eliminate these biases to improve the accuracy of scientific interpretation based on these data.

  6. Invited Commentary: Causal Diagrams and Measurement Bias

    OpenAIRE

    Hernán, Miguel A.; Cole, Stephen R.

    2009-01-01

    Causal inferences about the effect of an exposure on an outcome may be biased by errors in the measurement of either the exposure or the outcome. Measurement errors of exposure and outcome can be classified into 4 types: independent nondifferential, dependent nondifferential, independent differential, and dependent differential. Here the authors describe how causal diagrams can be used to represent these 4 types of measurement bias and discuss some problems that arise when using measured expo...

  7. Local Bias and Stock Market Conditions

    OpenAIRE

    Giannetti, Mariassunta; Laeven, Luc

    2012-01-01

    We show that the local bias in U.S. mutual fund portfolios varies significantly over time and is more pronounced at times of heightened market uncertainty, such as during financial crises. Similarly, the local bias is less pronounced in periods when market sentiment is strong. These results do not depend on past fund performance or fund inflows during good times. Additionally, we do not find that fund managers earn superior returns on local stocks during periods of heightened market uncertain...

  8. Time Series Properties of Expectation Biases

    OpenAIRE

    Kinari, Yusuke

    2011-01-01

    This study exammes time senes properties of expectation biases usmg a highfrequency survey on stock price forecasts, which required participants to forecast the Nikkei 225 over three forecasting horizons: one day, one week, and one month ahead. Constructing proxies for overconfidence and optimism as the expectation biases, this study shows that overconfidence is likely to remain stable over time while optimism is not. Moreover, a relationship exists between optimism and stock price movement, ...

  9. Constraints on Assembly Bias from Galaxy Clustering

    CERN Document Server

    Zentner, Andrew R; Bosch, Frank C van den; Lange, Johannes U; Villarreal, Antonio

    2016-01-01

    We constrain the newly-introduced decorated Halo Occupation Distribution (HOD) model using SDSS DR7 measurements of projected galaxy clustering or r-band luminosity threshold samples. The decorated HOD is a model for the galaxy-halo connection that augments the HOD by allowing for the possibility of galaxy assembly bias: galaxy luminosity may be correlated with dark matter halo properties besides mass, Mvir. We demonstrate that it is not possible to rule out galaxy assembly bias using DR7 measurements of galaxy clustering alone. Moreover, galaxy samples with Mr < -20 and Mr < -20.5 favor strong central galaxy assembly bias. These samples prefer scenarios in which high-concentration are more likely to host a central galaxy relative to low-concentration halos of the same mass. We exclude zero assembly bias with high significance for these samples. Satellite galaxy assembly bias is significant for the faintest sample, Mr < -19. We find no evidence for assembly bias in the Mr < -21 sample. Assembly bi...

  10. Microarray analyses reveal that plant mutagenesis may induce more transcriptomic changes than transgene insertion.

    Science.gov (United States)

    Batista, Rita; Saibo, Nelson; Lourenço, Tiago; Oliveira, Maria Margarida

    2008-03-01

    Controversy regarding genetically modified (GM) plants and their potential impact on human health contrasts with the tacit acceptance of other plants that were also modified, but not considered as GM products (e.g., varieties raised through conventional breeding such as mutagenesis). What is beyond the phenotype of these improved plants? Should mutagenized plants be treated differently from transgenics? We have evaluated the extent of transcriptome modification occurring during rice improvement through transgenesis versus mutation breeding. We used oligonucleotide microarrays to analyze gene expression in four different pools of four types of rice plants and respective controls: (i) a gamma-irradiated stable mutant, (ii) the M1 generation of a 100-Gy gamma-irradiated plant, (iii) a stable transgenic plant obtained for production of an anticancer antibody, and (iv) the T1 generation of a transgenic plant produced aiming for abiotic stress improvement, and all of the unmodified original genotypes as controls. We found that the improvement of a plant variety through the acquisition of a new desired trait, using either mutagenesis or transgenesis, may cause stress and thus lead to an altered expression of untargeted genes. In all of the cases studied, the observed alteration was more extensive in mutagenized than in transgenic plants. We propose that the safety assessment of improved plant varieties should be carried out on a case-by-case basis and not simply restricted to foods obtained through genetic engineering. PMID:18303117

  11. A mutagenesis-derived broad-spectrum disease resistance locus in wheat.

    Science.gov (United States)

    Campbell, Jackie; Zhang, Hongtao; Giroux, Michael J; Feiz, Leila; Jin, Yue; Wang, Meinan; Chen, Xianming; Huang, Li

    2012-07-01

    Wheat leaf rust, stem rust, stripe rust, and powdery mildew caused by the fungal pathogens Puccinia triticina, P. graminis f. sp. tritici, P. striiformis f. sp. tritici, and Blumeria graminis f. sp. tritici, respectively, are destructive diseases of wheat worldwide. Breeding durable disease resistance cultivars rely largely on continually introgressing new resistance genes, especially the genes with different defense mechanisms, into adapted varieties. Here, we describe a new resistance gene obtained by mutagenesis. The mutant, MNR220 (mutagenesis-derived new resistance), enhances resistance to three rusts and powdery mildew, with the characteristics of delayed disease development at the seedling stage and completed resistance at the adult plant stage. Genetic analysis demonstrated that the resistance in MNR220 is conferred by a single semidominant gene mapped on the short arm of chromosome 2B. Gene expression profiling of several pathogenesis-related genes indicated that MNR220 has an elevated and rapid pathogen-induced response. In addition to its potential use in breeding for resistance to multiple diseases, high-resolution mapping and cloning of the disease resistance locus in MNR220 may lead to a better understanding of the regulation of defense responses in wheat. PMID:22446929

  12. Characterization of a novel missense mutation on murine Pax3 through ENU mutagenesis

    Institute of Scientific and Technical Information of China (English)

    Yue Xiao; Lingling Zhang; Kuanjun He; Xiang Gao; Lun Yang; Lin He; Gang Ma

    2011-01-01

    N-ethyl-N-nitrosourea (ENU) mutagenesis has led to the elucidation of several regulator genes for melanocyte and skin development.Here we characterized a mutant from ENU mutagenesis with similar phenotype as that of Splotch mutant,including exencephaly,spina bifida and abnormal limbs in homozygotes as well as white belly spotting and occasionally loop-tail in heterozygotes.This novel mutant was named as SpxG..Through genome-wide linkage analysis in backcross progenies with microsatellite markers,the SpxG was confined to a region between D1MIT415 and D1M IT7 on chromosome 1,where notable Pax3 gene was located.Direct sequencing revealed that SpxG carried a nucleotide A894G missense transition in exon 6 of Pax3 gene that resulted in Asn to Asp substitution at amino acid 269 within the highly-conserved homeodomain (HD) DNA recognition module,which was the first point mutation found in this domain in mice.This N269D mutation impaired the transactivation capacity of Pax3 protein,but exerted no effect on Pax3 protein translation.The characterization of the new mutation expanded our understanding the transactivation and DNA-binding structure of Pax3 protein.

  13. Improving isopropanol tolerance and production of Clostridium beijerinckii DSM 6423 by random mutagenesis and genome shuffling.

    Science.gov (United States)

    Gérando, H Máté de; Fayolle-Guichard, F; Rudant, L; Millah, S K; Monot, F; Ferreira, Nicolas Lopes; López-Contreras, A M

    2016-06-01

    Random mutagenesis and genome shuffling was applied to improve solvent tolerance and isopropanol/butanol/ethanol (IBE) production in the strictly anaerobic bacteria Clostridium beijerinckii DSM 6423. Following chemical mutagenesis with N-methyl-N-nitro-N-nitrosoguanidine (NTG), screening of putatively improved strains was done by submitting the mutants to toxic levels of inhibitory chemicals or by screening for their tolerance to isopropanol (>35 g/L). Suicide substrates, such as ethyl or methyl bromobutyrate or alcohol dehydrogenase inhibitors like allyl alcohol, were tested and, finally, 36 mutants were isolated. The fermentation profiles of these NTG mutant strains were characterized, and the best performing mutants were used for consecutive rounds of genome shuffling. Screening of strains with further enhancement in isopropanol tolerance at each recursive shuffling step was then used to spot additionally improved strains. Three highly tolerant strains were finally isolated and able to withstand up to 50 g/L isopropanol on plates. Even if increased tolerance to the desired end product was not always accompanied by higher production capabilities, some shuffled strains showed increased solvent titers compared to the parental strains and the original C. beijerinckii DSM 6423. This study confirms the efficiency of genome shuffling to generate improved strains toward a desired phenotype such as alcohol tolerance. This tool also offers the possibility of obtaining improved strains of Clostridium species for which targeted genetic engineering approaches have not been described yet. PMID:26852409

  14. The effect of chronic alcohol consumption on mitochondrial DNA mutagenesis in human blood

    Energy Technology Data Exchange (ETDEWEB)

    Wurmb-Schwark, N. von [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany)], E-mail: nvonwurmb@rechtsmedizin.uni-kiel.de; Ringleb, A.; Schwark, T. [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany); Broese, T.; Weirich, S.; Schlaefke, D. [Clinic of Psychiatry and Psychotherapy, University of Rostock, Gehlsheimer Str. 20, Rostock (Germany); Wegener, R. [Institute of Legal Medicine, St-Georg-Str. 108, University of Rostock, 18055 Rostock (Germany); Oehmichen, M. [Institute of Legal Medicine, Christian Albrecht University of Kiel, Arnold-Heller-Str. 12, 24105 Kiel (Germany)

    2008-01-01

    The 4977 bp deletion of mitochondrial DNA (mtDNA) is known to accumulate with increasing age in post mitotic tissues. Recently, studies came out detecting this specific alteration also in fast replicating cells, e.g. in blood or skin tissue, often in correlation to specific diseases or - specifically in skin - external stressors such as UV radiation. In this study, we investigated mitochondrial mutagenesis in 69 patients with a chronic alcoholic disease and 46 age matched controls with a moderate drinking behavior. Two different fragments, specific for total and for deleted mtDNA (dmtDNA) were amplified in a duplex-PCR. A subsequent fragment analysis was performed and for relative quantification, the quotient of the peak areas of amplification products specific for deleted and total mtDNA was determined. Additionally, a real time PCR was performed to quantify mtDNA copy number. The relative amount of 4977 bp deleted mtDNA in alcoholics was significantly increased compared to controls. On the other hand, no difference regarding the mtDNA/nuclear DNA ratio in both investigated groups was detected. Additionally, no age dependence could be found nor in alcoholics, neither in the control group. These findings indicate that mtDNA mutagenesis in blood can be influenced by stressors such as alcohol. Ethanol seems to be a significant factor to alter mitochondrial DNA in blood and might be an additional contributor for the cellular aging process.

  15. Viral Bacterial Artificial Chromosomes: Generation, Mutagenesis, and Removal of Mini-F Sequences

    Directory of Open Access Journals (Sweden)

    B. Karsten Tischer

    2012-01-01

    Full Text Available Maintenance and manipulation of large DNA and RNA virus genomes had presented an obstacle for virological research. BAC vectors provided a solution to both problems as they can harbor large DNA sequences and can efficiently be modified using well-established mutagenesis techniques in Escherichia coli. Numerous DNA virus genomes of herpesvirus and pox virus were cloned into mini-F vectors. In addition, several reverse genetic systems for RNA viruses such as members of Coronaviridae and Flaviviridae could be established based on BAC constructs. Transfection into susceptible eukaryotic cells of virus DNA cloned as a BAC allows reconstitution of recombinant viruses. In this paper, we provide an overview on the strategies that can be used for the generation of virus BAC vectors and also on systems that are currently available for various virus species. Furthermore, we address common mutagenesis techniques that allow modification of BACs from single-nucleotide substitutions to deletion of viral genes or insertion of foreign sequences. Finally, we review the reconstitution of viruses from BAC vectors and the removal of the bacterial sequences from the virus genome during this process.

  16. Sleeping Beauty transposon insertional mutagenesis based mouse models for cancer gene discovery

    Science.gov (United States)

    Moriarity, Branden S; Largaespada, David A

    2016-01-01

    Large-scale genomic efforts to study human cancer, such as the cancer gene atlas (TCGA), have identified numerous cancer drivers in a wide variety of tumor types. However, there are limitations to this approach, the mutations and expression or copy number changes that are identified are not always clearly functionally relevant, and only annotated genes and genetic elements are thoroughly queried. The use of complimentary, nonbiased, functional approaches to identify drivers of cancer development and progression is ideal to maximize the rate at which cancer discoveries are achieved. One such approach that has been successful is the use of the Sleeping Beauty (SB) transposon-based mutagenesis system in mice. This system uses a conditionally expressed transposase and mutagenic transposon allele to target mutagenesis to somatic cells of a given tissue in mice to cause random mutations leading to tumor development. Analysis of tumors for transposon common insertion sites (CIS) identifies candidate cancer genes specific to that tumor type. While similar screens have been performed in mice with the PiggyBac (PB) transposon and viral approaches, we limit extensive discussion to SB. Here we discuss the basic structure of these screens, screens that have been performed, methods used to identify CIS. PMID:26051241

  17. Random mutagenesis of aspergillus niger and process optimization for enhanced production of glucose oxidase

    International Nuclear Information System (INIS)

    The study deals with the improvement of wild strain Aspergillus niger IIB-31 through random mutagenesis using chemical mutagens. The main aim of the work was to enhance the glucose oxidase (GOX) yield of wild strain (24.57+-0.01 U/g of cell mass) through random mutagenesis and process optimization. The wild strain of Aspergillus niger IIB-31 was treated with chemical mutagens such as Ethyl methane sulphonate (EMS) and nitrous acid for this purpose. Mutagen treated 98 variants indicating the positive results were picked and screened for the glucose oxidase production using submerged fermentation. EMS treated E45 mutant strain gave the highest glucose oxidase production (69.47 + 0.01 U/g of cell mass), which was approximately 3-folds greater than the wild strain IIB-31. The preliminary cultural conditions for the production of glucose oxidase using submerged fermentation from strain E45 were also optimized. The highest yield of GOD was obtained using 8% glucose as carbon and 0.3% peptone as nitrogen source at a medium pH of 7.0 after an incubation period of 72 hrs at 30 degree. (author)

  18. Novel patterns of ultraviolet mutagenesis and Weigle reactivation in Staphylococcus aureus and phage phi II

    International Nuclear Information System (INIS)

    The effects of u.v. irradiation on the survival of Staphylococcus aureus and its phage phi11 were studied. The recA and uvr mutations affected their survival like synonymous mutations in Escherichia coli. Weigle reactivation (W-reactivation) of phi11 occurred in wild-type S. aureus and in a uvr mutant. Reactivation was recA-dependent and was accompanied by u.v.-induced mutagenesis in a temperature-sensitive mutant of phi11. Bacterial mutation to streptomycin resistance was induced by u.v. and was also recA-dependent. In S. aureus, as in E. coli, u.v. was a more effective mutagen in the uvr genetic background. However, a dose-squared response for u.v.-induced mutation of wild-type and uvr strains of S. aureus to streptomycin resistance, and of a trp auxotroph to tryptophan independence, was found only with u.v. doses below 1 J m-2. In relation to the Uvr mechanism of DNA repair, u.v. mutagenesis in S. aureus may involve both repairable and non-repairable lesions. As in E. Coli, the uvr genetic background reduced the u.v. dose required for maximal W-reactivation of u.v.-irradiated phage. However, there was no enhancement of W-reactivation by post-irradiation broth incubation of S. aureus. The results are compatible with a non-inducible mechanism for this phenomenon. (author)

  19. Control of mammalian cell mutagenesis and differentiation by chemicals which initiate or promote tumor formation

    Energy Technology Data Exchange (ETDEWEB)

    Jones, C. A.; Huberman, E.

    1980-01-01

    A cell-mediated mutagenesis assay was developed to predict the potential carcinogenic hazard of some environmental chemicals. In this assay, Chinese hamster V79 cells, which are susceptible to mutagenesis, are co-cultivated with cells capable of metabolizing chemical carcinogens. Use of this assay made it possible to demonstrate a relationship between the degree of carcinogenicity and mutagenicity of a series of polycyclic hydrocarbons and nitrosamines and to study the organ specificity exhibited by some chemical carcinogens. However, most short-term in vitro assays are designed to detect mutagenic activity and therefore do not detect tumor promoting agents which are devoid of this activity. By analyzing various markers of terminal differentiation in cultured human melanoma and myeloid leukemia cells, we have established a relationship between the activity of a series of tumor promoting phorbol diesters in the mouse skin and their ability to induce terminal differentiation. We suggest that measuring alterations in the differentiation characteristics of some cultured cells may represent an approach by which environmental tumor promoting agents can be studied and detected.

  20. Fragile DNA motifs trigger mutagenesis at distant chromosomal loci in saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Natalie Saini

    2013-06-01

    Full Text Available DNA sequences capable of adopting non-canonical secondary structures have been associated with gross-chromosomal rearrangements in humans and model organisms. Previously, we have shown that long inverted repeats that form hairpin and cruciform structures and triplex-forming GAA/TTC repeats induce the formation of double-strand breaks which trigger genome instability in yeast. In this study, we demonstrate that breakage at both inverted repeats and GAA/TTC repeats is augmented by defects in DNA replication. Increased fragility is associated with increased mutation levels in the reporter genes located as far as 8 kb from both sides of the repeats. The increase in mutations was dependent on the presence of inverted or GAA/TTC repeats and activity of the translesion polymerase Polζ. Mutagenesis induced by inverted repeats also required Sae2 which opens hairpin-capped breaks and initiates end resection. The amount of breakage at the repeats is an important determinant of mutations as a perfect palindromic sequence with inherently increased fragility was also found to elevate mutation rates even in replication-proficient strains. We hypothesize that the underlying mechanism for mutagenesis induced by fragile motifs involves the formation of long single-stranded regions in the broken chromosome, invasion of the undamaged sister chromatid for repair, and faulty DNA synthesis employing Polζ. These data demonstrate that repeat-mediated breaks pose a dual threat to eukaryotic genome integrity by inducing chromosomal aberrations as well as mutations in flanking genes.

  1. Mutagenesis for improvement of activity and thermostability of amylomaltase from Corynebacterium glutamicum.

    Science.gov (United States)

    Nimpiboon, Pitchanan; Kaulpiboon, Jarunee; Krusong, Kuakarun; Nakamura, Shigeyoshi; Kidokoro, Shun-Ichi; Pongsawasdi, Piamsook

    2016-05-01

    This work aims to improve thermostability of amylomaltase from a mesophilic Corynebacterium glutamicum (CgAM) by random and site-directed mutagenesis. From error prone PCR, a mutated CgAM with higher thermostability at 50°C compared to the wild-type was selected and sequenced. The result showed that the mutant contains a single mutation of A406V. Site-directed mutagenesis was then performed to construct A406V and A406L. Both mutated CgAMs showed higher intermolecular transglucosylation activity with an upward shift in the optimum temperature and a slight increase in the optimum pH for disproportionation and cyclization reactions. Thermostability of both mutated CgAMs at 35-40°C was significantly increased with a higher peak temperature from DSC spectra when compared to the wild-type. A406V had a greater effect on activity and thermostability than A406L. The catalytic efficiency values kcat/Km of A406V- and A406L-CgAMs were 2.9 and 1.4 times higher than that of the wild-type, respectively, mainly due to a significant increase in kcat. LR-CD product analysis demonstrated that A406V gave higher product yield, especially at longer incubation time and higher temperature, in comparison to the wild-type enzyme. PMID:26875536

  2. The role of the bacterial mismatch repair system in SOS-induced mutagenesis: a theoretical background

    International Nuclear Information System (INIS)

    A theoretical study is performed of the possible role of the methyl-directed mismatch repair system in the ultraviolet-induced mutagenesis of Escherichia coli bacterial cells. For this purpose, a mathematical model of the bacterial mismatch repair system is developed. Within this model, the key pathways of this type of repair are simulated on the basis of modern experimental data related to its mechanisms. Here we have modelled in detail five main pathways of DNA misincorporation removal with different DNA exonucleases. Using our calculations, we have tested the hypothesis that the bacterial mismatch repair system is responsible for the removal of the nucleotides misincorporated by DNA polymerase V (the UmuD'2C complex) during ultraviolet-induced SOS response. For the theoretical analysis of the mutation frequency, we have combined the proposed mathematical approach with the model of SOS-induced mutagenesis in the E.coli bacterial cell developed earlier. Our calculations support the hypothesis that methyl-directed mismatch repair influences the mutagenic effect of ultraviolet radiation

  3. The effect of chronic alcohol consumption on mitochondrial DNA mutagenesis in human blood

    International Nuclear Information System (INIS)

    The 4977 bp deletion of mitochondrial DNA (mtDNA) is known to accumulate with increasing age in post mitotic tissues. Recently, studies came out detecting this specific alteration also in fast replicating cells, e.g. in blood or skin tissue, often in correlation to specific diseases or - specifically in skin - external stressors such as UV radiation. In this study, we investigated mitochondrial mutagenesis in 69 patients with a chronic alcoholic disease and 46 age matched controls with a moderate drinking behavior. Two different fragments, specific for total and for deleted mtDNA (dmtDNA) were amplified in a duplex-PCR. A subsequent fragment analysis was performed and for relative quantification, the quotient of the peak areas of amplification products specific for deleted and total mtDNA was determined. Additionally, a real time PCR was performed to quantify mtDNA copy number. The relative amount of 4977 bp deleted mtDNA in alcoholics was significantly increased compared to controls. On the other hand, no difference regarding the mtDNA/nuclear DNA ratio in both investigated groups was detected. Additionally, no age dependence could be found nor in alcoholics, neither in the control group. These findings indicate that mtDNA mutagenesis in blood can be influenced by stressors such as alcohol. Ethanol seems to be a significant factor to alter mitochondrial DNA in blood and might be an additional contributor for the cellular aging process

  4. Screening and characterization of a high taxol producing fungus by protoplast mutagenesis

    Institute of Scientific and Technical Information of China (English)

    Zhao Kai; Sun Qingshen; Zhang Yanjun; Ping Wenxiang; Jin Tao; Zhou Dongpo

    2009-01-01

    The preparation, regeneration and mutagenesis of the taxol-producing fungus UV40-19 protoplasts were discussed in the experiment. Totally 42 strains displayed hygromycin resistance. Six strains were found to be positive mutants when screened on plate containing 90μg/mL hygromycin. One hereditarily stable strain UN05-6 was obtained, which raised the taxol yield from (376.38±8.41)μg/L to (493.12±11.36)μg/L. The optimal conditions for the preparation, regeneration and mutagenesis of the taxol producing fungus UV40-19 were as follows: 1)enzymolysis in a solution containing 3% lywallzyme, 4% snailase, 1% lysozyme and 3% cellulose at 30℃ water bath, pH5.5~6.0 for 5h; 2) The prepared protoplasts were regenerated by using bilayer plate culturing method; 3)To mutagenize the fungus UV40-19, the protoplast suspension was treated with 0.8mg/mL NTG for 15min, followed by UV irradiation (30W, 30cm distance)for 40s under magnetic stirring. The purified products of the fungus UN05-6 fermented extracts have significant inhibitive effects on SMMC-7721 cell.

  5. Comparative Analysis of Context-Dependent Mutagenesis Using Human and Mouse Models

    Directory of Open Access Journals (Sweden)

    Sofya A. Medvedeva

    2013-01-01

    Full Text Available Substitution rates strongly depend on their nucleotide context. One of the most studied examples is the excess of C > T mutations in the CG context in various groups of organisms, including vertebrates. Studies on the molecular mechanisms underlying this mutation regularity have provided insights into evolution, mutagenesis, and cancer development. Recently several other hypermutable motifs were identified in the human genome. There is an increased frequency of T > C mutations in the second position of the words ATTG and ATAG and an increased frequency of A > C mutations in the first position of the word ACAA. For a better understanding of evolution, it is of interest whether these mutation regularities are human specific or present in other vertebrates, as their presence might affect the validity of currently used substitution models and molecular clocks. A comprehensive analysis of mutagenesis in 4 bp mutation contexts requires a vast amount of mutation data. Such data may be derived from the comparisons of individual genomes or from single nucleotide polymorphism (SNP databases. Using this approach, we performed a systematical comparison of mutation regularities within 2–4 bp contexts in Mus musculus and Homo sapiens and uncovered that even closely related organisms may have notable differences in context-dependent mutation regularities.

  6. Generation of a glucose de-repressed mutant of Trichoderma reesei using disparity mutagenesis.

    Science.gov (United States)

    Iwakuma, Hidekazu; Koyama, Yoshiyuki; Miyachi, Ayako; Nasukawa, Masashi; Matsumoto, Hitoshi; Yano, Shuntaro; Ogihara, Jun; Kasumi, Takafumi

    2016-03-01

    We obtained a novel glucose de-repressed mutant of Trichoderma reesei using disparity mutagenesis. A plasmid containing DNA polymerase δ lacking proofreading activity, and AMAI, an autonomously replicating sequence was introduced into T. reesei ATCC66589. The rate of mutation evaluated with 5-fluoroorotic acid resistance was approximately 30-fold higher than that obtained by UV irradiation. The transformants harboring incompetent DNA polymerase δ were then selected on 2-deoxyglucose agar plates with hygromycin B. The pNP-lactoside hydrolyzing activities of mutants were 2 to 5-fold higher than the parent in liquid medium containing glucose. Notably, the amino acid sequence of cre1, a key gene involved in glucose repression, was identical in the mutant and parent strains, and further, the cre1 expression levels was not abolished in the mutant. Taken together, these results demonstrate that the strains of T. reesei generated by disparity mutagenesis are glucose de-repressed variants that contain mutations in yet-unidentified factors other than cre1. PMID:26540299

  7. Contextual modulation of biases in face recognition.

    Directory of Open Access Journals (Sweden)

    Fatima Maria Felisberti

    Full Text Available BACKGROUND: The ability to recognize the faces of potential cooperators and cheaters is fundamental to social exchanges, given that cooperation for mutual benefit is expected. Studies addressing biases in face recognition have so far proved inconclusive, with reports of biases towards faces of cheaters, biases towards faces of cooperators, or no biases at all. This study attempts to uncover possible causes underlying such discrepancies. METHODOLOGY AND FINDINGS: Four experiments were designed to investigate biases in face recognition during social exchanges when behavioral descriptors (prosocial, antisocial or neutral embedded in different scenarios were tagged to faces during memorization. Face recognition, measured as accuracy and response latency, was tested with modified yes-no, forced-choice and recall tasks (N = 174. An enhanced recognition of faces tagged with prosocial descriptors was observed when the encoding scenario involved financial transactions and the rules of the social contract were not explicit (experiments 1 and 2. Such bias was eliminated or attenuated by making participants explicitly aware of "cooperative", "cheating" and "neutral/indifferent" behaviors via a pre-test questionnaire and then adding such tags to behavioral descriptors (experiment 3. Further, in a social judgment scenario with descriptors of salient moral behaviors, recognition of antisocial and prosocial faces was similar, but significantly better than neutral faces (experiment 4. CONCLUSION: The results highlight the relevance of descriptors and scenarios of social exchange in face recognition, when the frequency of prosocial and antisocial individuals in a group is similar. Recognition biases towards prosocial faces emerged when descriptors did not state the rules of a social contract or the moral status of a behavior, and they point to the existence of broad and flexible cognitive abilities finely tuned to minor changes in social context.

  8. piggyBac transposon somatic mutagenesis with an activated reporter and tracker (PB-SMART for genetic screens in mice.

    Directory of Open Access Journals (Sweden)

    Sean F Landrette

    Full Text Available Somatic forward genetic screens have the power to interrogate thousands of genes in a single animal. Retroviral and transposon mutagenesis systems in mice have been designed and deployed in somatic tissues for surveying hematopoietic and solid tumor formation. In the context of cancer, the ability to visually mark mutant cells would present tremendous advantages for identifying tumor formation, monitoring tumor growth over time, and tracking tumor infiltrations and metastases into wild-type tissues. Furthermore, locating mutant clones is a prerequisite for screening and analyzing most other somatic phenotypes. For this purpose, we developed a system using the piggyBac (PB transposon for somatic mutagenesis with an activated reporter and tracker, called PB-SMART. The PB-SMART mouse genetic screening system can simultaneously induce somatic mutations and mark mutated cells using bioluminescence or fluorescence. The marking of mutant cells enable analyses that are not possible with current somatic mutagenesis systems, such as tracking cell proliferation and tumor growth, detecting tumor cell infiltrations, and reporting tissue mutagenesis levels by a simple ex vivo visual readout. We demonstrate that PB-SMART is highly mutagenic, capable of tumor induction with low copy transposons, which facilitates the mapping and identification of causative insertions. We further integrated a conditional transposase with the PB-SMART system, permitting tissue-specific mutagenesis with a single cross to any available Cre line. Targeting the germline, the system could also be used to conduct F1 screens. With these features, PB-SMART provides an integrated platform for individual investigators to harness the power of somatic mutagenesis and phenotypic screens to decipher the genetic basis of mammalian biology and disease.

  9. piggyBac transposon somatic mutagenesis with an activated reporter and tracker (PB-SMART) for genetic screens in mice.

    Science.gov (United States)

    Landrette, Sean F; Cornett, Jonathan C; Ni, Thomas K; Bosenberg, Marcus W; Xu, Tian

    2011-01-01

    Somatic forward genetic screens have the power to interrogate thousands of genes in a single animal. Retroviral and transposon mutagenesis systems in mice have been designed and deployed in somatic tissues for surveying hematopoietic and solid tumor formation. In the context of cancer, the ability to visually mark mutant cells would present tremendous advantages for identifying tumor formation, monitoring tumor growth over time, and tracking tumor infiltrations and metastases into wild-type tissues. Furthermore, locating mutant clones is a prerequisite for screening and analyzing most other somatic phenotypes. For this purpose, we developed a system using the piggyBac (PB) transposon for somatic mutagenesis with an activated reporter and tracker, called PB-SMART. The PB-SMART mouse genetic screening system can simultaneously induce somatic mutations and mark mutated cells using bioluminescence or fluorescence. The marking of mutant cells enable analyses that are not possible with current somatic mutagenesis systems, such as tracking cell proliferation and tumor growth, detecting tumor cell infiltrations, and reporting tissue mutagenesis levels by a simple ex vivo visual readout. We demonstrate that PB-SMART is highly mutagenic, capable of tumor induction with low copy transposons, which facilitates the mapping and identification of causative insertions. We further integrated a conditional transposase with the PB-SMART system, permitting tissue-specific mutagenesis with a single cross to any available Cre line. Targeting the germline, the system could also be used to conduct F1 screens. With these features, PB-SMART provides an integrated platform for individual investigators to harness the power of somatic mutagenesis and phenotypic screens to decipher the genetic basis of mammalian biology and disease. PMID:22039523

  10. Biased diffusion in tubes of alternating diameter: Numerical study over a wide range of biasing force

    Energy Technology Data Exchange (ETDEWEB)

    Makhnovskii, Yurii A. [Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Leninsky Prospect 29, Moscow 119991 (Russian Federation); Berezhkovskii, Alexander M. [Mathematical and Statistical Computing Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20819 (United States); Antipov, Anatoly E. [Faculty of Fundamental Physics and Chemical Engineering, Moscow State University, GSP-1, 1-51 Leninskie Gory, Moscow 119991 (Russian Federation); Zitserman, Vladimir Yu. [Joint Institute for High Temperatures, Russian Academy of Sciences, Izhorskaya 13, Bldg. 2, Moscow 125412 (Russian Federation)

    2015-11-07

    This paper is devoted to particle transport in a tube formed by alternating wide and narrow sections, in the presence of an external biasing force. The focus is on the effective transport coefficients—mobility and diffusivity, as functions of the biasing force and the geometric parameters of the tube. Dependences of the effective mobility and diffusivity on the tube geometric parameters are known in the limiting cases of no bias and strong bias. The approximations used to obtain these results are inapplicable at intermediate values of the biasing force. To bridge the two limits Brownian dynamics simulations were run to determine the transport coefficients at intermediate values of the force. The simulations were performed for a representative set of tube geometries over a wide range of the biasing force. They revealed that there is a range of the narrow section length, where the force dependence of the mobility has a maximum. In contrast, the diffusivity is a monotonically increasing function of the force. A simple formula is proposed, which reduces to the known dependences of the diffusivity on the tube geometric parameters in both limits of zero and strong bias. At intermediate values of the biasing force, the formula catches the diffusivity dependence on the narrow section length, if the radius of these sections is not too small.

  11. Thinking in Black and White: Conscious thought increases racially biased judgments through biased face memory

    NARCIS (Netherlands)

    Strick, M.A.; Stoeckart, P.F.; Dijksterhuis, A.J.

    2015-01-01

    It is a common research finding that conscious thought helps people to avoid racial discrimination. These three experiments, however, illustrate that conscious thought may increase biased face memory, which leads to increased judgment bias (i.e., preferring White to Black individuals). In Experiment

  12. Placebo effect studies are susceptible to response bias and to other types of biases

    DEFF Research Database (Denmark)

    Hróbjartsson, Asbjørn; Kaptchuk, Ted J; Miller, Franklin G

    2011-01-01

    Investigations of the effect of placebo are often challenging to conduct and interpret. The history of placebo shows that assessment of its clinical significance has a real potential to be biased. We analyze and discuss typical types of bias in studies on placebo....

  13. Reciprocity-induced bias in digital reputation

    CERN Document Server

    Livan, Giacomo; Aste, Tomaso

    2016-01-01

    The peer-to-peer (P2P) economy relies on establishing trust in distributed networked systems, where the reliability of a user is assessed through digital peer-review processes that aggregate ratings into reputation scores. Here we present evidence of a network effect which biases the digital reputations of the users of P2P networks, showing that P2P networks display exceedingly high levels of reciprocity. In fact, these are so large that they are close to the highest levels structurally compatible with the networks' reputation landscape. This shows that the crowdsourcing process underpinning digital reputation is significantly distorted by the attempt of users to mutually boost reputation, or to retaliate, through the exchange of ratings. We show that the least active users are predominantly responsible for such reciprocity-induced bias, and that this fact can be exploited to suppress the bias itself.

  14. Motion, identity and the bias toward agency

    Directory of Open Access Journals (Sweden)

    Chris eFields

    2014-08-01

    Full Text Available The well-documented human bias toward agency as a cause and therefore an explanation of observed events is typically attributed to evolutionary selection for a social brain. Based on a review of developmental and adult behavioral and neurocognitive data, it is argued that the bias toward agency is a result of the default human solution, developed during infancy, to the computational requirements of object re-identification over gaps in observation of more than a few seconds. If this model is correct, overriding the bias toward agency to construct mechanistic explanations of observed events requires structure-mapping inferences, implemented by the pre-motor action planning system, that replace agents with mechanisms as causes of unobserved changes in contextual or featural properties of objects. Experiments that would test this model are discussed.

  15. Recognition bias and the physical attractiveness stereotype.

    Science.gov (United States)

    Rohner, Jean-Christophe; Rasmussen, Anders

    2012-06-01

    Previous studies have found a recognition bias for information consistent with the physical attractiveness stereotype (PAS), in which participants believe that they remember that attractive individuals have positive qualities and that unattractive individuals have negative qualities, regardless of what information actually occurred. The purpose of this research was to examine whether recognition bias for PAS congruent information is replicable and invariant across a variety of conditions (i.e. generalizable). The effects of nine different moderator variables were examined in two experiments. With a few exceptions, the effect of PAS congruence on recognition bias was independent of the moderator variables. The results suggest that the tendency to believe that one remembers information consistent with the physical attractiveness stereotype is a robust phenomenon. PMID:22416805

  16. Recursive bias estimation for high dimensional smoothers

    Energy Technology Data Exchange (ETDEWEB)

    Hengartner, Nicolas W [Los Alamos National Laboratory; Matzner-lober, Eric [UHB, FRANCE; Cornillon, Pierre - Andre [INRA

    2008-01-01

    In multivariate nonparametric analysis, sparseness of the covariates also called curse of dimensionality, forces one to use large smoothing parameters. This leads to biased smoothers. Instead of focusing on optimally selecting the smoothing parameter, we fix it to some reasonably large value to ensure an over-smoothing of the data. The resulting smoother has a small variance but a substantial bias. In this paper, we propose to iteratively correct the bias initial estimator by an estimate of the latter obtained by smoothing the residuals. We examine in detail the convergence of the iterated procedure for classical smoothers and relate our procedure to L{sub 2}-Boosting. We apply our method to simulated and real data and show that our method compares favorably with existing procedures.

  17. Systematic approach to establishing criticality biases

    International Nuclear Information System (INIS)

    A systematic approach has been developed to determine benchmark biases and apply those biases to code results to meet the requirements of DOE Order 5480.24 regarding documenting criticality safety margins. Previously, validation of the code against experimental benchmarks to prove reasonable agreement was sufficient. However, DOE Order 5480.24 requires contractors to adhere to the requirements of ANSI/ANS-8.1 and establish subcritical margins. A method was developed to incorporate biases and uncertainties from benchmark calculations into a keff value with quantifiable uncertainty. The method produces a 95% confidence level in both the keff value of the scenario modeled and the distribution of the keffS calculated by the Monte Carlo code. Application of the method to a group of benchmarks modeled using the KENO-Va code and the SCALE 27 group cross sections is also presented

  18. Racial bias in perceptions of others' pain.

    Directory of Open Access Journals (Sweden)

    Sophie Trawalter

    Full Text Available The present work provides evidence that people assume a priori that Blacks feel less pain than do Whites. It also demonstrates that this bias is rooted in perceptions of status and the privilege (or hardship status confers, not race per se. Archival data from the National Football League injury reports reveal that, relative to injured White players, injured Black players are deemed more likely to play in a subsequent game, possibly because people assume they feel less pain. Experiments 1-4 show that White and Black Americans-including registered nurses and nursing students-assume that Black people feel less pain than do White people. Finally, Experiments 5 and 6 provide evidence that this bias is rooted in perceptions of status, not race per se. Taken together, these data have important implications for understanding race-related biases and healthcare disparities.

  19. Observational biases in flux magnification measurements

    CERN Document Server

    Hildebrandt, Hendrik

    2015-01-01

    Flux magnification is an interesting complement to shear-based lensing measurements, especially at high redshift where sources are harder to resolve. One measures either changes in the source density (magnification bias) or in the shape of the flux distribution (e.g. magnitude-shift). The interpretation of these measurements relies on theoretical estimates of how the observables change under magnification. Here we present simulations to create multi-band photometric mock catalogues of Lyman-break galaxies in a CFHTLenS-like survey that include several observational effects that can change these relations, making simple theoretical estimates unusable. In particular, we show how the magnification bias can be affected by photometric noise, colour selection, and dust extinction. We find that a simple measurement of the slope of the number-counts is not sufficient for the precise interpretation of virtually all observations of magnification bias. We also explore how sensitive the shift in the mean magnitude of a s...

  20. Linearity Limits of Biased 1337 Trap Detectors

    CERN Document Server

    Balling, Petr

    2015-01-01

    The upper power limit of linear response of light trap detectors was recently measured [2,3]. We have completed this measurement with test of traps with bias voltage at several visible wavelengths using silicon photodiodes Hamamatsu S1337 1010 and made a brief test of S5227 1010. Bias extends the linearity limit by factor of more than 10 for very narrow beams and more than 30 for wide beams [5]. No irreversible changes were detected even for the highest irradiance of 33 W/cm2 at 406nm. Here we present measurement of minimal bias voltage necessary for 99%, 99.8% and 99.95% linearity for several beam sizes.

  1. Improved detection in CDMA for biased sources

    Energy Technology Data Exchange (ETDEWEB)

    Efraim, Hadar [Minerva Center and Department of Physics, Bar-Ilan University, Ramat-Gan 52900 (Israel); Yacov, Nadav [Minerva Center and Department of Physics, Bar-Ilan University, Ramat-Gan 52900 (Israel); Shental, Ori [Center for Magnetic Recording Research (CMRR), University of California, San Diego (UCSD), 9500 Gilman Drive, La Jolla, CA 92093 (United States); Kanter, Ido [Minerva Center and Department of Physics, Bar-Ilan University, Ramat-Gan 52900 (Israel); Saad, David [Neural Computing Research Group, Aston University, Birmingham B4 7ET (United Kingdom)

    2007-08-17

    We consider the detection of biased information sources in the ubiquitous code-division multiple-access (CDMA) scheme. We propose a simple modification to both the popular single-user matched-filter detector and a recently introduced near-optimal message-passing-based multiuser detector. This modification allows for detecting modulated biased sources directly with no need for source coding. Analytical results and simulations with excellent agreement are provided, demonstrating substantial improvement in bit error rate in comparison with the unmodified detectors and the alternative of source compression. The robustness of error-performance improvement is shown under practical model settings, including bias estimation mismatch and finite-length spreading codes.

  2. Improved detection in CDMA for biased sources

    International Nuclear Information System (INIS)

    We consider the detection of biased information sources in the ubiquitous code-division multiple-access (CDMA) scheme. We propose a simple modification to both the popular single-user matched-filter detector and a recently introduced near-optimal message-passing-based multiuser detector. This modification allows for detecting modulated biased sources directly with no need for source coding. Analytical results and simulations with excellent agreement are provided, demonstrating substantial improvement in bit error rate in comparison with the unmodified detectors and the alternative of source compression. The robustness of error-performance improvement is shown under practical model settings, including bias estimation mismatch and finite-length spreading codes

  3. Systematic review of the empirical evidence of study publication bias and outcome reporting bias.

    Directory of Open Access Journals (Sweden)

    Kerry Dwan

    Full Text Available BACKGROUND: The increased use of meta-analysis in systematic reviews of healthcare interventions has highlighted several types of bias that can arise during the completion of a randomised controlled trial. Study publication bias has been recognised as a potential threat to the validity of meta-analysis and can make the readily available evidence unreliable for decision making. Until recently, outcome reporting bias has received less attention. METHODOLOGY/PRINCIPAL FINDINGS: We review and summarise the evidence from a series of cohort studies that have assessed study publication bias and outcome reporting bias in randomised controlled trials. Sixteen studies were eligible of which only two followed the cohort all the way through from protocol approval to information regarding publication of outcomes. Eleven of the studies investigated study publication bias and five investigated outcome reporting bias. Three studies have found that statistically significant outcomes had a higher odds of being fully reported compared to non-significant outcomes (range of odds ratios: 2.2 to 4.7. In comparing trial publications to protocols, we found that 40-62% of studies had at least one primary outcome that was changed, introduced, or omitted. We decided not to undertake meta-analysis due to the differences between studies. CONCLUSIONS: Recent work provides direct empirical evidence for the existence of study publication bias and outcome reporting bias. There is strong evidence of an association between significant results and publication; studies that report positive or significant results are more likely to be published and outcomes that are statistically significant have higher odds of being fully reported. Publications have been found to be inconsistent with their protocols. Researchers need to be aware of the problems of both types of bias and efforts should be concentrated on improving the reporting of trials.

  4. Characterization of highly efficient heavy-ion mutagenesis in Arabidopsis thaliana

    Directory of Open Access Journals (Sweden)

    Kazama Yusuke

    2011-11-01

    Full Text Available Abstract Background Heavy-ion mutagenesis is recognised as a powerful technology to generate new mutants, especially in higher plants. Heavy-ion beams show high linear energy transfer (LET and thus more effectively induce DNA double-strand breaks than other mutagenic techniques. Previously, we determined the most effective heavy-ion LET (LETmax: 30.0 keV μm-1 for Arabidopsis mutagenesis by analysing the effect of LET on mutation induction. However, the molecular structure of mutated DNA induced by heavy ions with LETmax remains unclear. Knowledge of the structure of mutated DNA will contribute to the effective exploitation of heavy-ion beam mutagenesis. Results Dry Arabidopsis thaliana seeds were irradiated with carbon (C ions with LETmax at a dose of 400 Gy and with LET of 22.5 keV μm-1 at doses of 250 Gy or 450 Gy. The effects on mutation frequency and alteration of DNA structure were compared. To characterise the structure of mutated DNA, we screened the well-characterised mutants elongated hypocotyls (hy and glabrous (gl and identified mutated DNA among the resulting mutants by high-resolution melting curve, PCR and sequencing analyses. The mutation frequency induced by C ions with LETmax was two-fold higher than that with 22.5 keV μm-1 and similar to the mutation frequency previously induced by ethyl methane sulfonate. We identified the structure of 22 mutated DNAs. Over 80% of the mutations caused by C ions with both LETs were base substitutions or deletions/insertions of less than 100 bp. The other mutations involved large rearrangements. Conclusions The C ions with LETmax showed high mutation efficiency and predominantly induced base substitutions or small deletions/insertions, most of which were null mutations. These small alterations can be determined by single-nucleotide polymorphism (SNP detection systems. Therefore, C ions with LETmax might be useful as a highly efficient reverse genetic system in conjunction with SNP detection

  5. PCR-based site-specific mutagenesis of peptide antibiotics FALL-39 and its biologic activities

    Institute of Scientific and Technical Information of China (English)

    Yun-xia YANG; Yun FENG; Bo-yao WANG; Qi WU

    2004-01-01

    AIM: To construct PGEX-1λT-FALL-39 expression vector and its mutant vector, and study the relationship of function and structure. METHODS: A cDNA encoding mature FALL-39 was cloned from SPCA- 1 cell mRNA and the prokaryotic expression vector PGEX- 1λT-FALL-39 was constructed. Two kinds of polymerase chain reaction (PCR) for the site-direction mutagenesis were used to construct FALL-39 mutant expression vector, FALL-39-Lys-32 and FALL-39-Lys-24. Minimal effective concentration, minimal inhibitory concentration, and minimal bactericidal concentration were used to assay the antibacterial activities of these peptides. Effects of different solution on the antibacterial activity of FALL-39 and FALL-39-Lys-32 were observed by CFU determination. The hemolytic effects of these peptides were also examined on human red blood cells. RESULTS: Two site-specific mutants FALL-39-Lys-32 and FALL-39-Lys24 were obtained by PCR-induced mutagenesis. In comparison with two-step PCR which required two pairs of primers, one step PCR which required one pair of primers is a simple and efficient method for the PCR based site-specific mutagenesis. Using the prokaryotic expression system, the E coli-based products of recombinant FALL39 and its mutant peptides were also obtained. The antibacterial assay showed that FALL-39-Lys-32 and FALL-39-Lys24 were more potential in the antibacterial activity against E coli ML35p and Pseltdomonas aeruginosa ATCC27853 than that of FALL-39, and no increase in hemolysis was observed at the antibacterial concentrations. The antibacterial activity of FALL-39-Lys-32 against E coli was more potent than that of FALL-39 in NaCl-containing LB medium, while its activity was almost the same as FALL-39 in SO2-4 containing Medium E. CONCLUSION: PCR-based mutagensis is a useful model system for studying the structure and function relationship of antimicrobial peptides. Keeping α-helical conformation of FALL-39 and increasing net positive charge can increase the

  6. Traders, Courts and the Home Bias Puzzle

    OpenAIRE

    Turrini, Alessandro; Van Ypersele, Tanguy

    2001-01-01

    Recent evidence shows that the ‘home bias puzzle’ in international trade may be associated with the mere presence of national borders (McCallum (1995)). In this Paper we provide a theoretical framework to explain why borders may matter so much for trade. Our argument is that even between perfectly integrated and similar countries the legal system differs, so that legal costs are higher when business is done abroad. Using a matching model of trade, we show that the home bias is associated with...

  7. Motion, identity and the bias toward agency

    OpenAIRE

    Chris Fields

    2014-01-01

    The well-documented human bias toward agency as a cause and therefore an explanation of observed events is typically attributed to evolutionary selection for a “social brain.” Based on a review of developmental and adult behavioral and neurocognitive data, it is argued that the bias toward agency is a result of the default human solution, developed during infancy, to the computational requirements of object re-identification over gaps in observation of more than a few seconds. If this model...

  8. Motion, identity and the bias toward agency

    OpenAIRE

    Fields, Chris

    2014-01-01

    The well-documented human bias toward agency as a cause and therefore an explanation of observed events is typically attributed to evolutionary selection for a “social brain”. Based on a review of developmental and adult behavioral and neurocognitive data, it is argued that the bias toward agency is a result of the default human solution, developed during infancy, to the computational requirements of object re-identification over gaps in observation of more than a few seconds. If this model i...

  9. Recursive bias estimation and L2 boosting

    Energy Technology Data Exchange (ETDEWEB)

    Hengartner, Nicolas W [Los Alamos National Laboratory; Cornillon, Pierre - Andre [INRA, FRANCE; Matzner - Lober, Eric [RENNE, FRANCE

    2009-01-01

    This paper presents a general iterative bias correction procedure for regression smoothers. This bias reduction schema is shown to correspond operationally to the L{sub 2} Boosting algorithm and provides a new statistical interpretation for L{sub 2} Boosting. We analyze the behavior of the Boosting algorithm applied to common smoothers S which we show depend on the spectrum of I - S. We present examples of common smoother for which Boosting generates a divergent sequence. The statistical interpretation suggest combining algorithm with an appropriate stopping rule for the iterative procedure. Finally we illustrate the practical finite sample performances of the iterative smoother via a simulation study.

  10. BIAS GENDER: MASALAH UTAMA DALAM INTERPRETASI ARKEOLOGI

    Directory of Open Access Journals (Sweden)

    Mimi Savitri

    2007-06-01

    Full Text Available Gender bias is an important theme in Gender Archaeology. It is influenced by modern people thinking and it has influenced archaeological interpretation for a long time. As a result, archaeological interpretation of past society is not objective. This problem should be solved to reach an objective interpretation of people’s life in the past. The author argues that gender bias in archaeology can be solved by actively criticizing androcentrism and paying more attention to men and women’s relationship in the past.

  11. Optimal design of APD biasing circuit

    Institute of Scientific and Technical Information of China (English)

    SUN Chun-sheng; QIN Shi-qiao; WANG Xing-shu; ZHU Dong-hua

    2007-01-01

    This paper proposes a control method for avalanche photodiode (APD) reverse bias with temperature compensation and load resistance compensation. The influence of background light and load resistance on APD detection circuit is analyzed in detail. A theoretical model of temperature compensation and load resistance compensation is established, which is used for APD biasing circuit designing. It is predicted that this control method is especially suitable for LD laser range finder used on vehicles. Experimental results confirm thatthe design proposed in this paper can considerablely improve the performance of range finder.

  12. Attention Bias Variability and Symptoms of Posttraumatic Stress Disorder

    OpenAIRE

    Iacoviello, Brian M.; Wu, Gang; Abend, Rany; Murrough, James W.; Feder, Adriana; Fruchter, Eyal; Levinstein, Yoav; Wald, Ilan; Bailey, Christopher R.; Pine, Daniel S.; Neumeister, Alexander; Bar-Haim, Yair; Charney, Dennis S.

    2014-01-01

    Cognitive theories implicate information-processing biases in the etiology of anxiety disorders. Results of attention-bias studies in posttraumatic stress disorder (PTSD) have been inconsistent, suggesting biases towards and away from threat. Within-subject variability of attention biases in posttraumatic patients may be a useful marker for attentional control impairment and the development of posttrauma symptoms. This study reports 2 experiments investigating threat-related attention biases,...

  13. The influence of cognitive biases on psychophysiological vulnerability to stress

    OpenAIRE

    Randall, Kate

    2012-01-01

    Individuals who disproportionately attend to negative aspects of a situation (attention bias), or who unduly interpret ambiguity in a negative manner (interpretive bias) report more psychological ill-effects of stress than those with balanced or positively-skewed inclinations. Cognitive Bias Modification (CBM) techniques improve maladaptive biases through implicitly-based association learning, with induced positive biases buffering the future perception of stress. Six experimen...

  14. Information bias in health research: definition, pitfalls, and adjustment methods

    OpenAIRE

    Althubaiti, Alaa

    2016-01-01

    As with other fields, medical sciences are subject to different sources of bias. While understanding sources of bias is a key element for drawing valid conclusions, bias in health research continues to be a very sensitive issue that can affect the focus and outcome of investigations. Information bias, otherwise known as misclassification, is one of the most common sources of bias that affects the validity of health research. It originates from the approach that is utilized to obtain or confir...

  15. Agrobacterium tumefaciens-mediated transformation: An efficient tool for insertional mutagenesis and targeted gene disruption in Harpophora oryzae.

    Science.gov (United States)

    Liu, Ning; Chen, Guo-Qing; Ning, Guo-Ao; Shi, Huan-Bin; Zhang, Chu-Long; Lu, Jian-Ping; Mao, Li-Juan; Feng, Xiao-Xiao; Liu, Xiao-Hong; Su, Zhen-Zhu; Lin, Fu-Cheng

    2016-01-01

    The endophytic filamentous fungus Harpophora oryzae is a beneficial endosymbiont isolated from the wild rice. H. oryzae could not only effectively improve growth rate and biomass yield of rice crops, but also induce systemic resistance against the rice blast fungus, Magnaporthe oryzae. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was employed and optimized to modify the H. oryzae genes by either random DNA fragment integration or targeted gene replacement. Our results showed that co-cultivation of H. oryzae conidia with A. tumefaciens in the presence of acetosyringone for 48 h at 22 °C could lead to a relatively highest frequency of transformation, and 200 μM acetosyringone (AS) pre-cultivation of A. tumefaciens is also suggested. ATMT-mediated knockout mutagenesis was accomplished with the gene-deletion cassettes using a yeast homologous recombination method with a yeast-Escherichia-Agrobacterium shuttle vector pKOHo. Using the ATMT-mediated knockout mutagenesis, we successfully deleted three genes of H. oryzae (HoATG5, HoATG7, and HoATG8), and then got the null mutants ΔHoatg5, ΔHoatg7, and ΔHoatg8. These results suggest that ATMT is an efficient tool for gene modification including randomly insertional mutagenesis and gene deletion mutagenesis in H. oryzae. PMID:26686612

  16. Insertional Mutagenesis and Deep Profiling Reveals Gene Hierarchies and a Myc/p53-Dependent Bottleneck in Lymphomagenesis

    NARCIS (Netherlands)

    Huser, C.A.; Gilroy, K.L.; De Ridder, J.; Kilbey, A.; Borland, G.; Mackay, N.; Jenkins, A.; Bell, M.; Herzyk, P.; Van der Weyden, L.; et al.

    2014-01-01

    Retroviral insertional mutagenesis (RIM) is a powerful tool for cancer genomics that was combined in this study with deep sequencing (RIM/DS) to facilitate a comprehensive analysis of lymphoma progression. Transgenic mice expressing two potent collaborating oncogenes in the germ line (CD2-MYC, -Runx

  17. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    Directory of Open Access Journals (Sweden)

    Weir Jerry P

    2007-05-01

    Full Text Available Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2 BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. While the BAC mutagenesis procedure is a powerful method to generate HSV-2 recombinants, particularly in the absence of selective marker in eukaryotic culture, the mutagenesis procedure is still difficult and cumbersome. Results Here we describe the incorporation of a phage lambda recombination system into an allele replacement vector. This strategy enables any DNA fragment containing the phage attL recombination sites to be efficiently inserted into the attR sites of the allele replacement vector using phage lambda clonase. We also describe how the incorporation of EGFP into the allele replacement vector can facilitate the selection of the desired cross-over recombinant BACs when the allele replacement reaction is a viral gene deletion. Finally, we incorporate the lambda phage recombination sites directly into an HSV-2 BAC vector for direct recombination of gene cassettes using the phage lambda clonase-driven recombination reaction. Conclusion Together, these improvements to the techniques of HSV BAC mutagenesis will facilitate the construction of recombinant herpes simplex viruses and viral vectors.

  18. Predictive mutagenesis of ligation-independent cloning (LIC) vectors for protein expression and site-specific chemical conjugation

    DEFF Research Database (Denmark)

    Vernet, Erik; Sauer, Jørgen; Andersen, Peter Andreas;

    2011-01-01

    Ligation-independent cloning (LIC) allows for cloning of DNA constructs independent of insert restriction sites and ligases. However, any required mutations are typically introduced by additional, time-consuming steps. We present a rapid, inexpensive method for mutagenesis in the 5' LIC site...

  19. From Green to Blue: Site-Directed Mutagenesis of the Green Fluorescent Protein to Teach Protein Structure-Function Relationships

    Science.gov (United States)

    Giron, Maria D.; Salto, Rafael

    2011-01-01

    Structure-function relationship studies in proteins are essential in modern Cell Biology. Laboratory exercises that allow students to familiarize themselves with basic mutagenesis techniques are essential in all Genetic Engineering courses to teach the relevance of protein structure. We have implemented a laboratory course based on the…

  20. [Comparative mutagenesis of human cells in vivo and in vitro]. Progress report, January 1-December 30, 1985

    International Nuclear Information System (INIS)

    Annual progress report is made on project focusing on the comparative mutagenesis of human cells in vivo and in vitro. The study employs the HGPRT gene to explore the changes in nucleotide sequence which has occurred in spontaneous mutations or mutations induced by MNNG or ICR191. Reports on the individual projects have been abstracted and indexed for the Energy Data Base. (DT)

  1. Biological effects of DNA repair, including mutagenesis. Progress report, August 15, 1982-August 1, 1983. COO-3571-23

    International Nuclear Information System (INIS)

    The research supported by this contract for the period covered by this report has concerned mechanisms in mutagenesis. Specifically, the work has been aimed at determining the lesions in DNA formed by particular mutagenic agents which lead to mutations, and to characterization of the pathways by which these lesions lead to changes in the sequence of bases in the genomic DNA

  2. Effect of radiation-sensitive mutations and mutagens/carcinogens on bacterial recombination and mutagenesis. Progress report

    Energy Technology Data Exchange (ETDEWEB)

    Matney, T.S.

    1978-01-01

    Progress is reported on effects of temperature sensitive DNA-initiation mutation in E. coli K-12 mutants; the use of Bacillus subtilis transforming system as an in vitro mutagenesis system; characteristics of the E. coli lysogen used to test the permeability to polycyclic aromatic hydrocarbons; and the genetic toxicology of gentian violet. (PCS)

  3. Mutagenesis for ACMV resistance in a Ghanian cassava cultivar 'Bosom nsia'

    International Nuclear Information System (INIS)

    Breeding for resistance to the African Cassava Mosaic Virus (ACMV) disease in the Ghanian cassava cultivar 'Bosom nsia' has been on-going for the past four years at the Biotechnology and Nuclear Agricultural Research Institute. Protocols for in vitro culture from shoot meristems and acclimation of plantlets were established. Radiosensitivity tests on the regenerated plantlets indicated LD50 of 40 Gy, and doses of 25, 30 and 35 Gy were suitable for mutagenesis. These doses were applied to in vivo and in vitro grown plants, and selection was carried out in three propagations. Four variants, selected under field conditions with high viral incidence, were analyzed for virus particles with three virus indexing techniques. Polymerase chain reaction (PCR) product analysis of DNA extracts from Nicotiana benthamiana test plants, inoculated with sap from the leaves of variants, confirmed the presence of virus particles in all variants. Inoculation and ELISA tests suggested ACMV tolerance in selected variants. (author). 24 refs, 3 figs, 1 tab

  4. Crystal structure and site-directed mutagenesis of a nitroalkane oxidase from Streptomyces ansochromogenes.

    Science.gov (United States)

    Li, Yanhua; Gao, Zengqiang; Hou, Haifeng; Li, Lei; Zhang, Jihui; Yang, Haihua; Dong, Yuhui; Tan, Huarong

    2011-02-18

    Nitroalkane oxidase (NAO) catalyzes neutral nitroalkanes to their corresponding aldehydes or ketones, hydrogen peroxide and nitrite. The crystal structure of NAO from Streptomyces ansochromogenes was determined; it consists of two domains, a TIM barrel domain bound to FMN and C-terminal domain with a novel folding pattern. Site-directed mutagenesis of His179, which is spatially adjacent to FMN, resulted in the loss of enzyme activity, demonstrating that this amino acid residue is important for catalysis. The crystal structure of mutant H179D-nitroethane was also analyzed. Interestingly, Sa-NAO shows the typical function as nitroalkane oxidase but its structure is similar to that of 2-nitropropane dioxygenase. Overall, these results suggest that Sa-NAO is a novel nitroalkane oxidase with TIM barrel structure. PMID:21147069

  5. Utilization of experimental mutagenesis to create high protein forms of field beans

    International Nuclear Information System (INIS)

    To induce mutation variations F1, F2 and F3 seeds of the crossing Prelom and Tyrnovo 13 are utilized. Just before the sowing the seeds are treated independently or in combination with gamma rays (Cs 137) and ethylmethanesulfonate (EMS) solutions. It is established that the treatment of the seeds with mutagenes favours the variability in increasing of the protein content in the hybrid population. Highest number of transgressive forms characterized by both high protein content and good productivity is createdby the combined ttreatment of F2 seeds with gamma-rays and 0.15% EMS. The application of the hybridization and the experimental mutagenesis resulted in the creation of eleven lines characterized by protein content more than 28%. 8 refs., 3 tabs. (author)

  6. Genetic modification through oligonucleotide-mediated mutagenesis. A GMO regulatory challenge?

    Science.gov (United States)

    Breyer, Didier; Herman, Philippe; Brandenburger, Annick; Gheysen, Godelieve; Remaut, Erik; Soumillion, Patrice; Van Doorsselaere, Jan; Custers, René; Pauwels, Katia; Sneyers, Myriam; Reheul, Dirk

    2009-01-01

    In the European Union, the definition of a GMO is technology-based. This means that a novel organism will be regulated under the GMO regulatory framework only if it has been developed with the use of defined techniques. This approach is now challenged with the emergence of new techniques. In this paper, we describe regulatory and safety issues associated with the use of oligonucleotide-mediated mutagenesis to develop novel organisms. We present scientific arguments for not having organisms developed through this technique fall within the scope of the EU regulation on GMOs. We conclude that any political decision on this issue should be taken on the basis of a broad reflection at EU level, while avoiding discrepancies at international level. PMID:19833073

  7. Use of the radio mutagenesis gamma to diminish the germinative periods of the seeds

    International Nuclear Information System (INIS)

    Among the nuclear techniques that have been used in Cuba in to feasible way for their it lives it uses in the agriculture it dog think about that the radio mutagenesis is that of advance it lives. In this address the fundamental problem consists in that to the being to casuistically method forces to uses to great initial population. The Fruit Bomb Net Maradol was studied and it was obtained to diminish its germination period in 12 days without affecting the quality of the cultivation. The seeds were irradiated with an irradiator with source of Co-60, originator of radiations a (gamma) with to power of dose of 2,76 kGy/h and to half energy of 1,25 MeV. The dose range applied to the seeds was among 50 - 250 Gy

  8. Mutagenesis in the blood lymphocytes of the residents of Chernobyl NPP exclusion zone villages

    International Nuclear Information System (INIS)

    A comparative examination of the Chernobyl NPP exclusion zone self-settlers and Yagotin region of Kiev province village residents was carried out in 1998-99. The interindividual variability and the mean frequency of hypoxanthine guanine phosphoribosyl transferase mutations, chromosomal aberrations both of the chromosome and chromatid types and the chromosome sensitivity to bleomycin in vitro were substantially higher for the exclusion zone self-settlers than for the Yagotin region residents. An increase in the mean group frequency of cytogenetic damages for the self-settlers was caused mostly by individuals younger 60 years old. There were revealed no significant difference for the people of an older age. Chromosome sensitivity to bleomycin in vitro correlates with a mutagenesis frequency in vivo

  9. Some possibilities of using irradiation mutagenesis for obtaining soybean lines resistant to stem canker

    International Nuclear Information System (INIS)

    The electrophoretic spectra of soybean lines, developed by γ-irradiation from two soybean cultivars are checked for some deviations from the spectra of the initial cultivars. Dry seeds from cvs. Hodson and Daniela are subjected to irradiation (60Co) attended or not by treating with 0.1% ethylmethaneulfonate (EMS). The radiosensitivity of the two cultivars are compared. In M2 generation plants resistant to diaporthe are observed. Selected line are tested in M3 for resistance to three diseases: diaporthe, alternaria and rhisoctonia. All line except for line N 221 are resistant to the three diseases. Line N221 is susceptible to alternaria. Some quantitative deviations are observed in the spectra of the cv. Daniela. The developed lines can be used as initial genetic material for obtaining resistant soybean cultivars. It seems that irradiation mutagenesis is an effective method for genetic improvement of soybean

  10. Role of the supX gene in ultraviolet light-induced mutagenesis in Salmonella typhimurium

    International Nuclear Information System (INIS)

    Salmonella typhimurium strains with sup X mutations are more sensitive than wild type to killing by ultraviolet irradiation. Studies with strains bearing the leuD21 mutation revealed that inactivation of the supX locus by a nonsense mutation or a deletion results in a complete lack of ability to produce induced Leu+ reversion mutations after UV irradiation. Suppression of the nonsense supX mutation or the presence of an Escherichia coli K-12 F'-borne supX+ allele restored the capacity for induced reversions and increased cell survival after UV irradiation. Introduction of plasmid pKM101 into supX mutant strains also restored their capacity for UV mutagenesis as well as increased survival. The possible nature of the supX gene product and mechanisms by which it may affect expression of the inducible SOS error-prone repair system are considered

  11. Development of an inducible transposon system for efficient random mutagenesis in Clostridium acetobutylicum.

    Science.gov (United States)

    Zhang, Ying; Xu, Shu; Chai, Changsheng; Yang, Sheng; Jiang, Weihong; Minton, Nigel P; Gu, Yang

    2016-04-01

    Clostridium acetobutylicum is an industrially important Gram-positive organism, which is capable of producing economically important chemicals in the ABE (Acetone, Butanol and Ethanol) fermentation process. Renewed interests in the ABE process necessitate the availability of additional genetics tools to facilitate the derivation of a greater understanding of the underlying metabolic and regulatory control processes in operation through forward genetic strategies. In this study, a xylose inducible, mariner-based, transposon system was developed and shown to allow high-efficient random mutagenesis in the model strain ATCC 824. Of the thiamphenicol resistant colonies obtained, 91.9% were shown to be due to successful transposition of the catP-based mini-transposon element. Phenotypic screening of 200 transposon clones revealed a sporulation-defective clone with an insertion in spo0A, thereby demonstrating that this inducible transposon system can be used for forward genetic studies in C. acetobutylicum. PMID:27001972

  12. Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System

    Directory of Open Access Journals (Sweden)

    Andrew R. Bassett

    2013-07-01

    Full Text Available Here, we present a simple and highly efficient method for generating and detecting mutations of any gene in Drosophila melanogaster through the use of the CRISPR/Cas9 system (clustered regularly interspaced palindromic repeats/CRISPR-associated. We show that injection of RNA into the Drosophila embryo can induce highly efficient mutagenesis of desired target genes in up to 88% of injected flies. These mutations can be transmitted through the germline to make stable lines. Our system provides at least a 10-fold improvement in efficiency over previously published reports, enabling wider application of this technique. We also describe a simple and highly sensitive method of detecting mutations in the target gene by high-resolution melt analysis and discuss how the new technology enables the study of gene function.

  13. Enu mutagenesis identifies a novel platelet phenotype in a loss-of-function Jak2 allele.

    Directory of Open Access Journals (Sweden)

    Nicole M Anderson

    Full Text Available Utilizing ENU mutagenesis, we identified a mutant mouse with elevated platelets. Genetic mapping localized the mutation to an interval on chromosome 19 that encodes the Jak2 tyrosine kinase. We identified a A3056T mutation resulting in a premature stop codon within exon 19 of Jak2 (Jak2(K915X, resulting in a protein truncation and functionally inactive enzyme. This novel platelet phenotype was also observed in mice bearing a hemizygous targeted disruption of the Jak2 locus (Jak2(+/-. Timed pregnancy experiments revealed that Jak2(K915X/K915X and Jak2(-/- displayed embryonic lethality; however, Jak2(K915X/K915X embryos were viable an additional two days compared to Jak2(-/- embryos. Our data suggest that perturbing JAK2 activation may have unexpected consequences in elevation of platelet number and correspondingly, important implications for treatment of hematological disorders with constitutive Jak2 activity.

  14. Deletion of Helicobacter pylorivacuolating cytotoxin gene by introduction of directed mutagenesis

    Institute of Scientific and Technical Information of China (English)

    Jian-Ping Yuan; Tao Li; Xiao-Dong Shi; Bao-Yu Hu; Gui-Zhen Yang; Shan-Qing Tong; Xiao-Kui Guo

    2003-01-01

    AIM: To construct a vacA-knockout Helicobacter pylori mutant strain, whose only difference from the wild strain is its disrupted vacA gene.METHODS AND RESULTS: A clone containing kanamycin resistance gene used for homologous recombination was constructed in a directional cloning procedure into pBluescript ⅡSK, and then transformed into vacA+ H pylori by electroporation.Colonies growing on the selective media containing kanamycin were harvested for chromosomal DNA extraction,and the allelic exchange was determined by polymerase chain reactions and sequencing. Loss of vacuolating activity of the vaci-knockout strain was confirmed by examining the gastric cells co-cultured with cell-free supernatants from H pylori wild strain or the mutant.CONCLUSION: We constructed a vacA-knockout strain of H pylori through direct mutagenesis, which creates an important precondition for the future research on virulence comparison with gene expression analysis.

  15. UV-induced mutagenesis of oxidation activity of ferrous ion of Thiobacillus ferrooxidans

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    An excellent strain named T. f6 was isolated and screened, the dose and other condition for the UV-induced mutagenesis were studied and the richened positive mutant m+ T. f6 was applied in the column leaching of copper-contain ing sulfides. The results show that T. f6 is characterized by rapid oxidation of ferrous ion and cupric sulfide, high tolerance of toxic ion and short generation time. The best mutagenic effectiveness can be obtained under the dose of low kill rate of UV and low temperature treatment, under which the best richened m+ T. f6 can be shortened 1.4h. It was shown by the column leaching of copper that the leaching rate can be enhanced by at least 11% compared with the original one by the mutants.

  16. U.v.-induced and N-methyl-N'-nitrosoguanidine-induced mutagenesis in Bacillus thuringiensis

    International Nuclear Information System (INIS)

    The lethal and mutagenic effects of u.v. light and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) on Bacillus thuringiensis were investigated. Lethality studies demonstrated that B. thuringiensis was relatively sensitive to these agents. This bacterium was mutated at the rifampicin resistance marker by u.v. light and to a lesser extent by the direct acting alkylating agent MNNG. One mutant selected for its greater sensitivity to u.v. light expressed a higher frequency of mutagenesis after u.v. light treatment and appeared to be defective in an excision repair pathway. However, this mutant was only slightly mutable by MNNG in comparison with the wild-type strain. This unusual phenotype does not yet have a parallel among the radiation sensitive mutants described in other bacterial species. (author)

  17. Random Transposon Mutagenesis for Cell-Envelope Resistant to Phage Infection.

    Science.gov (United States)

    Reyes-Cortés, Ruth; Arguijo-Hernández, Emma S; Carballo-Ontiveros, Marco A; Martínez-Peñafiel, Eva; Kameyama, Luis

    2016-01-01

    In order to identify host components involved in the infective process of bacteriophages, we developed a wide-range strategy to obtain cell envelope mutants, using Escherichia coli W3110 and its specific phage mEp213. The strategy consisted in four steps: (1) random mutagenesis using transposon miniTn10Km(r); (2) selection of phage-resistant mutants by replica-plating; (3) electroporation of the phage-resistant mutants with mEp213 genome, followed by selection of those allowing phage development; and (4) sequencing of the transposon-disrupted genes. This strategy allowed us to distinguish the host factors related to phage development or multiplication within the cell, from those involved in phage infection at the level of the cell envelope. PMID:27311665

  18. Systematic analysis of the kalimantacin assembly line NRPS module using an adapted targeted mutagenesis approach.

    Science.gov (United States)

    Uytterhoeven, Birgit; Appermans, Kenny; Song, Lijiang; Masschelein, Joleen; Lathouwers, Thomas; Michiels, Chris W; Lavigne, Rob

    2016-04-01

    Kalimantacin is an antimicrobial compound with strong antistaphylococcal activity that is produced by a hybrid trans-acyltransferase polyketide synthase/nonribosomal peptide synthetase system in Pseudomonas fluorescens BCCM_ID9359. We here present a systematic analysis of the substrate specificity of the glycine-incorporating adenylation domain from the kalimantacin biosynthetic assembly line by a targeted mutagenesis approach. The specificity-conferring code was adapted for use in Pseudomonas and mutated adenylation domain active site sequences were introduced in the kalimantacin gene cluster, using a newly adapted ligation independent cloning method. Antimicrobial activity screens and LC-MS analyses revealed that the production of the kalimantacin analogues in the mutated strains was abolished. These results support the idea that further insight in the specificity of downstream domains in nonribosomal peptide synthetases and polyketide synthases is required to efficiently engineer these strains in vivo. PMID:26666990

  19. Rapid fine conformational epitope mapping using comprehensive mutagenesis and deep sequencing.

    Science.gov (United States)

    Kowalsky, Caitlin A; Faber, Matthew S; Nath, Aritro; Dann, Hailey E; Kelly, Vince W; Liu, Li; Shanker, Purva; Wagner, Ellen K; Maynard, Jennifer A; Chan, Christina; Whitehead, Timothy A

    2015-10-30

    Knowledge of the fine location of neutralizing and non-neutralizing epitopes on human pathogens affords a better understanding of the structural basis of antibody efficacy, which will expedite rational design of vaccines, prophylactics, and therapeutics. However, full utilization of the wealth of information from single cell techniques and antibody repertoire sequencing awaits the development of a high throughput, inexpensive method to map the conformational epitopes for antibody-antigen interactions. Here we show such an approach that combines comprehensive mutagenesis, cell surface display, and DNA deep sequencing. We develop analytical equations to identify epitope positions and show the method effectiveness by mapping the fine epitope for different antibodies targeting TNF, pertussis toxin, and the cancer target TROP2. In all three cases, the experimentally determined conformational epitope was consistent with previous experimental datasets, confirming the reliability of the experimental pipeline. Once the comprehensive library is generated, fine conformational epitope maps can be prepared at a rate of four per day. PMID:26296891

  20. Mutagenesis in sequence encoding of human factor VII for gene therapy of hemophilia

    Directory of Open Access Journals (Sweden)

    B Kazemi

    2009-12-01

    Full Text Available "nBackground: Current treatment of hemophilia which is one of the most common bleeding disorders, involves replacement therapy using concentrates of FVIII and FIX .However, these concentrates have been associated with viral infections and thromboembolic complications and development of antibodies. "nThe use of recombinant human factor VII (rhFVII is effective  for the treatment of patients with  hemophilia A or B, who develop antibodies ( referred as inhibitors against  replacement therapy , because it induces coagulation independent of FVIII and FIX. However, its short half-life and high cost have limited its use. One potential solution to this problem may be the use of FVIIa gene transfer, which would attain continuing therapeutic levels of expression from a single injection. The aim of this study was to engineer a novel hFVII (human FVII gene containing a cleavage site for the intracellular protease and furin, by PCR mutagenesis "nMethods: The sequence encoding light and heavy chains of hFVII, were amplified by using hFVII/pTZ57R and specific primers, separately. The PCR products were cloned in pTZ57R vector. "nResults and discussion: Cloning was confirmed by restriction analysis or PCR amplification using specific primers and plasmid universal primers. Mutagenesis of sequence encoding light and heavy chain was confirmed by restriction enzyme. "nConclusion: In the present study, it was provided recombinant plasmids based on mutant form of DNA encoding light and heavy chains.  Joining mutant form of DNA encoding light chain with mutant heavy chain led to a new variant of hFVII. This variant can be activated by furin and an increase in the proportion of activated form of FVII. This mutant form of hFVII may be used for gene therapy of hemophilia.

  1. BAX and tumor suppressor TRP53 are important in regulating mutagenesis in spermatogenic cells in mice.

    Science.gov (United States)

    Xu, Guogang; Vogel, Kristine S; McMahan, C Alex; Herbert, Damon C; Walter, Christi A

    2010-12-01

    During the first wave of spermatogenesis, and in response to ionizing radiation, elevated mutant frequencies are reduced to a low level by unidentified mechanisms. Apoptosis is occurring in the same time frame that the mutant frequency declines. We examined the role of apoptosis in regulating mutant frequency during spermatogenesis. Apoptosis and mutant frequencies were determined in spermatogenic cells obtained from Bax-null or Trp53-null mice. The results showed that spermatogenic lineage apoptosis was markedly decreased in Bax-null mice and was accompanied by a significantly increased spontaneous mutant frequency in seminiferous tubule cells compared to that of wild-type mice. Apoptosis profiles in the seminiferous tubules for Trp53-null were similar to control mice. Spontaneous mutant frequencies in pachytene spermatocytes and in round spermatids from Trp53-null mice were not significantly different from those of wild-type mice. However, epididymal spermatozoa from Trp53-null mice displayed a greater spontaneous mutant frequency compared to that from wild-type mice. A greater proportion of spontaneous transversions and a greater proportion of insertions/deletions 15 days after ionizing radiation were observed in Trp53-null mice compared to wild-type mice. Base excision repair activity in mixed germ cell nuclear extracts prepared from Trp53-null mice was significantly lower than that for wild-type controls. These data indicate that BAX-mediated apoptosis plays a significant role in regulating spontaneous mutagenesis in seminiferous tubule cells obtained from neonatal mice, whereas tumor suppressor TRP53 plays a significant role in regulating spontaneous mutagenesis between postmeiotic round spermatid and epididymal spermatozoon stages of spermiogenesis. PMID:20739667

  2. Somatic mutagenesis with a Sleeping Beauty transposon system leads to solid tumor formation in zebrafish.

    Directory of Open Access Journals (Sweden)

    Maura McGrail

    Full Text Available Large-scale sequencing of human cancer genomes and mouse transposon-induced tumors has identified a vast number of genes mutated in different cancers. One of the outstanding challenges in this field is to determine which genes, when mutated, contribute to cellular transformation and tumor progression. To identify new and conserved genes that drive tumorigenesis we have developed a novel cancer model in a distantly related vertebrate species, the zebrafish, Danio rerio. The Sleeping Beauty (SB T2/Onc transposon system was adapted for somatic mutagenesis in zebrafish. The carp ß-actin promoter was cloned into T2/Onc to create T2/OncZ. Two transgenic zebrafish lines that contain large concatemers of T2/OncZ were isolated by injection of linear DNA into the zebrafish embryo. The T2/OncZ transposons were mobilized throughout the zebrafish genome from the transgene array by injecting SB11 transposase RNA at the 1-cell stage. Alternatively, the T2/OncZ zebrafish were crossed to a transgenic line that constitutively expresses SB11 transposase. T2/OncZ transposon integration sites were cloned by ligation-mediated PCR and sequenced on a Genome Analyzer II. Between 700-6800 unique integration events in individual fish were mapped to the zebrafish genome. The data show that introduction of transposase by transgene expression or RNA injection results in an even distribution of transposon re-integration events across the zebrafish genome. SB11 mRNA injection resulted in neoplasms in 10% of adult fish at ∼10 months of age. T2/OncZ-induced zebrafish tumors contain many mutated genes in common with human and mouse cancer genes. These analyses validate our mutagenesis approach and provide additional support for the involvement of these genes in human cancers. The zebrafish T2/OncZ cancer model will be useful for identifying novel and conserved genetic drivers of human cancers.

  3. Sleeping Beauty transposon mutagenesis identifies genes that cooperate with mutant Smad4 in gastric cancer development.

    Science.gov (United States)

    Takeda, Haruna; Rust, Alistair G; Ward, Jerrold M; Yew, Christopher Chin Kuan; Jenkins, Nancy A; Copeland, Neal G

    2016-04-01

    Mutations in SMAD4 predispose to the development of gastrointestinal cancer, which is the third leading cause of cancer-related deaths. To identify genes driving gastric cancer (GC) development, we performed a Sleeping Beauty (SB) transposon mutagenesis screen in the stomach of Smad4(+/-) mutant mice. This screen identified 59 candidate GC trunk drivers and a much larger number of candidate GC progression genes. Strikingly, 22 SB-identified trunk drivers are known or candidate cancer genes, whereas four SB-identified trunk drivers, including PTEN, SMAD4, RNF43, and NF1, are known human GC trunk drivers. Similar to human GC, pathway analyses identified WNT, TGF-β, and PI3K-PTEN signaling, ubiquitin-mediated proteolysis, adherens junctions, and RNA degradation in addition to genes involved in chromatin modification and organization as highly deregulated pathways in GC. Comparative oncogenomic filtering of the complete list of SB-identified genes showed that they are highly enriched for genes mutated in human GC and identified many candidate human GC genes. Finally, by comparing our complete list of SB-identified genes against the list of mutated genes identified in five large-scale human GC sequencing studies, we identified LDL receptor-related protein 1B (LRP1B) as a previously unidentified human candidate GC tumor suppressor gene. In LRP1B, 129 mutations were found in 462 human GC samples sequenced, and LRP1B is one of the top 10 most deleted genes identified in a panel of 3,312 human cancers. SB mutagenesis has, thus, helped to catalog the cooperative molecular mechanisms driving SMAD4-induced GC growth and discover genes with potential clinical importance in human GC. PMID:27006499

  4. Nutritional value of quinua (chenopodium quinoa) seeds improved by radioinduced mutagenesis

    International Nuclear Information System (INIS)

    Quinua (Chenopodium quinoa), a pseudo cereal considered as an alternative crop for areas with marginal agricultural conditions has been subjected since 1990 to a radioinduced mutagenesis programme aiming to obtain lines with low saponin content, good yields and high nutritional value. Seeds obtained from lines grown in M7 generation which exhibited yields averaging 1.5 ton/ha, were analyzed regarding grain quality and nutritive value. Evaluated parameters were diameter and thickness of the seed, weight of 100 seeds and density. Regarding to bromatological analysis, determinations were made of moisture, ash, raw fiber, proteins, oil content and carbohydrates, following the procedures indicated in Official Mexican Norms (NOM). Evaluated genotypes were the varieties Sajama, Barandales and Amarilla de Marangani and the mutant lines 20R110, 94, 20R333, 20R227, 20R342, 20R37 and the advanced line obtained by selection 640304. Mutant genotypes 20R333 and 20R342 exhibited outstanding characteristics regarding to grain quality (diameter 2.0 mm, thickness 1.2mm, weight of 100 seeds 0.42 and 0.22 g respectively and density 710 and 686 grams per liter). In the bromatological analysis the protein content ranged from 11.82 % (genotype 20 R227) to 16.8% in mutant 20R333 while mutant 20R342 exhibited 15.6%. The lipid content was minimum on Barandales and 20R333 both with 3.8%, having the genotype 20R110 the highest value among evaluated genotypes with 4.35%, line 20R342 exhibited 4.2%.. The high percentages of proteins and lipids, found among some analyzed mutants exhibit the feasibility to obtain, through radioinduced mutagenesis, lines with low saponins and high nutritive value

  5. Factors influencing transformation and mutagenesis in vitro by high LET radiation

    International Nuclear Information System (INIS)

    We have shown that 125Iododeoxyuridine (125IdUrd) and 3H-thymidine are more effective than x-rays for the induction of specific gene mutations in TK6 human lymphoblastoid cells. The results of parallel transformation experiments with tritiated water suggest that the enhanced efficiency of 3H-thymidine as compared with x-rays is due to a higher RBE of the tritium beta particle for mutagenesis and transformation, rather than to the fact that the radioactive decay occurs within the DNA molecule. Studies of the cell cycle specificity for the induction of cell killing and mutagenesis by 125IdUrd indicate that late S-phase cells are more radiosensitive than early S-phase cells to the localized deposition of energy characteristic of 125I decay. Cellular localization studies have shown that 125I decay must occur in close proximity to cellular DNA in order to produce mutations; 125IdUrd was very mutagenic in cells which incorporated it into DNA, but not in cells in which it remained in the acid soluble pool. A similar result emerged from preliminary experiments with 131I. These results suggest that effects result largely from a transmutation/fragmentation. Continuous, low dose-rate exposure to fast neutrons (total doses of 1 to 40 rads protracted over periods of 5 to 20 days) was more mutagenic than acute neutron irradiation. No cytotoxicity was observed in cultures continuously irradiated with up to 2 rads/day for a 20 day period (total dose of 40 rads), whereas significant cell killing occurred with acute neutron exposures of 4.6 rads or greater. 11 refs., 6 figs., 1 tab

  6. 5-Azacytidine Enhances the Mutagenesis of HIV-1 by Reduction to 5-Aza-2'-Deoxycytidine.

    Science.gov (United States)

    Rawson, Jonathan M O; Daly, Michele B; Xie, Jiashu; Clouser, Christine L; Landman, Sean R; Reilly, Cavan S; Bonnac, Laurent; Kim, Baek; Patterson, Steven E; Mansky, Louis M

    2016-04-01

    5-Azacytidine (5-aza-C) is a ribonucleoside analog that induces the lethal mutagenesis of human immunodeficiency virus type 1 (HIV-1) by causing predominantly G-to-C transversions during reverse transcription. 5-Aza-C could potentially act primarily as a ribonucleotide (5-aza-CTP) or as a deoxyribonucleotide (5-aza-2'-deoxycytidine triphosphate [5-aza-dCTP]) during reverse transcription. In order to determine the primary form of 5-aza-C that is active against HIV-1, Illumina sequencing was performed using proviral DNA from cells treated with 5-aza-C or 5-aza-dC. 5-Aza-C and 5-aza-dC were found to induce highly similar patterns of mutation in HIV-1 in terms of the types of mutations observed, the magnitudes of effects, and the distributions of mutations at individual sequence positions. Further, 5-aza-dCTP was detected by liquid chromatography-tandem mass spectrometry in cells treated with 5-aza-C, demonstrating that 5-aza-C was a substrate for ribonucleotide reductase. Notably, levels of 5-aza-dCTP were similar in cells treated with equivalent effective concentrations of 5-aza-C or 5-aza-dC. Lastly, HIV-1 reverse transcriptase was found to incorporate 5-aza-CTPin vitroat least 10,000-fold less efficiently than 5-aza-dCTP. Taken together, these data support the model that 5-aza-C enhances the mutagenesis of HIV-1 primarily after reduction to 5-aza-dC, which can then be incorporated during reverse transcription and lead to G-to-C hypermutation. These findings may have important implications for the design of new ribonucleoside analogs directed against retroviruses. PMID:26833151

  7. Development of Therapeutic Chimeric Uricase by Exon Replacement/Restoration and Site-Directed Mutagenesis.

    Science.gov (United States)

    Xie, Guangrong; Yang, Weizhen; Chen, Jing; Li, Miaomiao; Jiang, Nan; Zhao, Baixue; Chen, Si; Wang, Min; Chen, Jianhua

    2016-01-01

    The activity of urate oxidase was lost during hominoid evolution, resulting in high susceptibility to hyperuricemia and gout in humans. In order to develop a more "human-like" uricase for therapeutic use, exon replacement/restoration and site-directed mutagenesis were performed to obtain porcine-human uricase with higher homology to deduced human uricase (dHU) and increased uricolytic activity. In an exon replacement study, substitution of exon 6 in wild porcine uricase (wPU) gene with corresponding exon in dhu totally abolished its activity. Substitutions of exon 5, 3, and 1-2 led to 85%, 60%, and 45% loss of activity, respectively. However, replacement of exon 4 and 7-8 did not significantly change the enzyme activity. When exon 5, 6, and 3 in dhu were replaced by their counterparts in wpu, the resulting chimera H1-2P₃H₄P5-6H7-8 was active, but only about 28% of wPU. Multiple sequence alignment and homology modeling predicted that mutations of E24D and E83G in H1-2P₃H₄P5-6H7-8 were favorable for further increase of its activity. After site-directed mutagenesis, H1-2P₃H₄P5-6H7-8 (E24D & E83G) with increased homology (91.45%) with dHU and higher activity and catalytic efficiency than the FDA-approved porcine-baboon chimera (PBC) was obtained. It showed optimum activity at pH 8.5 and 35 °C and was stable in a pH range of 6.5-11.0 and temperature range of 20-40 °C. PMID:27213357

  8. Development of Therapeutic Chimeric Uricase by Exon Replacement/Restoration and Site-Directed Mutagenesis

    Directory of Open Access Journals (Sweden)

    Guangrong Xie

    2016-05-01

    Full Text Available The activity of urate oxidase was lost during hominoid evolution, resulting in high susceptibility to hyperuricemia and gout in humans. In order to develop a more “human-like” uricase for therapeutic use, exon replacement/restoration and site-directed mutagenesis were performed to obtain porcine–human uricase with higher homology to deduced human uricase (dHU and increased uricolytic activity. In an exon replacement study, substitution of exon 6 in wild porcine uricase (wPU gene with corresponding exon in dhu totally abolished its activity. Substitutions of exon 5, 3, and 1–2 led to 85%, 60%, and 45% loss of activity, respectively. However, replacement of exon 4 and 7–8 did not significantly change the enzyme activity. When exon 5, 6, and 3 in dhu were replaced by their counterparts in wpu, the resulting chimera H1-2P3H4P5-6H7-8 was active, but only about 28% of wPU. Multiple sequence alignment and homology modeling predicted that mutations of E24D and E83G in H1-2P3H4P5-6H7-8 were favorable for further increase of its activity. After site-directed mutagenesis, H1-2P3H4P5-6H7-8 (E24D & E83G with increased homology (91.45% with dHU and higher activity and catalytic efficiency than the FDA-approved porcine–baboon chimera (PBC was obtained. It showed optimum activity at pH 8.5 and 35 °C and was stable in a pH range of 6.5–11.0 and temperature range of 20–40 °C.

  9. Site-Directed Mutagenesis to Improve Sensitivity of a Synthetic Two-Component Signaling System.

    Science.gov (United States)

    Olshefsky, Audrey; Shehata, Laila; Kuldell, Natalie

    2016-01-01

    Two-component signaling (2CS) systems enable bacterial cells to respond to changes in their local environment, often using a membrane-bound sensor protein and a cytoplasmic responder protein to regulate gene expression. Previous work has shown that Escherichia coli's natural EnvZ/OmpR 2CS could be modified to construct a light-sensing bacterial photography system. The resulting bacterial photographs, or "coliroids," rely on a phosphotransfer reaction between Cph8, a synthetic version of EnvZ that senses red light, and OmpR. Gene expression changes can be visualized through upregulation of a LacZ reporter gene by phosphorylated OmpR. Unfortunately, basal LacZ expression leads to a detectable reporter signal even when cells are grown in the light, diminishing the contrast of the coliroids. We performed site-directed mutagenesis near the phosphotransfer site of Cph8 to isolate mutants with potentially improved image contrast. Five mutants were examined, but only one of the mutants, T541S, increased the ratio of dark/light gene expression, as measured by β-galactosidase activity. The ratio changed from 2.57 fold in the starting strain to 5.59 in the T541S mutant. The ratio decreased in the four other mutant strains we examined. The phenotype observed in the T541S mutant strain may arise because the serine sidechain is chemically similar but physically smaller than the threonine sidechain. This may minimally change the protein's local structure, but may be less sterically constrained when compared to threonine, resulting in a higher probability of a phosphotransfer event. Our initial success pairing synthetic biology and site-directed mutagenesis to optimize the bacterial photography system's performance encourages us to imagine further improvements to the performance of this and other synthetic systems, especially those based on 2CS signaling. PMID:26799494

  10. Cognitive bias measurement and social anxiety disorder: Correlating self-report data and attentional bias

    Directory of Open Access Journals (Sweden)

    Alexander Miloff

    2015-09-01

    Full Text Available Social anxiety disorder (SAD and attentional bias are theoretically connected in cognitive behavioral therapeutic models. In fact, there is an emerging field focusing on modifying attentional bias as a stand-alone treatment. However, it is unclear to what degree these attentional biases are present before commencing treatment. The purpose of this study was to measure pre-treatment attentional bias in 153 participants diagnosed with SAD using a home-based Internet version of the dot-probe paradigm. Results showed no significant correlation for attentional bias (towards or away from negative words or faces and the self-rated version of the Liebowitz Social Anxiety Scale (LSAS-SR. However, two positive correlations were found for the secondary measures Generalized Anxiety Disorder 7 (GAD-7 and Patient Health Questionnaire 9 (PHQ-9. These indicated that those with elevated levels of anxiety and depression had a higher bias towards negative faces in neutral–negative and positive–negative valence combinations, respectively. The unreliability of the dot-probe paradigm and home-based Internet delivery are discussed to explain the lack of correlations between LSAS-SR and attentional bias. Changes to the dot-probe task are suggested that could improve reliability.

  11. Creating Culturally Considerate Schools: Educating without Bias

    Science.gov (United States)

    Anderson, Kim L.; Davis, Bonnie M.

    2012-01-01

    This unique collaboration between a veteran educator and a psychotherapist shows that the educators who are most effective in teaching diverse student populations are the ones who can "see students clearly and respond to their needs without hesitation or bias." Framed around an original, eight-stage model of diversity development, this book…

  12. Avoiding bias in safety testing design

    DEFF Research Database (Denmark)

    Calow, Peter

    2011-01-01

    All scientists are biased, no matter what their backgrounds or affiliations, so what is it about the scientific method that overcomes this and which makes science so successful? Key features are transparency and critical peer scrutiny. These general issues will be will be considered in terms...

  13. Exchange bias mediated by interfacial nanoparticles (invited)

    Energy Technology Data Exchange (ETDEWEB)

    Berkowitz, A. E., E-mail: aberk@ucsd.edu [Department of Physics, University of California, San Diego, La Jolla, California 92093 (United States); Center for Magnetic Recording Research, University of California, California 92093 (United States); Sinha, S. K. [Department of Physics, University of California, San Diego, La Jolla, California 92093 (United States); Fullerton, E. E. [Center for Magnetic Recording Research, University of California, California 92093 (United States); Smith, D. J. [Department of Physics, Arizona State University, Tempe, Arizona 85287 (United States)

    2015-05-07

    The objective of this study on the iconic exchange-bias bilayer Permalloy/CoO has been to identify those elements of the interfacial microstructure and accompanying magnetic properties that are responsible for the exchange-bias and hysteretic properties of this bilayer. Both epitaxial and polycrystalline samples were examined. X-ray and neutron reflectometry established that there existed an interfacial region, of width ∼1 nm, whose magnetic properties differed from those of Py or CoO. A model was developed for the interfacial microstructure that predicts all the relevant properties of this system; namely; the temperature and Permalloy thickness dependence of the exchange-bias, H{sub EX}, and coercivity, H{sub C}; the much smaller measured values of H{sub EX} from what was nominally expected; the different behavior of H{sub EX} and H{sub C} in epitaxial and polycrystalline bilayers. A surprising result is that the exchange-bias does not involve direct exchange-coupling between Permalloy and CoO, but rather is mediated by CoFe{sub 2}O{sub 4} nanoparticles in the interfacial region.

  14. A new polarization amplitude bias reduction method

    Science.gov (United States)

    Vidal, Matias; Leahy, J. P.; Dickinson, C.

    2016-09-01

    Polarization amplitude estimation is affected by a positive noise bias, particularly important in regions with low signal-to-noise ratio (SNR). We present a new approach to correct for this bias in the case there is additional information about the polarization angle. We develop the `known-angle estimator' that works in the special case when there is an independent and high SNR (≳ 2σ) measurement of the polarization angle. It is derived for the general case where the uncertainties in the Q, U Stokes parameters are not symmetric. This estimator completely corrects for the polarization bias if the polarization angle is perfectly known. In the realistic case, where the angle template has uncertainties, a small residual bias remains, but that is shown to be much smaller that the one left by other classical estimators. We also test our method with more realistic data, using the noise properties of the three lower frequency maps of Wilkinson Microwave Anisotropy Probe. In this case, the known-angle estimator also produces better results than methods that do not include the angle information. This estimator is therefore useful in the case where the polarization angle is expected to be constant over different data sets with different SNR.

  15. Clustering and Bias Measurements of SDSS Voids

    CERN Document Server

    Clampitt, Joseph; Sánchez, Carles

    2015-01-01

    Using a void catalog from the SDSS survey, we present the first measurements of void clustering and the corresponding void bias. Over the range 30-200 Mpc/h the void auto-correlation is detected at 5-sigma significance for voids of radius 15-20 Mpc/h. We also measure the void-galaxy cross-correlation at higher signal-to-noise and compare the inferred void bias with the autocorrelation results. Void bias is constant with scale for voids of a given size, but its value falls from 5.6 +/- 1.0 to below zero as the void radius increases from 15 to 30 Mpc/h. The comparison of our measurements with carefully matched galaxy mock catalogs, with no free parameters related to the voids, shows that model predictions can be reliably made for void correlations. We study the dependence of void bias on tracer density and void size with a view to future applications. In combination with our previous lensing measurements of void mass profiles, these clustering measurements provide another step towards using voids as cosmologica...

  16. Uncovering Racial Bias in Nursing Fundamentals Textbooks.

    Science.gov (United States)

    Byrne, Michelle M.

    2001-01-01

    The portrayal of African Americans in nursing fundamentals textbooks was analyzed, resulting in 11 themes in the areas of history, culture, and physical assessment. Few African American leaders were included, and racial bias and stereotyping were apparent. Differences were often discussed using Eurocentric norms, and language tended to minimize…

  17. Bounding the Bias of Contrastive Divergence Learning

    DEFF Research Database (Denmark)

    Fischer, Anja; Igel, Christian

    2011-01-01

    number of variables in the RBM, and the maximum change in energy that can be produced by changing a single variable. The last reflects the dependence on the absolute values of the RBM parameters. The magnitude of the bias is also affected by the distance in variation between the modeled distribution and...

  18. Examining Gender Bias in Studies of Innovation

    OpenAIRE

    Crowden, N.

    2003-01-01

    This paper examines the presence of a gender bias in studies of innovation. Using the Innovation Systems Research Network (ISRN) and its interview guide as a case study, this research project examines how accurately and completely such innovation studies present gender differences in the innovation process.

  19. Zero bias transformation and asymptotic expansions

    OpenAIRE

    Jiao, Ying

    2012-01-01

    Let W be a sum of independent random variables. We apply the zero bias transformation to deduce recursive asymptotic expansions for $\\mathbb {E}[h(W)]$ in terms of normal expectations, or of Poisson expectations for integer-valued random variables. We also discuss the estimates of remaining errors.

  20. Sociocognitive Biases in the Evaluation Process.

    Science.gov (United States)

    Perloff, Richard M.; And Others

    1980-01-01

    Causes of evaluator bias are: overemphasizing concrete, salient, and retrievable information; reporting only evidence which confirms hypothesis; focusing on stable personality factors, rather than on situation and environment; developing positive perceptions of a program as both an evaluator and a highly involved participant; statistical naivete;…

  1. Knowledge of Social Affiliations Biases Economic Decisions

    Science.gov (United States)

    Martinez, Joel E.; Mack, Michael L.; Gelman, Bernard D.; Preston, Alison R.

    2016-01-01

    An individual’s reputation and group membership can produce automatic judgments and behaviors toward that individual. Whether an individual’s social reputation impacts interactions with affiliates has yet to be demonstrated. We tested the hypothesis that during initial encounters with others, existing knowledge of their social network guides behavior toward them. Participants learned reputations (cooperate, defect, or equal mix) for virtual players through an iterated economic game (EG). Then, participants learned one novel friend for each player. The critical question was how participants treated the friends in a single-shot EG after the friend-learning phase. Participants tended to cooperate with friends of cooperators and defect on friends of defectors, indicative of a decision making bias based on memory for social affiliations. Interestingly, participants’ explicit predictions of the friends’ future behavior showed no such bias. Moreover, the bias to defect on friends of defectors was enhanced when affiliations were learned in a social context; participants who learned to associate novel faces with player faces during reinforcement learning did not show reputation-based bias for associates of defectors during single-shot EG. These data indicate that when faced with risky social decisions, memories of social connections influence behavior implicitly. PMID:27441563

  2. Assessing Projection Bias in Consumers' Food Preferences.

    Science.gov (United States)

    de-Magistris, Tiziana; Gracia, Azucena

    2016-01-01

    The aim of this study is to test whether projection bias exists in consumers' purchasing decisions for food products. To achieve our aim, we used a non-hypothetical experiment (i.e., experimental auction), where hungry and non-hungry participants were incentivized to reveal their willingness to pay (WTP). The results confirm the existence of projection bias when consumers made their decisions on food products. In particular, projection bias existed because currently hungry participants were willing to pay a higher price premium for cheeses than satiated ones, both in hungry and satiated future states. Moreover, participants overvalued the food product more when they were delivered in the future hungry condition than in the satiated one. Our study provides clear, quantitative and meaningful evidence of projection bias because our findings are based on economic valuation of food preferences. Indeed, the strength of this study is that findings are expressed in terms of willingness to pay which is an interpretable amount of money. PMID:26828930

  3. Assessing Projection Bias in Consumers’ Food Preferences

    Science.gov (United States)

    de-Magistris, Tiziana; Gracia, Azucena

    2016-01-01

    The aim of this study is to test whether projection bias exists in consumers’ purchasing decisions for food products. To achieve our aim, we used a non-hypothetical experiment (i.e., experimental auction), where hungry and non-hungry participants were incentivized to reveal their willingness to pay (WTP). The results confirm the existence of projection bias when consumers made their decisions on food products. In particular, projection bias existed because currently hungry participants were willing to pay a higher price premium for cheeses than satiated ones, both in hungry and satiated future states. Moreover, participants overvalued the food product more when they were delivered in the future hungry condition than in the satiated one. Our study provides clear, quantitative and meaningful evidence of projection bias because our findings are based on economic valuation of food preferences. Indeed, the strength of this study is that findings are expressed in terms of willingness to pay which is an interpretable amount of money. PMID:26828930

  4. Exchange bias of conetic thin films

    Science.gov (United States)

    Eggers, Tatiana; Kirby, Hillary; Jayathilaka, Priyanga; Campbell, Scott; Miller, Casey

    2012-02-01

    In this work, we study the exchange bias and coercivity of Ni77Fe14Cu5Mo4 (Conetic, also known as mu-metal) exchange coupled with FeMn as functions of Conetic thickness and buffer layer material. The samples studied were BL(30nm)/Conetic(9nm-30nm)/FeMn(10nm)/Ta(5nm), where BL = Cu or Ta. All samples were grown by magnetron sputtering in a deposition field of ˜150 Oe during growth to set the exchange bias axis. Room temperature hysteresis loops were measured by a magneto-optical Kerr effect magnetometer as a function of applied-field angle. For each variety of sample, the exchange bias and coercivity were inversely proportional to Conetic thickness. With Cu buffer layers grown on Si, the Heb decreased from 300 Oe to 62 Oe, and Hc decreased from 99 Oe to 9 Oe. Similar results were found when the Cu buffer layer was grown on SiOx, though the maximum coercivity was only 67 Oe. For the samples grown on Si(001)/Ta(5nm), the exchange bias decreased from 80 Oe to 14 Oe, while the coercivity increases only slightly from 2 Oe to 10 Oe. These results indicate a trade-off between preserving the softness of the ferromagnet and having a large exchange, which may be useful for tuning the performance of low-field sensing materials

  5. A new method to measure galaxy bias

    CERN Document Server

    Pollack, Jennifer E; Porciani, Cristiano

    2013-01-01

    We present a new approach for modelling halo bias that utilizes the full non-linear information contained in the moments of the matter density field. The basis of our technique is to derive this information directly from a set of numerical simulations. Although our method is general, we perform a case study based on the local Eulerian bias scheme truncated to second-order. Using 200 N-body simulations that cover a total comoving volume of 675 (Gpc/h)^3, we measure several 2- and 3-point statistics of the halo distribution to unprecedented accuracy. We then use the bias model to fit the halo-halo power spectrum, the halo-matter cross spectrum and the corresponding three bispectra for wavenumbers in the range 0.04 < k < 0.12 h Mpc^-1. While all fits accurately describe the data, we find that the constraints on the bias parameters obtained using the full non-linear information differ significantly from those derived using leading-order standard perturbation theory. Hence, neglecting the full non-linear inf...

  6. Researching Sex Bias in the Classroom.

    Science.gov (United States)

    Donlan, Dan

    This paper outlines five methods of research on sex bias in the classroom: one-time survey, one class/one treatment, two class/two treatment, one class/random assignment to treatment, and analysis of differentiated effect. It shows how each method could be used in attempting to measure the effect of a unit on Norma Klein's "Mom, the Wolfman and…

  7. Linguistic Abstractness, Intergroup Bias and National Essentialism

    Czech Academy of Sciences Publication Activity Database

    Kouřilová, Sylvie; Geschke, D.; Finell, E.; Bilewicz, M.; Casini, A.

    2007, s. 25-25. [Transfer of Knowledge Conference. Brno (CZ), 05.09.2007-09.09.2007] R&D Projects: GA ČR GA406/07/1561 Institutional research plan: CEZ:AV0Z70250504 Keywords : language abstraction * linguistic category model * intergroup bias, national essentialism Subject RIV: AN - Psychology

  8. Bias sensitive multispectral structures for imaging applications

    International Nuclear Information System (INIS)

    In this paper we present results on the optimization of an pinpii'n' type a-Si:H based three color detector with voltage controlled spectral sensitivity. The sensor element was fabricated on a glass covered with Indium Tin Oxide (ITO) and consists of a p-i-n a-SiC:H multilayer structure which faces the incident illumination, followed by a-SiC:H(-p)/a-SiC:H(-i)/a-Si:H(-i')/a-SiC:H(-n')/ITO heterostructure, that allows the optically addressed readout. Results show that this approach leads to regionally different collection parameters resulting in multispectral photodiodes. In the polychromatic operation mode different sensitivity ranges are programmed by switching between different biases so that the basic colors can be resolved with a single device. Positive bias is needed under blue irradiation and moderated reverse bias under green. The threshold voltage between green and red sensitivity depends on the thickness of the bottom a-SiC:H (-i) layer, and corresponds to the complete confinement of the absorbed green photons across the pinpi sequence. As the thickness of the a-Si:H i'-layer increases, the self-reverse effect due to the front absorption will be balanced by the decrease of the self-forward effect due to the back absorption shifting the threshold voltage to lower reverse bias. The various design parameters are discussed and supported by a 2D numerical simulation

  9. Teaching EFL Students about Language Bias

    Science.gov (United States)

    Randolph, Justus J.

    2005-01-01

    In this article, I discuss a method for teaching EFL students about language bias. The method involves (A) introducing vocabulary, (B) activating knowledge, (C) giving instruction, (D) group and individual practice, and (E) reflection. I also summarize guidelines for teaching students about the use of gendered pronouns, gender-loaded nouns and…

  10. Very Massive Tracers and Higher Derivative Biases

    CERN Document Server

    Fujita, Tomohiro; Senatore, Leonardo; Vlah, Zvonimir; Angulo, Raul

    2016-01-01

    Most of the upcoming cosmological information will come from analyzing the clustering of the Large Scale Structures (LSS) of the universe through LSS or CMB observations. It is therefore essential to be able to understand their behavior with exquisite precision. The Effective Field Theory of Large Scale Structures (EFTofLSS) provides a consistent framework to make predictions for LSS observables in the mildly non-linear regime. In this paper we focus on biased tracers. We argue that in calculations at a given order in the dark matter perturbations, highly biased tracers will underperform because of their larger higher derivative biases. A natural prediction of the EFTofLSS is therefore that by simply adding higher derivative biases, all tracers should perform comparably well. We implement this prediction for the halo-halo and the halo-matter power spectra at one loop, and the halo-halo-halo, halo-halo-matter, and halo-matter-matter bispectra at tree-level, and compare with simulations. We find good agreement ...

  11. Assessing Projection Bias in Consumers' Food Preferences.

    Directory of Open Access Journals (Sweden)

    Tiziana de-Magistris

    Full Text Available The aim of this study is to test whether projection bias exists in consumers' purchasing decisions for food products. To achieve our aim, we used a non-hypothetical experiment (i.e., experimental auction, where hungry and non-hungry participants were incentivized to reveal their willingness to pay (WTP. The results confirm the existence of projection bias when consumers made their decisions on food products. In particular, projection bias existed because currently hungry participants were willing to pay a higher price premium for cheeses than satiated ones, both in hungry and satiated future states. Moreover, participants overvalued the food product more when they were delivered in the future hungry condition than in the satiated one. Our study provides clear, quantitative and meaningful evidence of projection bias because our findings are based on economic valuation of food preferences. Indeed, the strength of this study is that findings are expressed in terms of willingness to pay which is an interpretable amount of money.

  12. Bias and variance in continuous EDA

    OpenAIRE

    Teytaud, Fabien; Teytaud, Olivier

    2009-01-01

    Estimation of Distribution Algorithms are based on statistical estimates. We show that when combining classical tools from statistics, namely bias/variance decomposition, reweighting and quasi-randomization, we can strongly improve the convergence rate. All modifications are easy, compliant with most algorithms, and experimentally very efficient in particular in the parallel case (large offsprings).

  13. Audibility and visual biasing in speech perception

    Science.gov (United States)

    Clement, Bart Richard

    Although speech perception has been considered a predominantly auditory phenomenon, large benefits from vision in degraded acoustic conditions suggest integration of audition and vision. More direct evidence of this comes from studies of audiovisual disparity that demonstrate vision can bias and even dominate perception (McGurk & MacDonald, 1976). It has been observed that hearing-impaired listeners demonstrate more visual biasing than normally hearing listeners (Walden et al., 1990). It is argued here that stimulus audibility must be equated across groups before true differences can be established. In the present investigation, effects of visual biasing on perception were examined as audibility was degraded for 12 young normally hearing listeners. Biasing was determined by quantifying the degree to which listener identification functions for a single synthetic auditory /ba-da-ga/ continuum changed across two conditions: (1)an auditory-only listening condition; and (2)an auditory-visual condition in which every item of the continuum was synchronized with visual articulations of the consonant-vowel (CV) tokens /ba/ and /ga/, as spoken by each of two talkers. Audibility was altered by presenting the conditions in quiet and in noise at each of three signal-to- noise (S/N) ratios. For the visual-/ba/ context, large effects of audibility were found. As audibility decreased, visual biasing increased. A large talker effect also was found, with one talker eliciting more biasing than the other. An independent lipreading measure demonstrated that this talker was more visually intelligible than the other. For the visual-/ga/ context, audibility and talker effects were less robust, possibly obscured by strong listener effects, which were characterized by marked differences in perceptual processing patterns among participants. Some demonstrated substantial biasing whereas others demonstrated little, indicating a strong reliance on audition even in severely degraded acoustic

  14. Single-Receiver GPS Phase Bias Resolution

    Science.gov (United States)

    Bertiger, William I.; Haines, Bruce J.; Weiss, Jan P.; Harvey, Nathaniel E.

    2010-01-01

    Existing software has been modified to yield the benefits of integer fixed double-differenced GPS-phased ambiguities when processing data from a single GPS receiver with no access to any other GPS receiver data. When the double-differenced combination of phase biases can be fixed reliably, a significant improvement in solution accuracy is obtained. This innovation uses a large global set of GPS receivers (40 to 80 receivers) to solve for the GPS satellite orbits and clocks (along with any other parameters). In this process, integer ambiguities are fixed and information on the ambiguity constraints is saved. For each GPS transmitter/receiver pair, the process saves the arc start and stop times, the wide-lane average value for the arc, the standard deviation of the wide lane, and the dual-frequency phase bias after bias fixing for the arc. The second step of the process uses the orbit and clock information, the bias information from the global solution, and only data from the single receiver to resolve double-differenced phase combinations. It is called "resolved" instead of "fixed" because constraints are introduced into the problem with a finite data weight to better account for possible errors. A receiver in orbit has much shorter continuous passes of data than a receiver fixed to the Earth. The method has parameters to account for this. In particular, differences in drifting wide-lane values must be handled differently. The first step of the process is automated, using two JPL software sets, Longarc and Gipsy-Oasis. The resulting orbit/clock and bias information files are posted on anonymous ftp for use by any licensed Gipsy-Oasis user. The second step is implemented in the Gipsy-Oasis executable, gd2p.pl, which automates the entire process, including fetching the information from anonymous ftp

  15. Self-bias technique improves amplifier gain and noise figure

    Science.gov (United States)

    Fithian, Michael J.

    1988-05-01

    A nover self-bias technique, which provides optimum amplifier performance from low-noise GaAs FET amplifiers, is described. The self-bias scheme employs small thin-film substrates to mount packaged FETs to amplifier's main microstrip substrates. The substrates, which feature high dielectric constant, are placed under each FET source lead. The use of self-biased amplifiers results in several benefits. Thus, with a single bias supply, proper bias sequencing is not requried among amplifier stages; in a self-bias layout, the active devices are not damaged by a bias-supply failure; finally, proper self-biasing is not complex, requiring only two resistors per stage. The results of an experimental testing of the self-bias technique, evaluated for a 5.0 to 5.6 GHz low-noise amplifier with the aid of commercially available CAD software, are presented.

  16. Thinking in Black and White: Conscious thought increases racially biased judgments through biased face memory.

    Science.gov (United States)

    Strick, Madelijn; Stoeckart, Peter F; Dijksterhuis, Ap

    2015-11-01

    It is a common research finding that conscious thought helps people to avoid racial discrimination. These three experiments, however, illustrate that conscious thought may increase biased face memory, which leads to increased judgment bias (i.e., preferring White to Black individuals). In Experiments 1 and 2, university students formed impressions of Black and White housemate candidates. They judged the candidates either immediately (immediate decision condition), thought about their judgments for a few minutes (conscious thought condition), or performed an unrelated task for a few minutes (unconscious thought condition). Conscious thinkers and immediate decision-makers showed a stronger face memory bias than unconscious thinkers, and this mediated increased judgment bias, although not all results were significant. Experiment 3 used a new, different paradigm and showed that a Black male was remembered as darker after a period of conscious thought than after a period of unconscious thought. Implications for racial prejudice are discussed. PMID:26164254

  17. Selection and Biased Gene Conversion in a Multigene Family: Consequences of Interallelic Bias and Threshold Selection

    OpenAIRE

    Walsh, James Bruce

    1986-01-01

    In a previous paper, I investigated the interactions in a gene family of additive selection and biased gene conversion in a finite population when conversion events are rare. Here I extend my "weak-conversion limit" model by allowing biased interallelic conversion (conversion between alleles at the same locus) of arbitrary frequency and various threshold selection schemes for rare interlocus conversion events. I suggest that it is not unreasonable for gene families to experience threshold fit...

  18. Where Has All the Bias Gone? Detecting Gender Bias in the Intrahousehold Allocation of Educational Expenditure

    OpenAIRE

    Kingdon, Geeta Gandhi

    2005-01-01

    The reliability of the household consumption-based (Engel curve) methodology in detecting gender bias has been called into question because it has generally failed to confirm bias even where it exists. This article seeks to find explanations for this failure by exploiting a data set that has educational expenditure information at the individual level and also, by aggregation, at the household level. I find that, in the basic education age groups, the discriminatory mechanism in education is v...

  19. Constructing a Bias-Free Trade Governance Indicator: Revealing the Biases of Existing Survey Indicators

    OpenAIRE

    Hamanaka, Shintaro; Tafgar, Aiken; Ico, Ronald

    2015-01-01

    Governance is one of the key factors that shape the economic performance of an economy in terms of economic and trade growth. However, accurately measuring the quality of governance is not an easy task. Research typically uses governance indicators from surveys, which may have biases and inherent errors. In this paper, we attempt to construct an alternative governance indicator, which is free from perception and subjective biases. Our exercise is based on the inference that economies with goo...

  20. Addressing bias in the forensic assessment of sexual harassment claims.

    Science.gov (United States)

    Gold, L H

    1998-01-01

    This article addresses unique biases that arise in the assessment of sexual harassment claims by forensic psychiatrists. These include gender biases, diagnostic biases, sociopolitical biases, and bias that arises from lack of knowledge regarding sexual harassment or lack of formal psychiatric training. Forensic psychiatrists are ethically obligated to strive for objectivity and honesty in their assessments. By becoming aware of these biases and attempting to minimize them, we can meet our ethical obligations as forensic psychiatrists. In addition, we can provide more credible and valuable assessments to the courts in this increasingly litigated and partisan issue. PMID:9894213

  1. When bias binds: Effect of implicit outgroup bias on ingroup affiliation.

    Science.gov (United States)

    Jacoby-Senghor, Drew S; Sinclair, Stacey; Smith, Colin Tucker

    2015-09-01

    We tested a novel process we term implicit homophily in which perceivers' implicit outgroup bias shapes their affiliative responses toward ingroup targets with outgroup friends as a function of perceived similarity. Across 4 studies, we tested implicit homophily in the context of racial groups. We found that White participants with higher implicit anti-Black bias reported less affiliative responses toward White targets with Black friends compared with White targets with White friends, and this effect persisted above and beyond the effects of implicit pro-White bias and explicit racial bias (Studies 1-3). We further found evidence that this relationship between implicit anti-Black bias and affiliation exists because participants infer how comfortable targets are around outgroup members (Preliminary Study) and use this information to infer similarity on this dimension (Studies 1-3). Our findings also suggested that stigma transference and expectancy violation were not viable alternative mediators (Preliminary Study and Study 1). Finally, women's implicit anti-Black bias predicted their likelihood of having Facebook friends with Black friends, providing ecological and behavioral evidence of implicit homophily (Study 4). Implications for research on stigma by association, extended contact, affiliation, and network formation are discussed. PMID:26280842

  2. Mutagenesis, by methylating and ethylating agents, in mutH, mutL, mutS, and uvrD mutants of Salmonella typhimurium LT2.

    OpenAIRE

    Shanabruch, W G; Rein, R P; Behlau, I; Walker, G C

    1983-01-01

    Salmonella typhimurium LT2 mutH, mutL, mutS, and uvrD mutants were especially sensitive to mutagenesis by both the recA+-dependent mutagen methyl methane sulfonate and the recA+-independent mutagen ethyl methane sulfonate, but not to mutagenesis by agents such as 4-nitroquinoline-1-oxide and UV irradiation. Similarly, these mutator strains were very sensitive to mutagenesis by the methylating agents N-methyl-N'-nitro-N-nitrosoguanidine and N-methyl-N-nitrosourea. The increased susceptibility ...

  3. Quantitative Bias Analysis in Regulatory Settings.

    Science.gov (United States)

    Lash, Timothy L; Fox, Matthew P; Cooney, Darryl; Lu, Yun; Forshee, Richard A

    2016-07-01

    Nonrandomized studies are essential in the postmarket activities of the US Food and Drug Administration, which, however, must often act on the basis of imperfect data. Systematic errors can lead to inaccurate inferences, so it is critical to develop analytic methods that quantify uncertainty and bias and ensure that these methods are implemented when needed. "Quantitative bias analysis" is an overarching term for methods that estimate quantitatively the direction, magnitude, and uncertainty associated with systematic errors influencing measures of associations. The Food and Drug Administration sponsored a collaborative project to develop tools to better quantify the uncertainties associated with postmarket surveillance studies used in regulatory decision making. We have described the rationale, progress, and future directions of this project. PMID:27196652

  4. Is there gender bias in nursing research?

    Science.gov (United States)

    Polit, Denise F; Beck, Cheryl Tatano

    2008-10-01

    Using data from a consecutive sample of 259 studies published in four leading nursing research journals in 2005-2006, we examined whether nurse researchers favor females as study participants. On average, 75.3% of study participants were female, and 38% of studies had all-female samples. The bias favoring female participants was statistically significant and persistent. The bias was observed regardless of funding source, methodological features, and other participant and researcher characteristics, with one exception: studies that had male investigators had more sex-balanced samples. When designing studies, nurse researchers need to pay close attention to who will benefit from their research and to whether they are leaving out a specific group about which there is a gap in knowledge. PMID:18324681

  5. Bias and spread in EVT performance tests.

    Science.gov (United States)

    Smith, J. G.

    1971-01-01

    Performance tests (error probability measurements) of communications systems characterized by low bit rates and high reliability requirements frequently utilize classical extreme value theory (EVT) to avoid the excessive test times encountered with bit error rate (BER) tests. If the underlying noise is Gaussian or perturbed Gaussian, the EVT error estimates have either excessive bias or excessive variance if an insufficient number of test samples is used. EVT is examined to explain the cause of this bias and spread. Experimental verification is made by testing a known Gaussian source, and procedures that minimize these effects are described. It seems apparent that even under the best of conditions the EVT test results are not particularly better than those of BER tests.

  6. Calibration biases in logical reasoning tasks

    Directory of Open Access Journals (Sweden)

    Guillermo Macbeth

    2013-08-01

    Full Text Available The aim of this contribution is to present an experimental study about calibration in deductive reasoning tasks. Calibration is defi ned as the empirical convergence or divergence between the objective and the subjective success. The underconfi dence bias is understood as the dominance of the former over the latter. The hypothesis of this study states that the form of the propositions presented in the experiment is critical for calibration phenomena. Affi rmative and negative propositions are distinguished in their cognitive processing. Results suggests that monotonous compound propositions are prone to underconfi dence. An heuristic approach to this phenomenon is proposed. The activation of a monotony heuristic would produce an illusion of simplicity that generates the calibration bias. These evidence is analysed in the context of the metacognitive modeling of calibration phenomena.

  7. Leveraging Pileup as a Zero Bias Trigger

    CERN Document Server

    Nachman, Benjamin

    2016-01-01

    At the Large Hadron Collider, each event recorded by the ATLAS and CMS collaborations contains many nearly simultaneous pp collisions occurring at nearly the same time as the primary interaction of interest. These pileup collisions are usually a nuisance, degrading the energy resolution of jets and the missing transverse momentum, as well as affecting other reconstructed physics objects. However, interesting processes can also occur in the pileup interactions, and by construction they are recorded without selection bias since the triggering signal originates from the primary interaction in the event. These zero bias events have a large effective prescale, but can be useful for searches and measurements of processes that are difficult or not possible to record with an online trigger. As one example, we show a significant improvement in the sensitivity to low mass dijet resonances using pileup interactions.

  8. Biased trapping issue on weighted hierarchical networks

    Indian Academy of Sciences (India)

    Meifeng Dai; Jie Liu; Feng Zhu

    2014-10-01

    In this paper, we present trapping issues of weight-dependent walks on weighted hierarchical networks which are based on the classic scale-free hierarchical networks. Assuming that edge’s weight is used as local information by a random walker, we introduce a biased walk. The biased walk is that a walker, at each step, chooses one of its neighbours with a probability proportional to the weight of the edge. We focus on a particular case with the immobile trap positioned at the hub node which has the largest degree in the weighted hierarchical networks. Using a method based on generating functions, we determine explicitly the mean first-passage time (MFPT) for the trapping issue. Let parameter (0 < < 1) be the weight factor. We show that the efficiency of the trapping process depends on the parameter a; the smaller the value of a, the more efficient is the trapping process.

  9. Plutino Detection Biases, Including the Kozai Resonance

    CERN Document Server

    Lawler, S M

    2013-01-01

    Because of their proximity within the transneptunian region, the plutinos (objects in the 3:2 mean-motion resonance with Neptune) are numerous in flux-limited catalogs, and well-studied theoretically. We perform detailed modelling of the on-sky detection biases for plutinos, with special attention to those that are simultaneously in the Kozai resonance. In addition to the normal 3:2 resonant argument libration, Kozai plutinos also show periodic oscillations in eccentricity and inclination, coupled to the argument of perihelion (omega) oscillation. Due to the mean-motion resonance, plutinos avoid coming to pericenter near Neptune's current position in the ecliptic plane. Because Kozai plutinos are restricted to certain values of omega, perihelion always occurs out of the ecliptic plane, biasing ecliptic surveys against finding these objects. The observed Kozai plutino fraction (fkoz) has been measured by several surveys, finding values between 8% and 25%, while the true fkoz has been predicted to be between 10...

  10. Vowel bias in Danish word-learning

    DEFF Research Database (Denmark)

    Højen, Anders; Nazzi, Thierry

    2016-01-01

    The present study explored whether the phonological bias favoring consonants found in French-learning infants and children when learning new words (Havy & Nazzi, 2009; Nazzi, 2005) is language-general, as proposed by Nespor, Peña and Mehler (2003), or varies across languages, perhaps as a function...... of the phonological or lexical properties of the language in acquisition. To do so, we used the interactive word-learning task set up by Havy and Nazzi (2009), teaching Danish-learning 20-month-olds pairs of phonetically similar words that contrasted either on one of their consonants or one of their...... one or two phonological features were changed. The implication of these findings is that the phonological biases found in early lexical processing are not language-general but develop during language acquisition, depending on the phonological or lexical properties of the native language....

  11. Human language reveals a universal positivity bias.

    Science.gov (United States)

    Dodds, Peter Sheridan; Clark, Eric M; Desu, Suma; Frank, Morgan R; Reagan, Andrew J; Williams, Jake Ryland; Mitchell, Lewis; Harris, Kameron Decker; Kloumann, Isabel M; Bagrow, James P; Megerdoomian, Karine; McMahon, Matthew T; Tivnan, Brian F; Danforth, Christopher M

    2015-02-24

    Using human evaluation of 100,000 words spread across 24 corpora in 10 languages diverse in origin and culture, we present evidence of a deep imprint of human sociality in language, observing that (i) the words of natural human language possess a universal positivity bias, (ii) the estimated emotional content of words is consistent between languages under translation, and (iii) this positivity bias is strongly independent of frequency of word use. Alongside these general regularities, we describe interlanguage variations in the emotional spectrum of languages that allow us to rank corpora. We also show how our word evaluations can be used to construct physical-like instruments for both real-time and offline measurement of the emotional content of large-scale texts. PMID:25675475

  12. Components of visual bias: a multiplicative hypothesis.

    Science.gov (United States)

    Bundesen, Claus; Vangkilde, Signe; Habekost, Thomas

    2015-03-01

    Attentional selection can be viewed as having two aspects: selection with respect to particular objects and selection with respect to particular categories. Both aspects are mathematically modeled in the theory of visual attention (TVA). In this paper, we expand the rate equation of the TVA and propose that the visual bias toward seeing an object x as a member of category i is a product of three factors: the expectancy (prior probability) of being presented with members of category i, the subjective importance (utility) of seeing objects in category i as members of that category, and the general level of alertness. Together, the three factors also determine the level of arousal in the visual system. The hypothesized multiplicative interaction between the three components of visual bias seems consistent with the function of an ideal observer and also paves the way for a Bayesian interpretation of the TVA. PMID:25675882

  13. Biased liquid crystal infiltrated photonic bandgap fiber

    DEFF Research Database (Denmark)

    Weirich, Johannes; Lægsgaard, Jesper; Scolari, Lara;

    2009-01-01

    A simulation scheme for the transmission spectrum of a photonic crystal fiber infiltrated with a nematic liquid crystal and subject to an external bias is presented. The alignment of the biased liquid crystal is simulated using the finite element method to solve the relevant system of coupled...... partial differential equations. From the liquid crystal alignment the full tensorial dielectric permittivity in the capillaries is derived. The transmission spectrum for the photonic crystal fiber is obtained by solving the generalized eigenvalue problem deriving from Maxwell’s equations using a vector...... element based finite element method. We demonstrate results for a splay aligned liquid crystal infiltrated into the capillaries of a four-ring photonic crystal fiber and compare them to corresponding experiments....

  14. Bias in emerging biomarkers for bipolar disorder

    DEFF Research Database (Denmark)

    Carvalho, A F; Köhler, C A; Fernandes, B S;

    2016-01-01

    BACKGROUND: To date no comprehensive evaluation has appraised the likelihood of bias or the strength of the evidence of peripheral biomarkers for bipolar disorder (BD). Here we performed an umbrella review of meta-analyses of peripheral non-genetic biomarkers for BD. METHOD: The Pubmed/Medline, E......BACKGROUND: To date no comprehensive evaluation has appraised the likelihood of bias or the strength of the evidence of peripheral biomarkers for bipolar disorder (BD). Here we performed an umbrella review of meta-analyses of peripheral non-genetic biomarkers for BD. METHOD: The Pubmed......) was observed in 11 meta-analyses. Heterogeneity was high for (I 2 ⩾ 50%) 16 meta-analyses. Only two biomarkers met criteria for suggestive evidence namely the soluble IL-2 receptor and morning cortisol. The median power of included studies, using the effect size of the largest dataset as the plausible...

  15. Limiter biasing experiments on the tokamak ISTTOK

    Czech Academy of Sciences Publication Activity Database

    Silva, C.; Nedzelskiy, I.; Figueiredo, H.; Cabral, J. A. C.; Varandas, C. A. F.; Stöckel, Jan

    2003-01-01

    Roč. 53, č. 10 (2003), s. 937-944. ISSN 0011-4626. [Workshop "Electric Fields Structures and Relaxation in Edge Plasmas"/6th./. St. Petersburg, 13.06.2003-14.06.2003] Institutional research plan: CEZ:AV0Z2043910 Keywords : biasing, edge plasma, particle confinement Subject RIV: BL - Plasma and Gas Discharge Physics Impact factor: 0.263, year: 2003

  16. Edge biasing in the WEGA stellarator

    Energy Technology Data Exchange (ETDEWEB)

    Lischtschenko, Oliver

    2009-02-27

    The WEGA stellarator is used to confine low temperature, overdense (densities exceeding the cut-off density of the heating wave) plasmas by magnetic fields in the range of B=50-500 mT. Microwave heating systems are used to ignite gas discharges using hydrogen, helium, neon or argon as working gases. The produced plasmas have been analyzed using Langmuir and emissive probes, a single-channel interferometer and ultra-high resolution Doppler spectroscopy. For a typical argon discharge in the low field operation, B=56 mT, the maximum electron density is n{sub e}{proportional_to}10{sup 18} m{sup -3} with temperatures in the range of T=4-12 eV. The plasma parameters are determined by using Langmuir probes and are cross-checked with interferometry. It is demonstrated within this work that the joint use of emissive probes and ultra-high resolution Doppler spectroscopy allows a precise measurement of the radial electric field. The focus of this work is on demonstrating the ability to modify the existing radial electric field in a plasma by using the biasing probe. This work commences with a basic approach and first establishes the diagnostic tools in a well-known discharge. Then the perturbation caused by the biasing probe is assessed. Following the characterization of the unperturbed plasmas, plasma states altered by the operation of the energized biasing probe are characterized. During biasing the plasma two different stable plasma states have been found. The two observed plasma states differ in plasma parameter profiles, such as density, temperature, electric field and confined energy. (orig.)

  17. Calibration biases in logical reasoning tasks

    OpenAIRE

    Guillermo Macbeth; Alfredo López Alonso; Eugenia Razumiejczyk; Rodrigo Sosa; Carolina Pereyra; Humberto Fernández

    2013-01-01

    The aim of this contribution is to present an experimental study about calibration in deductive reasoning tasks. Calibration is defi ned as the empirical convergence or divergence between the objective and the subjective success. The underconfi dence bias is understood as the dominance of the former over the latter. The hypothesis of this study states that the form of the propositions presented in the experiment is critical for calibration phenomena. Affi rmative and negative propositions are...

  18. A Protectionist Bias in Majoritarian Politics

    OpenAIRE

    Grossman, Gene; Helpman, Elhanan

    2005-01-01

    We develop a novel model of campaigns, elections, and policymaking in which the ex ante objectives of national party leaders differ from the ex post objectives of elected legislators. This generates a distinction between "policy rhetoric" and "policy reality" and introduces an important role for "party discipline" in the policymaking process. We identify a protectionist bias in majoritarian politics. When trade policy is chosen by the majority delegation and legislators in the minority have l...

  19. Bias During the Evaluation of Animal Studies?

    OpenAIRE

    Andrew Knight

    2012-01-01

    Simple Summary Animal experimentation evokes strong emotional responses in people on both sides of the debate surrounding its ethical status. However, the true level of its usefulness to society may only be discerned by careful examination of reliable scientific evidence. My recent book, The Costs and Benefits of Animal Experiments, reviewed more than 500 relevant scientific publications. Recently in this journal, however, a reviewer essentially accused me of bias. Yet the conclusions of my b...

  20. Substitution biases in price indices during transition

    Czech Academy of Sciences Publication Activity Database

    Hanousek, Jan; Filer, Randall K.

    2004-01-01

    Roč. 21, č. 2 (2004), s. 167-177. ISSN 0167-8000 R&D Projects: GA MŠk ME 595 Institutional research plan: CEZ:AV0Z7085904 Keywords : price liberalization * substitution bias * transition economies Subject RIV: AH - Economics http://search.ebscohost.com/login.aspx?direct=true&db=a9h&AN=17109091&site=ehost-live

  1. Edge biasing in the WEGA stellarator

    International Nuclear Information System (INIS)

    The WEGA stellarator is used to confine low temperature, overdense (densities exceeding the cut-off density of the heating wave) plasmas by magnetic fields in the range of B=50-500 mT. Microwave heating systems are used to ignite gas discharges using hydrogen, helium, neon or argon as working gases. The produced plasmas have been analyzed using Langmuir and emissive probes, a single-channel interferometer and ultra-high resolution Doppler spectroscopy. For a typical argon discharge in the low field operation, B=56 mT, the maximum electron density is ne∝1018 m-3 with temperatures in the range of T=4-12 eV. The plasma parameters are determined by using Langmuir probes and are cross-checked with interferometry. It is demonstrated within this work that the joint use of emissive probes and ultra-high resolution Doppler spectroscopy allows a precise measurement of the radial electric field. The focus of this work is on demonstrating the ability to modify the existing radial electric field in a plasma by using the biasing probe. This work commences with a basic approach and first establishes the diagnostic tools in a well-known discharge. Then the perturbation caused by the biasing probe is assessed. Following the characterization of the unperturbed plasmas, plasma states altered by the operation of the energized biasing probe are characterized. During biasing the plasma two different stable plasma states have been found. The two observed plasma states differ in plasma parameter profiles, such as density, temperature, electric field and confined energy. (orig.)

  2. Plutino Detection Biases, Including the Kozai Resonance

    OpenAIRE

    Lawler, S. M.; Gladman, B.

    2013-01-01

    Because of their proximity within the transneptunian region, the plutinos (objects in the 3:2 mean-motion resonance with Neptune) are numerous in flux-limited catalogs, and well-studied theoretically. We perform detailed modelling of the on-sky detection biases for plutinos, with special attention to those that are simultaneously in the Kozai resonance. In addition to the normal 3:2 resonant argument libration, Kozai plutinos also show periodic oscillations in eccentricity and inclination, co...

  3. The Scarcity Bias: Some Theoretical Notes

    OpenAIRE

    Mittone, Luigi; Soraperra, Ivan

    2006-01-01

    The bias generated by the subjective perception of scarcity on the consumer’s choice is discussed from a theoretical perspective. The core idea here discussed is that scarcity is an Lancasterian attribute of the goods which is not endogenously built in the goods, like many physical attributes, color, weight, etc. but which is dependent from the context where the good is consumed. The exogenously nature of scarcity requires a specific theoretical treatment which is here attempted.

  4. Interpretive biases in socially anxious adults

    OpenAIRE

    Godfree, Ross

    2013-01-01

    Social phobia is a highly prevalent and debilitating anxiety disorder that can significantly impact quality of life and produce extreme distress in social situations. Cognitive models of social phobia suggest that information-processing biases are involved in the maintenance of social anxiety. Treatment typically involves a course of Cognitive Behavioural Therapy (CBT). Recent advancements in the understanding of the mechanisms underlying social anxiety have led to specific adjunctive treatme...

  5. Home Biases, 19th Century Style

    OpenAIRE

    Marc Flandreau

    2005-01-01

    This paper discusses the existence of 'home' biases in the 19th century global capital market, whereby colonies appear to have received a 'disproportionate' amount of capital from their metropolis. Starting from a discussion of the Bulow Rogoff (1989) problem, we argue that imperial links provided a natural institutional framework to make pre-commitment credible by ensuring an adequate degree of willingness to pay. This was not because imperial rule provided coercion or punishment, but rather...

  6. Frictions, behavioral biases and active portfolio management

    OpenAIRE

    Eisele, Alexander; Nowak, Eric

    2015-01-01

    The three chapters of this thesis contribute to the following research questions: (i) What is the role of agency frictions for the performance of mutual funds? (ii) What is the role of market frictions for the performance of hedge funds? (iii) Do hedge funds profit from the behavioral biases of other market participants? The first chapter of this thesis comprises the article "Are Star Funds really Shining? Cross-trading and Performance Shifting in Mutual Fund Families", which is joint wo...

  7. Reference bias in reports of drug trials.

    OpenAIRE

    Dickersin, K

    1987-01-01

    Articles published before 1985 describing double blind trials of two or more non-steroidal anti-inflammatory drugs in rheumatoid arthritis were examined to see whether there was any bias in the references they cited. Althogether 244 articles meeting the criteria were found through a Medline search and through examining the reference lists of the articles retrieved. The drugs compared in the studies were classified as new or as control drugs and the outcome of the trial as positive or not posi...

  8. Team formation and biased self-attribution

    OpenAIRE

    Corgnet, Brice

    2005-01-01

    We analyze the impact of individuals' self-attribution biases on the formation of teams in the workplace. We consider a two periods model in which workers jointly decide whether to form a team or work alone. We assume workers' abilities are unknown. Agents update their beliefs about abilities after receiving a signal at the end of the first period. We show that allowing workers to learn about their abilities undermines cooperation when a fixed allocation of the group outcome is assumed. Consi...

  9. Using biased discriminant analysis for email filtering

    OpenAIRE

    Gomez, Juan Carlos; Moens, Marie-Francine

    2010-01-01

    This paper reports on email filtering based on content features. We test the validity of a novel statistical feature extraction method, which relies on dimensionality reduction to retain the most informative and discriminative features from messages. The approach, named Biased Discriminant Analysis (BDA), aims at finding a feature space transformation that closely clusters positive examples while pushing away the negative ones. This method is an extension of Linear Discriminant Analysis (L...

  10. The bias in time series volatility forecasts

    OpenAIRE

    Ederington, Louis H; Wei Guan

    2010-01-01

    By Jensen's inequality, a model's forecasts of the variance and standard deviation of returns cannot both be unbiased. This study explores the bias in GARCH type model forecasts of the standard deviation of returns, which we argue is the more appropriate volatility measure for most financial applications. For a wide variety of markets, the GARCH, EGARCH, and GJR (or TGARCH) models tend to persistently over‐estimate the standard deviation of returns, whereas the ARLS model of L. Ederington and...

  11. The natalist bias of pollution control

    OpenAIRE

    De La Croix, David; GOSSERIES, Axel

    2011-01-01

    For a given technology, two ways are available to achieve low polluting emissions: reducing production per capita or reducing population size. This paper insists on the tension between the former and the latter. Controlling pollution either through Pigovian taxes or through tradable quotas schemes encourages agents to shift away from production to tax free activities such as procreation and leisure. This natalist bias will deteriorate the environment further, entailing the need to impose ever...

  12. Gender Roles:Biases or Differences?

    Institute of Scientific and Technical Information of China (English)

    魏静

    2013-01-01

    This paper aims to probe into the two distinct gender roles-males and females-in several ways, and further answers the question“what on earth cause the salient differentiation in gender roles, biases or differences? ”In conclusion, the author holds that it is the physiological and psychological differences in the two sexes that result in the differed distribution of such vari-ous duties which males and females are supposed to fulfill as the current society has expected.

  13. Bias Adaptation for Vocal Tract Length Normalization

    OpenAIRE

    Saheer, Lakshmi; Yamagishi, Junichi; Garner, Philip N.; Dines, John

    2013-01-01

    Vocal tract length normalisation (VTLN) is a well known rapid adaptation technique. VTLN as a linear transformation in the cepstral domain results in the scaling and translation factors. The warping factor represents the spectral scaling parameter. While, the translation factor represented by bias term captures more speaker characteristics especially in a rapid adaptation framework without having the risk of over-fitting. This paper presents a complete and comprehensible derivation of the bia...

  14. Different efficiency of UmuDC and MucAB proteins in UV light induced mutagenesis in Escherichia coli

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, M.; Herrera, G.; Aleixandre, V.

    1986-11-01

    Two multicopy plasmids carrying either the umuDC or the mucAB operon were used to compare the efficiency of UmuDC and MucAB proteins in UV mutagenesis of Escherichia coli K12. It was found that in recA/sup +/ uvr/sup +/ bacteria, plasmid pIC80, mucAB/sup +/ mediated UV mutagenesis more efficiently than did plasmid pSE 117, umuDC/sup +/. A similar result was obtained in lex A51(Def) cells, excluding the possibility that this was due to a differential regulation by LexA of the umuDC and mucAB operons. We conclude that some structural characteristic of the UmuDC and MucAB proteins determines their different efficiency in UV mutagenesis. This characteristic could be also responsible for the observation that in the recA430 mutant, pIC80 but no pSE117 can mediate UV mutagenesis. In the recAS142 mutant pIC80 also promoted UV mutagenesis more efficiently than pSE117. In this mutant, the recombination proficiency, the protease activity toward LexA and the mutation frequency were increased by the presence of adenine in the medium. In recA/sup +/ uvrB5 bacteria, plasmid pSE117, umuDC caused both an increase in UV sensitivity as well as a reduction in the mutation frequency. These negative effects resulting from the overproduction of UmuDC proteins were higher in recA142 uvrB5 than in recA/sup +/ uvrB5 cells. In contrast, overproduction of MucAB proteins in excision-deficient bacteria containing pIC80 led to a large increase in the mutation frequency. We suggest that the functional differences between UmuDC and MucAB proteins might be due to their different dependence on the direct role of RecA protease in UV mutagenesis.

  15. Biases in Cometary Catalogues and Planet X

    CERN Document Server

    Horner, J

    2002-01-01

    Two sets of investigators -- Murray (1999) and Matese, Whitman & Whitmire (1999) -- have recently claimed evidence for an undiscovered Solar System planet from possible great circle alignments in the aphelia directions of the long period comets. However, comet discoveries are bedevilled by selection effects. These include anomalies caused by the excess of observers in the northern as against the southern hemisphere, seasonal and diurnal biases, directional effects which make it harder to discover comets in certain regions of the sky, as well as sociological biases. The stream proposed by Murray is shown on an equal area Hammer-Aitoff projection. The addition of newer data weakens the case for the alignment. There is also evidence that the subsample in the stream is affected by seasonal and north-south biases. The stream proposed by Matese et al. is most obvious in the sample of dynamically new comets, and especially in those whose orbits are best known. The most recent data continues to maintain the overp...

  16. Primordial black holes as biased tracers

    CERN Document Server

    Tada, Yuichiro

    2015-01-01

    Primordial black holes (PBHs) are theoretical black holes which may be formed during the radiation dominant era and, basically, caused by the gravitational collapse of radiational overdensities. It has been well known that in the context of the structure formation in our Universe such collapsed objects, e.g., halos/galaxies, could be considered as bias tracers of underlying matter fluctuations and the halo/galaxy bias has been studied well. Employing a peak-background split picture which is known to be a useful tool to discuss the halo bias, we consider the large scale clustering behavior of the PBH and propose an almost mass-independent constraint to the scenario that dark matters (DMs) consist of PBHs. We consider the case where the statistics of the primordial curvature perturbations is almost Gaussian, but with small local-type non-Gaussianity. If PBHs account for the DM abundance, such a large scale clustering of PBHs behaves as nothing but the matter isocurvature perturbation and constrained strictly by...

  17. A Model of Inductive Bias Learning

    CERN Document Server

    Baxter, J

    2011-01-01

    A major problem in machine learning is that of inductive bias: how to choose a learner's hypothesis space so that it is large enough to contain a solution to the problem being learnt, yet small enough to ensure reliable generalization from reasonably-sized training sets. Typically such bias is supplied by hand through the skill and insights of experts. In this paper a model for automatically learning bias is investigated. The central assumption of the model is that the learner is embedded within an environment of related learning tasks. Within such an environment the learner can sample from multiple tasks, and hence it can search for a hypothesis space that contains good solutions to many of the problems in the environment. Under certain restrictions on the set of all hypothesis spaces available to the learner, we show that a hypothesis space that performs well on a sufficiently large number of training tasks will also perform well when learning novel tasks in the same environment. Explicit bounds are also de...

  18. Anandamide mediates cognitive judgement bias in rats.

    Science.gov (United States)

    Kregiel, J; Malek, N; Popik, P; Starowicz, K; Rygula, R

    2016-02-01

    In the present study, we investigated the effects of acute pharmacological manipulation of the endocannabinoid (EC) system on the valence of cognitive judgement bias of rats in the ambiguous-cue interpretation (ACI) paradigm. To accomplish this goal, after initial behavioural training, different groups of rats received single, systemic injections of the irreversible anandamide (AEA) hydrolysis inhibitor URB597, the cannabinoid receptor type 1 (CB1) inverse agonist AM251, the cannabinoid receptor type 2 (CB2) inverse agonist AM630, the combination of URB597 and AM251, and a combination of URB597 and AM630 and were subsequently tested with the ACI paradigm. We report that URB597 at a dose of 1 mg/kg significantly biased animals towards positive interpretation of the ambiguous cue and that this effect was abolished by pre-treatment with AM251 (1 mg/kg) or AM630 (1 mg/kg). The CB1 and CB2 inverse agonists administered alone (1 mg/kg) had no statistically significant effects on the interpretation of the ambiguous cue by rats. Our findings suggest involvement of the endocannabinoid system in the mediation of optimistic judgement bias. PMID:26363193

  19. Perceptive biases in major depressive episode.

    Directory of Open Access Journals (Sweden)

    Marine Naudin

    Full Text Available INTRODUCTION: Alterations in emotional processing occur during a major depressive episode (MDE, and olfaction and facial expressions have implications in emotional and social interactions. To gain a better understanding of these processes, we characterized the perceptive sensorial biases, potential links, and potential remission after antidepressant treatment of MDE. METHODS: We recruited 22 patients with acute MDE, both before and after three months of antidepressant treatment, and 41 healthy volunteers matched by age and smoking status. The participants underwent a clinical assessment (Mini International Neuropsychiatry Interview, Montgomery-Åsberg Depression Rating Scale, State-Trait Anxiety Inventory, Physical and Social Anhedonia scales, Pleasure-Displeasure Scale, an olfactory evaluation (hedonic aspect, familiarity and emotional impact of odors, and a computerized Facial Affect Recognition task. RESULTS: MDE was associated with an olfactory bias concerning hedonic and emotional aspects, including negative olfactory alliesthesia (unpleasant odorants perceived as more unpleasant, facial emotion expression recognition (happy facial expressions, and in part olfactory anhedonia (pleasant odorants perceived as less pleasant. In addition, the results revealed that these impairments represent state markers of MDE, suggesting that the patients recovered the same sensory processing as healthy subjects after antidepressant treatment. DISCUSSION: This study demonstrated that MDE is associated with negative biases toward olfactory perception and the recognition of facial emotional expressions. The link between these two sensory parameters suggests common underlying processes.

  20. Bias temperature instability for devices and circuits

    CERN Document Server

    2014-01-01

    This book provides a single-source reference to one of the more challenging reliability issues plaguing modern semiconductor technologies, negative bias temperature instability.  Readers will benefit from state-of-the art coverage of research in topics such as time dependent defect spectroscopy, anomalous defect behavior, stochastic modeling with additional metastable states, multiphonon theory, compact modeling with RC ladders and implications on device reliability and lifetime.  ·         Enables readers to understand and model negative bias temperature instability, with an emphasis on dynamics; ·         Includes coverage of DC vs. AC stress, duty factor dependence and bias dependence; ·         Explains time dependent defect spectroscopy, as a measurement method that operates on nanoscale MOSFETs; ·         Introduces new defect model for metastable defect states, nonradiative multiphonon theory and stochastic behavior.

  1. [Notion of threshold in mutagenesis: implications for mutagenic and carcinogenic risk assessment].

    Science.gov (United States)

    Marzin, D

    2007-11-01

    During years, it has been widely admitted in the scientific community that there was no threshold in mutagenesis: a compound was or not a mutagen. The meaning of such a proposition was that a risk existed at all exposure level, because, at least theoretically, one molecule is sufficient to cause the formation of a DNA adduct which is able to induce a mutation. However, works carried out in the last few years have shown that in the case of some specific mechanisms of mutagenesis, a threshold could be demonstrated essentially in the case of compounds that do not react directly with DNA. Several types of thresholds exist, and the simple statistical threshold is not sufficient in terms of risk assessment. A biological threshold that is consistent with a mechanism of action of the mutagen should be established. Amongst these mechanisms, we can mention some mechanism with a demonstrated threshold: effects of aneugens, effects of topoisomerases inhibitors, effects of DNA polymerases inhibitors, effects of compounds with a different metabolism at high doses compared to low doses. On the contrary, for some mechanisms, the demonstration of the mechanism is suspected, but not totally demonstrated. It is the case of compounds which induce nucleotides pool imbalance or compounds which are DNA repair inhibitors. In some cases, when a redundancy exists in the repair of damages, like oxidative DNA damage, a threshold is suspected. Some authors even recently proposed the possibility of a threshold in the case of alkylating agents. The majority of mutagenic thresholds were demonstrated in vitro, however some mechanisms were demonstrated in vivo, for example in the case of micronucleus induction by hypo or hyperthermia in rodents bone marrow. The use of threshold in risk assessment requires the use of the most sensitive endpoint for example, non disjunction in the case of aneugens, confusing factors like apoptosis should be eliminated and species sensitivities should be taken into

  2. Induction of novel genetic recombinants through chemical mutagenesis of microspores in Indian Mustard B. juncea

    International Nuclear Information System (INIS)

    The microspore embryogenesis and DH production protocol developed in our lab [In Vitro Cellular and Development Biology - Plant. 2005, 41: 266-273] was used for microspores isolation and their chemical mutagenesis to widen the genetic base of three widely cultivated B. juncea species, Pusa Bold, Varuna and Bio- 902. The regenerated three to four leaf growth stage plantlets were diploidized, hardened and transplanted to develop doubled haploid plants. The microspores of genotype BIO-902 treated with either ENU/EMS did not produce any embryos while the control produced 85.4 ± 10.9 embryos/ Petri dish. Treatment with 5.0 μM ENU/EMS resulted in maximum embryo induction from the other two genotypes, Pusa Bold and Varuna. Irrespective of the concentration used, EMS mutated microspores produced embryos with higher frequency (239) as compared to those treated with ENU (106). The control embryos exhibited 85 to 90% germination against the mutant microspore derived embryos (16.7 to 31.5%). Overall lower concentrations of EMS (1.0 to 2.5 μM) compared to that of ENU (2.5 to 5.0 μM) promoted higher frequency of positive mutants with promising yield potential. Both EMS and ENU generated considerable variability for agro morphological and biochemical traits; appressed pod phenotype, number of pods, leaf size, total glucosinolate content and FA profile. Desirable phenotypes with reduced glucosinolate ( 100 μM) per g oil free meal were recovered from 2.5 to 5.0 μM EMS mutagenesis. Mutants with 45% oleic acid (against 40-45% erucic and 15-20% oleic in controls) were obtained in mutagenized plants from EMS (2.5 μM) and ENU (5.0 μM ). Useful variability was identified in mutant plants for their disease response to the most devastating fungal diseases Albugo candida (DI 0.6-2.0) and Alternaria brassicae (DI 1.3- 2.6) under artificial inoculation. (author)

  3. Identification of critical residues of the mycobacterial dephosphocoenzyme a kinase by site-directed mutagenesis.

    Directory of Open Access Journals (Sweden)

    Guneet Walia

    Full Text Available Dephosphocoenzyme A kinase performs the transfer of the γ-phosphate of ATP to dephosphocoenzyme A, catalyzing the last step of coenzyme A biosynthesis. This enzyme belongs to the P-loop-containing NTP hydrolase superfamily, all members of which posses a three domain topology consisting of a CoA domain that binds the acceptor substrate, the nucleotide binding domain and the lid domain. Differences in the enzymatic organization and regulation between the human and mycobacterial counterparts, have pointed out the tubercular CoaE as a high confidence drug target (HAMAP database. Unfortunately the absence of a three-dimensional crystal structure of the enzyme, either alone or complexed with either of its substrates/regulators, leaves both the reaction mechanism unidentified and the chief players involved in substrate binding, stabilization and catalysis unknown. Based on homology modeling and sequence analysis, we chose residues in the three functional domains of the enzyme to assess their contributions to ligand binding and catalysis using site-directed mutagenesis. Systematically mutating the residues from the P-loop and the nucleotide-binding site identified Lys14 and Arg140 in ATP binding and the stabilization of the phosphoryl intermediate during the phosphotransfer reaction. Mutagenesis of Asp32 and Arg140 showed catalytic efficiencies less than 5-10% of the wild type, indicating the pivotal roles played by these residues in catalysis. Non-conservative substitution of the Leu114 residue identifies this leucine as the critical residue from the hydrophobic cleft involved in leading substrate, DCoA binding. We show that the mycobacterial enzyme requires the Mg(2+ for its catalytic activity. The binding energetics of the interactions of the mutant enzymes with the substrates were characterized in terms of their enthalpic and entropic contributions by ITC, providing a complete picture of the effects of the mutations on activity. The properties of

  4. Spontaneous inflammatory pain model from a mouse line with N-ethyl-N-nitrosourea mutagenesis

    Directory of Open Access Journals (Sweden)

    Chen Tsung-Chieh

    2012-05-01

    Full Text Available Abstract Background N-ethyl-N-nitrosourea mutagenesis was used to induce a point mutation in C57BL/6 J mice. Pain-related phenotype screening was performed in 915 G3 mice. We report the detection of a heritable recessive mutant in meiotic recombinant N1F1 mice that caused an abnormal pain sensitivity phenotype with spontaneous skin inflammation in the paws and ears. Methods We investigated abnormal sensory processing, neuronal peptides, and behavioral responses after the induction of autoinflammatory disease. Single-nucleotide polymorphism (SNP markers and polymerase chain reaction product sequencing were used to identify the mutation site. Results All affected mice developed paw inflammation at 4–8 weeks. Histological examinations revealed hyperplasia of the epidermis in the inflamed paws and increased macrophage expression in the spleen and paw tissues. Mechanical and thermal nociceptive response thresholds were reduced in the affected mice. Locomotor activity was decreased in affected mice with inflamed hindpaws, and this reduction was attributable to the avoidance of contact of the affected paw with the floor. Motor strength and daily activity in the home cage in the affected mice did not show any significant changes. Although Fos immunoreactivity was normal in the dorsal horn of affected mice, calcitonin gene-related peptide immunoreactivity significantly increased in the deep layer of the dorsal horn. The number of microglia increased in the spinal cord, hippocampus, and cerebral cortex in affected mice, and the proliferation of microglia was maintained for a couple of months. Two hundred eighty-five SNP markers were used to reveal the affected gene locus, which was found on the distal part of chromosome 18. A point mutation was detected at A to G in exon 8 of the pstpip2 gene, resulting in a conserved tyrosine residue at amino acid 180 replaced by cysteine (Y180 C. Conclusions The data provide definitive evidence that a mutation

  5. Structural insights from random mutagenesis of Campylobacter jejuni oligosaccharyltransferase PglB

    Directory of Open Access Journals (Sweden)

    Ihssen Julian

    2012-09-01

    Full Text Available Abstract Background Protein glycosylation is of fundamental importance in many biological systems. The discovery of N-glycosylation in bacteria and the functional expression of the N-oligosaccharyltransferase PglB of Campylobacter jejuni in Escherichia coli enabled the production of engineered glycoproteins and the study of the underlying molecular mechanisms. A particularly promising application for protein glycosylation in recombinant bacteria is the production of potent conjugate vaccines where polysaccharide antigens of pathogenic bacteria are covalently bound to immunogenic carrier proteins. Results In this study capsular polysaccharides of the clinically relevant pathogen Staphylococcus aureus serotype 5 (CP5 were expressed in Escherichia coli and linked in vivo to a detoxified version of Pseudomonas aeruginosa exotoxin (EPA. We investigated which amino acids of the periplasmic domain of PglB are crucial for the glycosylation reaction using a newly established 96-well screening system enabling the relative quantification of glycoproteins by enzyme-linked immunosorbent assay. A random mutant library was generated by error-prone PCR and screened for inactivating amino acid substitutions. In addition to 15 inactive variants with amino acid changes within the previously known, strictly conserved WWDYG motif of N-oligosaccharyltransferases, 8 inactivating mutations mapped to a flexible loop in close vicinity of the amide nitrogen atom of the acceptor asparagine as revealed in the crystal structure of the homologous enzyme C. lari PglB. The importance of the conserved loop residue H479 for glycosylation was confirmed by site directed mutagenesis, while a change to alanine of the adjacent, non-conserved L480 had no effect. In addition, we investigated functional requirements in the so-called MIV motif of bacterial N-oligosaccharyltransferases. Amino acid residues I571 and V575, which had been postulated to interact with the acceptor peptide, were

  6. Impact of Continued Biased Disenrollment from the Medic...

    Data.gov (United States)

    U.S. Department of Health & Human Services — Impact of Continued Biased Disenrollment from the Medicare Advantage Program to Fee-for-Service As reported in Impact of Continued Biased Disenrollment from the...

  7. Comparing measures of cognitive bias relating to eating behaviour

    OpenAIRE

    Pothos, E. M.; Calitri, R.; Tapper, K.; Brunstrom, J M; Rogers, P J

    2009-01-01

    Consumption of and/or abstinence from substances with a high reward value (e.g., heroin, marijuana, alcohol, nicotine, certain foods) are associated with cognitive biases for information related to the substance. Such cognitive biases are important since they may contribute to difficulties in controlling intake of the substance. We examine cognitive biases for stimuli related to food. For the first time, we concurrently employ and compare five conceptually distinct measures of cognitive bias ...

  8. Application and investigation of a bound for outcome reporting bias

    OpenAIRE

    Gamble Carrol; Williamson Paula R

    2007-01-01

    Abstract Background Direct empirical evidence for the existence of outcome reporting bias is accumulating and this source of bias is recognised as a potential threat to the validity of meta-analysis of randomised clinical trials. Methods A method for calculating the maximum bias in a meta-analysis due to publication bias is adapted for the setting where within-study selective non-reporting of outcomes is suspected, and compared to the alternative approach of missing data imputation. The prope...

  9. Biased quantitative measurement of interval ordered homothetic preferences

    OpenAIRE

    Le Menestrel, Marc; LEMAIRE, Bertrand

    2004-01-01

    We represent interval ordered homothetic preferences with a quantitative homothetic utility function and a multiplicative bias. When preferences are weakly ordered (i.e. when indifference is transitive), such a bias equals 1. When indifference is intransitive, the biasing factor is a positive function smaller than 1 and measures a threshold of indifference. We show that the bias is constant if and only if preferences are semiordered, and we identify conditions ensuring a linear utility functi...

  10. Simulation of HPIB propagation in biased charge collector

    International Nuclear Information System (INIS)

    A 2.5D PIC simulation using KARAT code for inner charge propagation within biased charge collector for measuring HPIB is presented. The simulation results indicate that the charges were neutralized but the current non-neutralized in the biased charge collector. The influence of ions collected vs biased voltage of the collector was also simulated. -800 V biased voltage can meet the measurement of 500 keV HPIB, and this is consistent with the experimental results

  11. Multiple Adaptive Fading Schmidt-Kalman Filter for Unknown Bias

    OpenAIRE

    Tai-Shan Lou; Zhi-Hua Wang; Meng-Li Xiao; Hui-Min Fu

    2014-01-01

    Unknown biases in dynamic and measurement models of the dynamic systems can bring greatly negative effects to the state estimates when using a conventional Kalman filter algorithm. Schmidt introduces the “consider” analysis to account for errors in both the dynamic and measurement models due to the unknown biases. Although the Schmidt-Kalman filter “considers” the biases, the uncertain initial values and incorrect covariance matrices of the unknown biases still are not considered. To solve th...

  12. Information bias in health research: definition, pitfalls, and adjustment methods

    OpenAIRE

    Althubaiti A

    2016-01-01

    Alaa Althubaiti Department of Basic Medical Sciences, College of Medicine, King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia Abstract: As with other fields, medical sciences are subject to different sources of bias. While understanding sources of bias is a key element for drawing valid conclusions, bias in health research continues to be a very sensitive issue that can affect the focus and outcome of investigations. Information bias, otherwise known as misclassific...

  13. Modifying Threat-Related Interpretive Bias in Adolescents

    Science.gov (United States)

    Salemink, Elske; Wiers, Reinout W.

    2011-01-01

    Socially anxious feelings sharply increase during adolescence and such feelings have been associated with interpretive biases. Studies in adults have shown that interpretive biases can be modified using Cognitive Bias Modification procedures (CBM-I) and subsequent effects on anxiety have been observed. The current study was designed to examine…

  14. CEO emotional bias and dividend policy: Bayesian network method

    OpenAIRE

    Azouzi Mohamed Ali; Jarboui Anis

    2012-01-01

    This paper assumes that managers, investors, or both behave irrationally. In addition, even though scholars have investigated behavioral irrationality from three angles, investor sentiment, investor biases and managerial biases, we focus on the relationship between one of the managerial biases, overconfidence and dividend policy. Previous research investigating the relationship between overconfidence and financial decisions has studied investment, financing decisions and firm values. However,...

  15. Development of Heuristic Bias Detection in Elementary School

    Science.gov (United States)

    De Neys, Wim; Feremans, Vicky

    2013-01-01

    Although human reasoning is often biased by intuitive heuristics, recent studies have shown that adults and adolescents detect the biased nature of their judgments. The present study focused on the development of this critical bias sensitivity by examining the detection skills of young children in elementary school. Third and 6th graders were…

  16. Cultural Bias in Children's Storybooks: Implications for Education.

    Science.gov (United States)

    Timm, Joan S.

    This study addresses concern about bias in educational materials for elementary school pupils. Children's storybooks were examined for the appearance of biases across the cultural categories of race, ethnicity, gender, age, socioeconomic level, religion, and environmental background. These biases included stereotyping, invisibility (omission of…

  17. MMPI Profiles of Black Americans: Is There a Bias?

    Science.gov (United States)

    Sturmer, Paul J.; Gerstein, Lawrence H.

    1997-01-01

    Reviews literature on Minnesota Multiphasic Personality Inventory (MMPI) racial bias since 1977. Research indicates cases in which racial bias is present and cases where it is not. Anticipates the onslaught of research on racial bias with the MMPI-2 and provides recommendations to researchers and mental-health counselors. (RJM)

  18. Questioning Children: Interactional Evidence of Implicit Bias in Medical Interviews

    Science.gov (United States)

    Stivers, Tanya; Majid, Asifa

    2007-01-01

    Social psychologists have shown experimentally that implicit race bias can influence an individual's behavior. Implicit bias has been suggested to be more subtle and less subject to cognitive control than more explicit forms of racial prejudice. Little is known about how implicit bias is manifest in naturally occurring social interaction. This…

  19. The effect of optimism bias on time preference

    OpenAIRE

    Tal Shavit

    2013-01-01

    This paper examines the effect of optimism bias on monetary time preference and risk tolerance. The results of a survey show that preference towards the present increases with optimism bias. I argue that the factor which affects time preference is the individual’s concern regarding future events, as measured by optimism bias.

  20. Perturbation theory for nonlinear halo power spectrum: the renormalized bias and halo bias

    CERN Document Server

    Nishizawa, Atsushi J; Nishimichi, Takahiro

    2013-01-01

    We revisit an analytical model to describe the halo-matter cross-power spectrum and the halo auto-power spectrum in the weakly nonlinear regime, by combining the perturbation theory (PT) for matter clustering, the local bias model, and the halo bias. Nonlinearities in the power spectra arise from the nonlinear clustering of matter as well as the nonlinear relation between the matter and halo density fields. By using the "renormalization" approach, we express the nonlinear power spectra by a sum of the two contributions: the nonlinear matter power spectrum with the effective linear bias parameter, and the higher-order PT spectra having the halo bias parameters as the coefficients. The halo auto-power spectrum includes the residual shot noise contamination that needs to be treated as additional free parameter. The term(s) of the higher-order PT spectra and the residual shot noise cause a scale-dependent bias function relative to the nonlinear matter power spectrum in the weakly nonlinear regime. We show that th...

  1. Mutagenesis of lambda phage by tif-expression or host-irradiation functions is largely independent of damage in the phage DNA

    International Nuclear Information System (INIS)

    The survival and mutagenesis of UV-irradiated phage lambda, as well as bacterial mutagenesis, are enhanced in tif mutants of Escherichia coli when these strains are grown at 430C (Castellazzi et al., 1972). This was interpreted on the basis of a hypothesis (the SOS hypothesis) according to which the UV-inducible phenomena connected with reactivation and mutagenesis of UV-irradiated bacteriophages (Weigle, 1953; Radman, 1975) are constitutively expressed in tif-bacteria at high temperature (Witkin, 1974). In unpublished experiments with phage T3 we found that the survival of UV-irradiated phage is also better at 430C than at 320C in tif + cells and this made us reexamine the significance and nature of tif expression and examine its effects on both unirradiated and UV-irradiated phage lambda. Our results indicate that tif-induced mutagenesis and possibly reactivation of UV-irradiated phage lambda should be reinterpreted. (orig./AJ)

  2. Over-expression of gluconic acid in Aspergillus oryzae RP-21 mutants generated by a random mutagenesis approach

    OpenAIRE

    Raksha, Sunhare; Srinivasan, Sharmila; Prasant, Garima; Prabu, Rajagopalan

    2012-01-01

    Random mutagenesis with N-methyl-N′ nitro-N-nitrosoguanidine (NTG) was used to mutate Aspergillus oryzae RP-21 to develop high gluconic acid-producing mutants. Forty mutant colonies (designated as A. oryzae strains RP-NTG-01 to RP-NTG-40) screened for gluconic acid, glucose dehydrogenase and glucose oxidase production using a 12-well plate method showed that 17 strains (positive mutants) produced high concentrations of these three products, whereas 12 strains (negative mutants) showed low con...

  3. The bacterial transposon Tn7 causes premature polyadenylation of mRNA in eukaryotic organisms: TAGKO mutagenesis in filamentous fungi

    OpenAIRE

    Lo, Clive; Adachi, Kiichi; Shuster, Jeffrey R.; Hamer, John E.; Hamer, Lisbeth

    2003-01-01

    TAGKO is a Tn7-based transposition system for genome wide mutagenesis in filamentous fungi. The effects of transposon insertion on the expression of TAGKO alleles were examined in Magnaporthe grisea and Mycosphaerella graminicola. Northern analysis showed that stable, truncated transcripts were expressed in the TAGKO mutants. Mapping of the 3′-ends of TAGKO cDNAs revealed that they all contain Tn7 end sequences, regardless of the transposon orientation. Polyadenylation signals characteristic ...

  4. High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop

    OpenAIRE

    Shapter, Frances M.; Michael Cross; Gary Ablett; Sylvia Malory; Chivers, Ian H.; King, Graham J.; Henry, Robert J.

    2013-01-01

    Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited...

  5. Mutation Breeding of Extracellular Polysaccharide-Producing Microalga Crypthecodinium cohnii by a Novel Mutagenesis with Atmospheric and Room Temperature Plasma

    OpenAIRE

    Bin Liu; Zheng Sun; Xiaonian Ma; Bo Yang; Yue Jiang; Dong Wei; Feng Chen

    2015-01-01

    Extracellular polysaccharides (EPS) produced by marine microalgae have the potential to be used as antioxidants, antiviral agents, immunomodulators, and anti-inflammatory agents. Although the marine microalga Crypthecodinium cohnii releases EPS during the process of docosahexaenoic acid (DHA) production, the yield of EPS remains relatively low. To improve the EPS production, a novel mutagenesis of C. cohnii was conducted by atmospheric and room temperature plasma (ARTP). Of the 12 mutants o...

  6. Gene-scrambling mutagenesis: generation and analysis of insertional mutations in the alginate regulatory region of Pseudomonas aeruginosa.

    OpenAIRE

    Mohr, C D; Deretic, V.

    1990-01-01

    A novel method for random mutagenesis of targeted chromosomal regions in Pseudomona aeruginosa was developed. This method can be used with a cloned DNA fragment of indefinite size that contains a putative gene of interest. Cloned DNA is digested to produce small fragments that are then randomly reassembled into long DNA inserts by using cosmid vectors and lambda packaging reaction. This DNA is then transferred into P. aeruginosa and forced into the chromosome via homologous recombination, pro...

  7. Rice improvement involving altered flower structure more suitable to cross-pollination, using in vitro culture in combination with mutagenesis

    International Nuclear Information System (INIS)

    Anther and somatic tissue culture in combination with mutagenesis were carried out to evaluate the efficiency of different mutagenic treatments of various in vitro culture materials, and to obtain some promising variants for rice improvement. Results indicated that in japonica rice radiation treatment of dry seeds and young panicles influenced the percentage of green plantlets regeneration from anther culture. Both treatments increased significantly the percentage of regenerated green plant lets in comparison with the control

  8. Insertional mutagenesis and marker rescue in a protozoan parasite: cloning of the uracil phosphoribosyltransferase locus from Toxoplasma gondii.

    OpenAIRE

    Donald, R G; Roos, D. S.

    1995-01-01

    Nonhomologous integration vectors have been used to demonstrate the feasibility of insertional mutagenesis in haploid tachyzoites of the protozoan parasite Toxoplasma gondii. Mutant clones resistant to 5-fluorouracil were identified at a frequency of approximately 10(-6) (approximately 2 x 10(-5) of the stable transformants). Four independent mutants were isolated, all of which were shown to lack uracil phosphoribosyl-transferase (UPRT) activity and harbor transgenes integrated at closely lin...

  9. An efficient PCR mutagenesis strategy without gel purification [correction of "purificiation"] step that is amenable to automation.

    OpenAIRE

    Séraphin, B; Kandels-Lewis, S

    1996-01-01

    We describe here an improved megaprimer PCR mutagenesis strategy. The cumbersome gel purification step that is usually used can be omitted by appropriately cleaving the first and second DNA templates with restriction enzymes and enzymatically removing remaining primers from the first PCR reaction. We show that this improved procedure is reproducible and highly efficient. Furthermore this method is suitable for automation because all the steps are now carried out in reaction tubes.

  10. Differences in temporal aspects of mutagenesis and cytotoxicity in Chinese hamster cells treated with methylating agents and thymidine.

    Science.gov (United States)

    Peterson, A R; Peterson, H

    1982-03-01

    Equitoxic concentrations of N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) and methyl methanesulfonate (MeMes) produced different frequencies of 8-azaguanine-resistant mutants and different amounts of N7-methylguanine, O6-methylguanine (m6G), and N3-methyladenine in the DNA of V79 Chinese hamster cells. Thus, neither the cytotoxicities nor the mutagenicities of these methylating agents could be attributed solely to nitrogen or to oxygen methylations in the DNA. However, MNNG produced 12-fold more m6G and 5-fold more mutants than did MeMes, indicating that a substantial part of the MNNG-induced mutations resulted from m6G--thymine mispairing during DNA replication. The expression as mutants of mutagenic oxygen methylations in the DNA of cells treated with MNNG was enhanced by thymidine (dThd) and deoxycytidine (dCyd), but these nucleosides did not significantly enhance MeMes-induced mutagenesis. The cytotoxicities of MNNG and MeMes were also increased by 10 microM dThd in proportion to the amount of m6G in the DNA. These increases in cytotoxicity were abolished by dCyd, which did not greatly reduce the dThd-induced enhancements of mutagenesis. Moreover, when dThd was present only during the 2-hr treatment with MNNG, maximal cytotoxicity occurred, but MNNG-induced mutagenesis was not increased. Maximal mutagenesis occurred when the dThd was present throughout the first doubling time of the MNNG-treated cells. Thus, the expression of the cytotoxicity and the mutagenicity associated with m6G in the DNA of V79 cells occurred by quite different mechanisms. PMID:6951203

  11. Bacterial Stationary-State Mutagenesis and Mammalian Tumorigenesis as Stress-Induced Cellular Adaptations and the Role of Epigenetics

    OpenAIRE

    Karpinets, TV; Greenwood, DJ; Pogribny, IP; Samatova, NF

    2006-01-01

    Mechanisms of cellular adaptation may have some commonalities across different organisms. Revealing these common mechanisms may provide insight in the organismal level of adaptation and suggest solutions to important problems related to the adaptation. An increased rate of mutations, referred as the mutator phenotype, and beneficial nature of these mutations are common features of the bacterial stationary-state mutagenesis and of the tumorigenic transformations in mammalian cells. We argue th...

  12. Incorporation of a lambda phage recombination system and EGFP detection to simplify mutagenesis of Herpes simplex virus bacterial artificial chromosomes

    OpenAIRE

    Weir Jerry P; Schmeisser Falko

    2007-01-01

    Abstract Background Targeted mutagenesis of the herpesvirus genomes has been facilitated by the use of bacterial artificial chromosome (BAC) technology. Such modified genomes have potential uses in understanding viral pathogenesis, gene identification and characterization, and the development of new viral vectors and vaccines. We have previously described the construction of a herpes simplex virus 2 (HSV-2) BAC and the use of an allele replacement strategy to construct HSV-2 recombinants. Whi...

  13. SiteFind: A software tool for introducing a restriction site as a marker for successful site-directed mutagenesis

    OpenAIRE

    Evans Paul M; Liu Chunming

    2005-01-01

    Abstract Background Site-directed mutagenesis is a widely-used technique for introducing mutations into a particular DNA sequence, often with the goal of creating a point mutation in the corresponding amino acid sequence but otherwise leaving the overall sequence undisturbed. However, this method provides no means for verifying its success other than sequencing the putative mutant construct: This can quickly become an expensive method for screening for successful mutations. An alternative to ...

  14. Site-directed mutagenesis of lysine 193 in Escherichia coli isocitrate lyase by use of unique restriction enzyme site elimination.

    OpenAIRE

    Diehl, P; McFadden, B A

    1993-01-01

    By a newly developed double-stranded mutagenesis technique, histidine (H), glutamate (E), arginine (R) and leucine (L) have been substituted for the lysyl 193 residue (K-193) in isocitrate lyase from Escherichia coli. The substitutions for this residue, which is present in a highly conserved, cationic region, significantly affect both the Km for Ds-isocitrate and the apparent kcat of isocitrate lyase. Specifically, the conservative substitutions, K-193-->H (K193H) and K193R, reduce catalytic ...

  15. Identification of New Genes Involved in the Virulence of Listeria monocytogenes by Signature-Tagged Transposon Mutagenesis

    OpenAIRE

    Autret, Nicolas; Dubail, Iharilalao; Trieu-Cuot, Patrick; Berche, Patrick; Charbit, Alain

    2001-01-01

    Listeria monocytogenes is a gram-positive, facultative intracellular pathogen that can cause severe food-born infections in humans and animals. We have adapted signature-tagged transposon mutagenesis to L. monocytogenes to identify new genes involved in virulence in the murine model of infection. We used transposon Tn1545 carried on the integrative vector pAT113. Forty-eight tagged transposons were constructed and used to generate banks of L. monocytogenes mutants. Pools of 48 mutants were as...

  16. Identification of the genes affecting the regulation of riboflavin synthesis in the flavinogenic yeast Pichia guilliermondii using insertion mutagenesis

    OpenAIRE

    Boretsky, Yuriy R.; Pynyaha, Yuriy V.; Boretsky, Volodymyr Y.; Fedorovych, Dariya V.; Fayura, Lyubov R.; Protchenko, Olha; Philpott, Caroline C.; Andriy A Sibirny

    2011-01-01

    Pichia guilliermondii is a representative of a group of so-called flavinogenic yeast species that overproduce riboflavin (vitamin B2) in response to iron limitation. Using insertion mutagenesis, we isolated P. guilliermondii mutants overproducing riboflavin. Analysis of nucleotide sequence of recombination sites revealed that insertion cassettes integrated into the genome disrupting P. guilliermondii genes similar to the VMA1 gene of Ashbya gossypii and Saccharomyces cerevisiae and FES1 and F...

  17. Enhancement of antiviral activity of collectin trimers through cross-linking and mutagenesis of the carbohydrate recognition domain

    DEFF Research Database (Denmark)

    White, Mitchell R; Boland, Patrick; Tecle, Tesfaldet; Gantz, Donald; Sørensen, Grith Lykke; Tornøe, Ida; Holmskov, Uffe; McDonald, Barbara; Crouch, Erika C; Hartshorn, Kevan L

    2010-01-01

    Surfactant protein D (SP-D) plays important roles in innate defense against respiratory viruses [including influenza A viruses (IAVs)]. Truncated trimers composed of its neck and carbohydrate recognition domains (NCRDs) bind various ligands; however, they have minimal inhibitory activity for IAV......, complementary strategies, namely cross-linking of NCRDs through various means and mutagenesis of CRD residues to increase viral binding. These findings may be relevant for antiviral therapy....

  18. Development of an Asymbiotic Reference Line for Pea cv. Bohatýr by De Novo Mutagenesis

    Czech Academy of Sciences Publication Activity Database

    Novák, Karel; Šlajs, Martin; Biedermannová, Eva; Vondrys, Josef

    2005-01-01

    Roč. 45, - (2005), s. 1837-1843. ISSN 0011-183X R&D Projects: GA ČR GA521/00/0937; GA ČR GA521/03/0192 Institutional research plan: CEZ:AV0Z50200510 Keywords : mutagenesis * bohatýr * nitrogen fixation Subject RIV: EE - Microbiology, Virology Impact factor: 0.925, year: 2005

  19. Studies of the in vitro selection of novel disease resistant plants and mutagenesis of cultured cells

    International Nuclear Information System (INIS)

    Plants of Brassica napus ssp. oleifera cv Primor which had been regenerated from secondary embryoids were found to be more susceptible to Leptosphaeria maculans than those grown from seed, but were generally more resistant to Alternaria brassicicola. In vitro selection of secondary embryoids on medium containing toxic filtrates of A. brassicicola did not result in significantly higher levels of resistance to the pathogen, and in the case of L. maculans, the plants were found to be more susceptible after the selection steps. When tissues were challenged with pycnidiospores of L. maculans it was possible to define growth conditions in which differential reactions correlated with in vivo responses. Studies on in vitro mutagenesis revealed that low doses of gamma rays enhanced the production of anther embryoids, although, whereas both gamma and X-rays reduced the regeneration capacity of treated tissues, irradiation with UV did not. Increased resistance to A. brassicicola was detected in doubled haploid plants following a seed treatment with EMS and from microspore culture following UV irradiation. In vitro studies of Helianthus annuus and Macrophomina phaseolina, and Zea mays and Fusarium moniliforme are also reported. (author). 28 refs, 2 figs, 2 tabs

  20. Insertional Mutagenesis Identifies a STAT3/Arid1b/β-catenin Pathway Driving Neurofibroma Initiation

    Directory of Open Access Journals (Sweden)

    Jianqiang Wu

    2016-03-01

    Full Text Available To identify genes and signaling pathways that initiate Neurofibromatosis type 1 (NF1 neurofibromas, we used unbiased insertional mutagenesis screening, mouse models, and molecular analyses. We mapped an Nf1-Stat3-Arid1b/β-catenin pathway that becomes active in the context of Nf1 loss. Genetic deletion of Stat3 in Schwann cell progenitors (SCPs and Schwann cells (SCs prevents neurofibroma formation, decreasing SCP self-renewal and β-catenin activity. β-catenin expression rescues effects of Stat3 loss in SCPs. Importantly, P-STAT3 and β-catenin expression correlate in human neurofibromas. Mechanistically, P-Stat3 represses Gsk3β and the SWI/SNF gene Arid1b to increase β-catenin. Knockdown of Arid1b or Gsk3β in Stat3fl/fl;Nf1fl/fl;DhhCre SCPs rescues neurofibroma formation after in vivo transplantation. Stat3 represses Arid1b through histone modification in a Brg1-dependent manner, indicating that epigenetic modification plays a role in early tumorigenesis. Our data map a neural tumorigenesis pathway and support testing JAK/STAT and Wnt/β-catenin pathway inhibitors in neurofibroma therapeutic trials.