mRNA processing in mutant zebrafish lines generated by chemical and CRISPR-mediated mutagenesis produces unexpected transcripts that escape nonsense-mediated decay.

Directory of Open Access Journals (Sweden)

Jennifer L Anderson

2017-11-01

Full Text Available As model organism-based research shifts from forward to reverse genetics approaches, largely due to the ease of genome editing technology, a low frequency of abnormal phenotypes is being observed in lines with mutations predicted to lead to deleterious effects on the encoded protein. In zebrafish, this low frequency is in part explained by compensation by genes of redundant or similar function, often resulting from the additional round of teleost-specific whole genome duplication within vertebrates. Here we offer additional explanations for the low frequency of mutant phenotypes. We analyzed mRNA processing in seven zebrafish lines with mutations expected to disrupt gene function, generated by CRISPR/Cas9 or ENU mutagenesis methods. Five of the seven lines showed evidence of altered mRNA processing: one through a skipped exon that did not lead to a frame shift, one through nonsense-associated splicing that did not lead to a frame shift, and three through the use of cryptic splice sites. These results highlight the need for a methodical analysis of the mRNA produced in mutant lines before making conclusions or embarking on studies that assume loss of function as a result of a given genomic change. Furthermore, recognition of the types of adaptations that can occur may inform the strategies of mutant generation.

Gel shift analysis of the empA promoter region in Vibrio anguillarum

Directory of Open Access Journals (Sweden)

Denkin Steven M

2004-10-01

Full Text Available Abstract Background The induction of metalloprotease encoded by empA in Vibrio anguillarum occurs at high cell density in salmon intestinal mucus. Previously we have shown that there are significant differences in empA expression in two strains of V. anguillarum, M93Sm and NB10. It is hypothesized that differences in empA regulation are due to differences in binding of regulatory elements. Results Two strains of V. anguillarum, M93Sm and NB10, were examined and compared for the presence of DNA regulatory proteins that bind to and control the empA promoter region. Gel mobility shift assays, using a digoxigenin (DIG-labeled oligomer containing a lux box-like element and the promoter for empA, were done to demonstrate the presence of a DNA-binding protein. Protein extracts from NB10 cells incubated in Luria Bertani broth + 2% NaCl (LB20, nine salts solution + 200 μg/ml mucus (NSSM, 3M (marine minimal medium, or NSS resulted in a gel mobility shift. No gel mobility shift was seen when protein extracts from either LB20- or NSSM-grown M93Sm cells were mixed with the DIG-labeled empA oligomer. The azocasein assay detected protease activity in all incubation conditions for NB10 culture supernatants. In contrast, protease activity was detected in M93Sm culture supernatants only when incubated in NSSM. Since the luxR homologue in V. anguillarum, vanT, has been cloned, sequenced, and shown to be required for protease activity, we wanted to determine if vanT mutants of NB10 exhibit the same gel shift observed in the wild-type. Site-directed mutagenesis was used to create vanT mutants in V. anguillarum M93Sm and NB10 to test whether VanT is involved with the gel mobility shift. Both vanT mutants, M02 and NB02, did not produce protease activity in any conditions. However, protein extracts from NB02 incubated in each condition still exhibited a gel shift when mixed with the DIG-labeled empA oligomer. Conclusions The data demonstrate that protein extracts of V

Modification of Antibody Function by Mutagenesis.

Science.gov (United States)

Dasch, James R; Dasch, Amy L

2017-09-01

The ability to "fine-tune" recombinant antibodies by mutagenesis separates recombinant antibodies from hybridoma-derived antibodies because the latter are locked with respect to their properties. Recombinant antibodies can be modified to suit the application: Changes in isotype, format (e.g., scFv, Fab, bispecific antibodies), and specificity can be made once the heavy- and light-chain sequences are available. After immunoglobulin heavy and light chains for a particular antibody have been cloned, the binding site-namely, the complementarity determining regions (CDR)-can be manipulated by mutagenesis to obtain antibody variants with improved properties. The method described here is relatively simple, uses commercially available reagents, and is effective. Using the pComb3H vector, a commercial mutagenesis kit, PfuTurbo polymerase (Agilent), and two mutagenic primers, a library of phage with mutagenized heavy and light CDR3 can be obtained. © 2017 Cold Spring Harbor Laboratory Press.

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. © 2016. Published by The Company of Biologists Ltd.

Characterization of Oblique Dual Frame Pairs

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Christensen Ole

2006-01-01

Full Text Available Given a frame for a subspace of a Hilbert space , we consider all possible families of oblique dual frame vectors on an appropriately chosen subspace . In place of the standard description, which involves computing the pseudoinverse of the frame operator, we develop an alternative characterization which in some cases can be computationally more efficient. We first treat the case of a general frame on an arbitrary Hilbert space, and then specialize the results to shift-invariant frames with multiple generators. In particular, we present explicit versions of our general conditions for the case of shift-invariant spaces with a single generator. The theory is also adapted to the standard frame setting in which the original and dual frames are defined on the same space.

umuC-mediated misrepair mutagenesis in Escherichia coli: Extent and specificity of SOS mutagenesis

International Nuclear Information System (INIS)

Shinoura, Y.; Ise, T.; Kato, T.; Glickman, B.W.

1983-01-01

The role of the error-prone misrepair pathway in mutagenesis was examined for a series of mutagens in umuC + and umuC36 strains of Escherichia coli. Mutagenesis by ENU, MNU, MNNG and EMS was independent of the umuC + gene function, while mutagenesis by MMS, 4NQO, γ-rays and UV was largely umuC + -dependent. Residual mutagenesis following UV-treatment of a umuC - strain showed the same mutational specificity seen in the umuC + strain. In contrast, the umuC mutation altered specificity substantially in an excision-repair-defective strain that showed a UV-spectrum strikingly different from that seen in an excision-repair-proficient strain. Only one of nine trpE frameshift mutations examined was reverted by UV-light and its reversion was umuC-dependent. In comparison, the dependence of frameshift mutagenesis following ICR191 treatment was site-specific, suggesting at least two mechanisms of frameshift mutagenesis, one dependent upon misrepair, the other not. (orig./AJ)

Transitions in students’ epistemic framing along two axes

Directory of Open Access Journals (Sweden)

Paul W. Irving

2013-04-01

Full Text Available We use epistemological framing to interpret participants’ behavior during group problem-solving sessions in an intermediate mechanics course. We are interested in how students frame discussion and in how the groups shift discussion framings. Our analysis includes two framing axes, expansive vs narrow and serious vs silly, which together incorporate and extend prior work on how students frame discussions in physics education research. We present markers for where discussion falls on these axes. We support our conclusions with both microanalytic excerpts of discussion and overall analysis of 75 hours of video-based data. We find that the group spends most of its time in more serious framings, and slightly more than half of its time in more narrow ones. The teaching assistant is the participant who initiates the largest number of frame shifts, and her shifts include bids to all quadrants in the expansive or narrow and serious or silly plane.

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.

Suppression of radiation mutagenesis by dactinomycin in Chinese hamster cells

International Nuclear Information System (INIS)

Tokita, N.; Capenter, S.G.; Chen, D.J.; MacInnes, M.A.; Raju, M.R.

1985-01-01

Dactinomycin (AMD) suppression of radiation mutagenesis was investigated using an in vitro mutation assay (6-thioguanine resistance) in Chinese hamster ovary cells. Cells were exposed to acute single doses of x rays followed by 1 hr-treatment with 0.1 or 1 μg/ml AMD. The cell survival curves plotted as a function of x-ray doses were similar for radiation alone and radiation plus AMD. The results suggest that AMD treatment was only slightly mutagenic, however, when given immediately after irradiation, it suppressed radiatiion mutagenesis at higher x-ray dose regions (below 10% survival levels). Higher AMD concentrations appeared more suppressive than lower concentrations. Dose-response data analyzed based on Poisson distribution models suggest the stochastic dependence of x-ray mutagenesis and AMD cytotoxity

Chemical and UV Mutagenesis.

Science.gov (United States)

Bose, Jeffrey L

2016-01-01

The ability to create mutations is an important step towards understanding bacterial physiology and virulence. While targeted approaches are invaluable, the ability to produce genome-wide random mutations can lead to crucial discoveries. Transposon mutagenesis is a useful approach, but many interesting mutations can be missed by these insertions that interrupt coding and noncoding sequences due to the integration of an entire transposon. Chemical mutagenesis and UV-based random mutagenesis are alternate approaches to isolate mutations of interest with the potential of only single nucleotide changes. Once a standard method, difficulty in identifying mutation sites had decreased the popularity of this technique. However, thanks to the recent emergence of economical whole-genome sequencing, this approach to making mutations can once again become a viable option. Therefore, this chapter provides an overview protocol for random mutagenesis using UV light or DNA-damaging chemicals.

[Stress-induced cellular adaptive mutagenesis].

Science.gov (United States)

Zhu, Linjiang; Li, Qi

2014-04-01

The adaptive mutations exist widely in the evolution of cells, such as antibiotic resistance mutations of pathogenic bacteria, adaptive evolution of industrial strains, and cancerization of human somatic cells. However, how these adaptive mutations are generated is still controversial. Based on the mutational analysis models under the nonlethal selection conditions, stress-induced cellular adaptive mutagenesis is proposed as a new evolutionary viewpoint. The hypothetic pathway of stress-induced mutagenesis involves several intracellular physiological responses, including DNA damages caused by accumulation of intracellular toxic chemicals, limitation of DNA MMR (mismatch repair) activity, upregulation of general stress response and activation of SOS response. These responses directly affect the accuracy of DNA replication from a high-fidelity manner to an error-prone one. The state changes of cell physiology significantly increase intracellular mutation rate and recombination activity. In addition, gene transcription under stress condition increases the instability of genome in response to DNA damage, resulting in transcription-associated DNA mutagenesis. In this review, we summarize these two molecular mechanisms of stress-induced mutagenesis and transcription-associated DNA mutagenesis to help better understand the mechanisms of adaptive mutagenesis.

Cultural Frame Switching and Emotion among Mexican Americans

Science.gov (United States)

Kreitler, Crystal Mata; Dyson, Kara S.

2016-01-01

Recent evidence indicates that bicultural individuals shift between interpretive frames rooted in different cultures in response to cues encountered in a given situation. The explanation for these shifts has been labeled "cultural frame switching." The current research sought to investigate the effect of priming culture among Mexican…

Mechanisms of umuC-dependent mutagenesis

International Nuclear Information System (INIS)

Kato, Takeji; Kitagawa, Yoshinori

1985-01-01

Present status of studies on umcDC genes-induced mutagenesis is introduced. Specificity of umuCD-dependent and -independent base substitution and frameshift mutagenesis is presented. Biochemical examinations of U.V.-induced umuCD gene function are described. Previous studies suggest that umuCD genes are induced by SOS inhibitory systems, that gene products are directly responsible for mutagenesis, that base substitution is largely involved in inducible mutagenesis, and that many of frameshifts are induced irrespective of gene function. (Namekawa, K.)

A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome

DEFF Research Database (Denmark)

Clendenning, Mark; Senter, Leigha; Hampel, Heather

2008-01-01

BACKGROUND: When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (Lynch syndrome cases...... on immunohistochemical analysis. RESULTS: We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n=61). These individuals all display the rare allele (population...... are caused by PMS2. This disparity is primarily due to complications in the study of this gene caused by interference from pseudogene sequences. METHODS: Using a recently developed method for detecting PMS2 specific mutations, we have screened 99 patients who are likely candidates for PMS2 mutations based...

A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome

DEFF Research Database (Denmark)

Clendenning, Mark; Senter, Leigha; Hampel, Heather

2008-01-01

BACKGROUND: When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (Lynch syndrome cases...... on immunohistochemical analysis. RESULTS: We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n=61). These individuals all display the rare allele (population...... and Swedish ancestry. We estimate that there are >10,000 carriers of this mutation in the United States alone. The identification of both the mutation and the common haplotype in one Swedish control sample (n = 225), along with evidence that Lynch syndrome associated cancers are rarer than expected...

Buckling collapse analysis of framed structures by using adaptively shifted integration technique. Junnogata shifted intergration ho ni yoru honegumi kozo no zakutsu hokai kaiseki

Energy Technology Data Exchange (ETDEWEB)

Toi, Y.; Isobe, D. (The University of Tokyo, Tokyo (Japan). Institute of Industrial Science)

1993-09-01

This paper describes the following matters on application of an adaptively shifted integration technique to a buckling collapse analysis of framed structures: This method is a method in a finite element analysis using three-dimensional girder elements to arrange value integration points at optimal locations in a linear analysis if the elements are in an elastic transform condition on the whole. The method then moves the value integration points so that plastic hinge will occur in these locations immediately after part of the elements has yielded. The method was applied to analyzing an elastic buckling problem in several loading patterns for either a both-end supported or a one-end fixed beam member. A result was obtained that a number of elements required for one member is four at minimum. In a buckling analysis of framed structures, a satisfactory result was obtained by using an automatic element segmenting algorithm, which begins the analysis with one element one member, and immediately after a member is determined with a possibility of generation of buckling, splits that member only into four elements. 6 refs., 5 figs.

Interacting Regional-Scale Regime Shifts for Biodiversity and Ecosystem Services

NARCIS (Netherlands)

Leadley, P.; Proenca, V.; Fernandez-Manjarres, J.; Pereira, H.M.; Alkemade, J.R.M.; Biggs, R.; Bruley, E.; Cheung, W.; Cooper, D.; Figueiredo, J.; Gilman, E.; Guenette, S.; Hurtt, G.; Mbow, C.; Oberdorff, T.; Revenga, C.; Scharlemann, J.P.W.; Scholes, R.; Smith, M.S.; Sumaila, U.R.; Walpole, M.

2014-01-01

Current trajectories of global change may lead to regime shifts at regional scales, driving coupled human-environment systems to highly degraded states in terms of biodiversity, ecosystem services, and human well-being. For business-as-usual socioeconomic development pathways, regime shifts are

Dynamic frame selection for in vivo ultrasound temperature estimation during radiofrequency ablation

International Nuclear Information System (INIS)

Daniels, Matthew J; Varghese, Tomy

2010-01-01

Minimally invasive therapies such as radiofrequency ablation have been developed to treat cancers of the liver, prostate and kidney without invasive surgery. Prior work has demonstrated that ultrasound echo shifts due to temperature changes can be utilized to track the temperature distribution in real time. In this paper, a motion compensation algorithm is evaluated to reduce the impact of cardiac and respiratory motion on ultrasound-based temperature tracking methods. The algorithm dynamically selects the next suitable frame given a start frame (selected during the exhale or expiration phase where extraneous motion is reduced), enabling optimization of the computational time in addition to reducing displacement noise artifacts incurred with the estimation of smaller frame-to-frame displacements at the full frame rate. A region of interest that does not undergo ablation is selected in the first frame and the algorithm searches through subsequent frames to find a similarly located region of interest in subsequent frames, with a high value of the mean normalized cross-correlation coefficient value. In conjunction with dynamic frame selection, two different two-dimensional displacement estimation algorithms namely a block matching and multilevel cross-correlation are compared. The multi-level cross-correlation method incorporates tracking of the lateral tissue expansion in addition to the axial deformation to improve the estimation performance. Our results demonstrate the ability of the proposed motion compensation using dynamic frame selection in conjunction with the two-dimensional multilevel cross-correlation to track the temperature distribution.

What's in a word? The framing of health at the regional level: ASEAN, EU, SADC and UNASUR.

Science.gov (United States)

Amaya, Ana B; Rollet, Vincent; Kingah, Stephen

2015-12-01

The Association of Southeast Asian Nations, the European Union, the Southern African Development Community and the Union of South American Nations have increasingly been involved in health diplomacy in the past decade, yet little is known about how they frame health as a foreign policy issue and how this has an impact on their prioritisation of policies. For this, we conducted a review of existing grey and peer-reviewed literature that address regional integration and health, as well as a documentary review according to security, development, trade, human rights, moral/ethical reasonings and global public goods frames identified in the literature. The policy frames identified responded to the challenges these regions currently face. The Association of Southeast Asian Nation's struggle with re-emerging diseases has led to favouring a securitisation approach to health, the European Union approaches health as a cross-cutting policy issue, the Southern African Development Community presents health as a driver for development, and while the Union of South American Nations emphasises health as a human right and addresses the social determinants of health as an ethical imperative. Overall, these policy frames were useful in analysing the framing of health in foreign policy at the regional level. However, within our analysis, we identified a new frame that approaches health as an intersectoral issue. The impact of regional organisations' forward will depend on their ability to harness their convening power and speak in a coherent voice on health matters.

Ultraviolet light protection, enhancement of ultraviolet light mutagenesis, and mutator effect of plasmid R46 in Salmonella typhimurium

International Nuclear Information System (INIS)

Mortelmans, K.E.; Stocker, B.A.D.

1976-01-01

Plasmid R46 partially protected Salmonella typhimurium, wild type or uvrB or polA, against the lethal effect of ultraviolet (uv) irradiation, but did not protect recA mutants. The plasmid also increased frequency of uv-induced reversion to His + in all tested his point mutants (wild type for uv sensitivity), including amber, ochre, UGA, missense, and frame-shift mutants. Plasmid R46 also increased uv-induced reversion to His + in uvrB and polA strains, but no uv mutagenic effect was detected in R - or R46-carrying recA derivatives of a his(amber) mutant. The spontaneous reversion frequency of his nonsense mutants of all classes, and of some his missense mutants, was increased about 10-fold when the strains carried R46, but the plasmid had no effect on the spontaneous reversion frequency of some other his missense mutations or of reversion rate of his frame-shift mutants (except for two uvrB derivatives of one single-base insertion mutant). The plasmid increased the ability of wild type, polA, and uvrB hosts to support plaque production by uv-irradiated phage, and made strain LT2 his G46 less sensitive to methyl methane sulfonate and to x rays and more responsive to the mutagenic effect of visible-light irradiation. R46 increased spontaneous reversion frequency of a his(amber) rec + strain, but had no such effect in its recA sublines. Since the plasmid in the absence of host recA function fails to produce its mutator effect, or to confer uv protection or to enhance uv mutagenesis, these three effects may be produced via some mechanism involved in recA-dependent deoxyribonucleic acid repair, perhaps by an increase in activity of the ''error-prone'' component of the inducible repair pathway

Transitions in Students' Epistemic Framing along Two Axes

Science.gov (United States)

Irving, Paul W.; Martinuk, Mathew Sandy; Sayre, Eleanor C.

2013-01-01

We use epistemological framing to interpret participants' behavior during group problem-solving sessions in an intermediate mechanics course. We are interested in how students frame discussion and in how the groups shift discussion framings. Our analysis includes two framing axes, expansive vs narrow and serious vs silly, which together…

Forward and reverse mutagenesis in C. elegans

Science.gov (United States)

Kutscher, Lena M.; Shaham, Shai

2014-01-01

Mutagenesis drives natural selection. In the lab, mutations allow gene function to be deciphered. C. elegans is highly amendable to functional genetics because of its short generation time, ease of use, and wealth of available gene-alteration techniques. Here we provide an overview of historical and contemporary methods for mutagenesis in C. elegans, and discuss principles and strategies for forward (genome-wide mutagenesis) and reverse (target-selected and gene-specific mutagenesis) genetic studies in this animal. PMID:24449699

Population genetical investigation of the level of mutagenesis and teratological events frequency in ecologically different regions of Kazakhstan

International Nuclear Information System (INIS)

Kashaganova, Zh.A.; Zhapbasov, R.; Kadyrova, N.Zh.; Karimbaeva, K.S.; Mamyrbaeva, A.N.; Altaeva, N.Z.

2008-01-01

Full text: Kazakhstan territory is unique including regions with radioactive pollution of Semipalatinsk nuclear test territory and storage of radioactive waste of uranium mines and metallurgy enterprises, and regions of drying Aral sea. These technogenic factors may cause some types of chromosome aberrations and developmental anomalies in mammals. The level of mutagenesis was estimated basing on chromosome aberrations and genomic mutation frequencies in bone marrow cells of natural rodents populations (Allactaga major Kern, Allactaga saltator Eversman, Cytellus eritrogenus Br.) and domestic animals (sheep, cattle, horse), which inhabit these regions. Sheep populations which are bred in the regions with different climatic conditions were used for teratological investigations. Different generations are met in the populations of mice family rodents caught in the nature. So studying the animals of different ages separately we can estimate the frequency of mutations in the animals of different age inhabiting the same radiation polluted regions. The frequency of chromosome abe rations in mice family rodents from such territories was twice as high as from the clear territories. In some animals chromosome aberration types characteristic for radiation mutagenesis (dicentrics, double acentric fragments) were found. High level of cytogenetical instability in somatic cells of agricultural animals which were bred on the pastures within former nuclear test territories for several generations may be caused by chronic radiation in low doses. The analysis of the spectrum of recorder chromosome aberrations in somatic cells and their dynamics in different animal species inhabiting for several generations these territories being chronically irradiated, allows us to investigate the direction of genetical evolution of mammals genofond structure induced by ecological factors. Comparative analysis of the frequencies of spontaneous abortuses, deadborn and newborn animals with innate

Theories of Lethal Mutagenesis: From Error Catastrophe to Lethal Defection.

Science.gov (United States)

Tejero, Héctor; Montero, Francisco; Nuño, Juan Carlos

2016-01-01

RNA viruses get extinct in a process called lethal mutagenesis when subjected to an increase in their mutation rate, for instance, by the action of mutagenic drugs. Several approaches have been proposed to understand this phenomenon. The extinction of RNA viruses by increased mutational pressure was inspired by the concept of the error threshold. The now classic quasispecies model predicts the existence of a limit to the mutation rate beyond which the genetic information of the wild type could not be efficiently transmitted to the next generation. This limit was called the error threshold, and for mutation rates larger than this threshold, the quasispecies was said to enter into error catastrophe. This transition has been assumed to foster the extinction of the whole population. Alternative explanations of lethal mutagenesis have been proposed recently. In the first place, a distinction is made between the error threshold and the extinction threshold, the mutation rate beyond which a population gets extinct. Extinction is explained from the effect the mutation rate has, throughout the mutational load, on the reproductive ability of the whole population. Secondly, lethal defection takes also into account the effect of interactions within mutant spectra, which have been shown to be determinant for the understanding the extinction of RNA virus due to an augmented mutational pressure. Nonetheless, some relevant issues concerning lethal mutagenesis are not completely understood yet, as so survival of the flattest, i.e. the development of resistance to lethal mutagenesis by evolving towards mutationally more robust regions of sequence space, or sublethal mutagenesis, i.e., the increase of the mutation rate below the extinction threshold which may boost the adaptability of RNA virus, increasing their ability to develop resistance to drugs (including mutagens). A better design of antiviral therapies will still require an improvement of our knowledge about lethal

Protracted radiation mutagenesis

International Nuclear Information System (INIS)

Dubinina, L.G.; Shanazarova, A.S.; Chernikova, O.P.

1976-01-01

The aim of the work is investigation of the dynamics of structural mutations of Cr.capillaris chromosomes induced by irradiation of seeds at different stages of the cell cycle with subsequent storage. The results obtained show that irradiation is followed by mutagenesis wave kinetics under such conditions. The level and the character of this phenomenon depends on the functional state of the nucleus or on the relationship between this state and the amount of water in the seeds. Studies of this phenomenon will bring better understanding to the mechanism of radiation mutagenesis [ru

Ethyl methanesulfonate mutagenesis in Schizosaccharomyces pombe

DEFF Research Database (Denmark)

Ekwall, Karl; Thon, Genevieve

2017-01-01

Here we provide an ethyl methanesulfonate (EMS) mutagenesis protocol for Schizosaccharomyces pombe cells.......Here we provide an ethyl methanesulfonate (EMS) mutagenesis protocol for Schizosaccharomyces pombe cells....

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

Science.gov (United States)

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

2017-04-01

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

Optogenetic mutagenesis in Caenorhabditis elegans.

Science.gov (United States)

Noma, Kentaro; Jin, Yishi

2015-12-03

Reactive oxygen species (ROS) can modify and damage DNA. Here we report an optogenetic mutagenesis approach that is free of toxic chemicals and easy to perform by taking advantage of a genetically encoded ROS generator. This method relies on the potency of ROS generation by His-mSOG, the mini singlet oxygen generator, miniSOG, fused to a histone. Caenorhabditis elegans expressing His-mSOG in the germline behave and reproduce normally, without photoinduction. Following exposure to blue light, the His-mSOG animals produce progeny with a wide range of heritable phenotypes. We show that optogenetic mutagenesis by His-mSOG induces a broad spectrum of mutations including single-nucleotide variants (SNVs), chromosomal deletions, as well as integration of extrachromosomal transgenes, which complements those derived from traditional chemical or radiation mutagenesis. The optogenetic mutagenesis expands the toolbox for forward genetic screening and also provides direct evidence that nuclear ROS can induce heritable and specific genetic mutations.

An introduction to frames and Riesz bases

CERN Document Server

Christensen, Ole

2016-01-01

This revised and expanded monograph presents the general theory for frames and Riesz bases in Hilbert spaces as well as its concrete realizations within Gabor analysis, wavelet analysis, and generalized shift-invariant systems.  Compared with the first edition, more emphasis is put on explicit constructions with attractive properties.  Based on the exiting development of frame theory over the last decade, this second edition now includes new sections on the rapidly growing fields of LCA groups, generalized shift-invariant systems, duality theory for as well Gabor frames as wavelet frames, and open problems in the field.   Key features include: *Elementary introduction to frame theory in finite-dimensional spaces * Basic results presented in an accessible way for both pure and applied mathematicians * Extensive exercises make the work suitable as a textbook for use in graduate courses * Full proofs includ ed in introductory chapters; only basic knowledge of functional analysis required * Explicit constructi...

Mutagenesis: Interactions with a parallel universe.

Science.gov (United States)

Miller, Jeffrey H

Unexpected observations in mutagenesis research have led to a new perspective in this personal reflection based on years of studying mutagenesis. Many mutagens have been thought to operate via a single principal mechanism, with secondary effects usually resulting in only minor changes in the observed mutation frequencies and spectra. For example, we conceive of base analogs as resulting in direct mispairing as their main mechanism of mutagenesis. Recent studies now show that in fact even these simple mutagens can cause very large and unanticipated effects both in mutation frequencies and in the mutational spectra when used in certain pair-wise combinations. Here we characterize this leap in mutation frequencies as a transport to an alternate universe of mutagenesis. Copyright © 2018 Elsevier B.V. All rights reserved.

Mechanisms of uv mutagenesis in yeast

International Nuclear Information System (INIS)

Lawrence, C.W.; Christensen, R.; Schwartz, A.

1982-01-01

The uv mutagenesis in yeast depends on the function of the RAD6 locus, a gene that is also responsible for a substantial fraction of wild-type resistance, suggesting that this eukaryote may possess a misrepair mechanism analogous to that proposed for Escherichia coli. The molecular mechanism responsible for RAD6 repair or recovery is not yet known, but it is different from either excision or recombination-dependent repair, processes carried out by the other two main repair pathways in yeast. RAD6-dependent mutagenesis has been found to have the following characteristics. It is associated at best with only a small fraction of RAD6-dependent repair, the majority of the sensitivity of rad6 mutants being due to their lack of nonmutagenic repair. SRS2 metabolic suppressors restore a substantial fraction of uv resistance to rad6 mutants but do not restore their uv mutability. Strains containing mutations at loci (rev, umr) that are probably more directly involved in mutagenesis are only mildly sensitive, and there is a poor correlation between their sensitivity and mutational deficiency. The uv mutagenesis appears to require a large number of gene functions, perhaps ten or more. Where examined in detail, these genes have been found to be concerned in the production of only a specific range of mutational events, not all of them. Mating experiments have shown that a substantial fraction, probably 40% or more, of uv-induced mutations are untargeted, that is, occur in lesion-free regions of DNA. The uv irradiation, therefore, produces a general reduction in the normally high fidelity with which DNA is replicated on undamaged templates. It does not appear to be necessary for the causal lesion to be present in the same chromosome as the mutation it induces. The reduction in fidelity may be the consequence of the production of a diffusible factor in uv-irradiated cells, but definite evidence supporting this proposal has not yet been obtained

Receptor mutagenesis strategies for examination of structure-function relationships

NARCIS (Netherlands)

Blomenröhr, Marion; Vischer, Henry F; Bogerd, Jan

2004-01-01

This chapter describes three different strategies of receptor mutagenesis with their advantages, disadvantages, and limitations. Oligonucleotide-directed mutagenesis using either the Altered Sites II in vitro mutagenesis system or the GeneTailor site-directed mutagenesis system can generate base

What’s in a word? The framing of health at the regional level: ASEAN, EU, SADC and UNASUR

Science.gov (United States)

Amaya, Ana B; Rollet, Vincent; Kingah, Stephen

2015-01-01

The Association of Southeast Asian Nations, the European Union, the Southern African Development Community and the Union of South American Nations have increasingly been involved in health diplomacy in the past decade, yet little is known about how they frame health as a foreign policy issue and how this has an impact on their prioritisation of policies. For this, we conducted a review of existing grey and peer-reviewed literature that address regional integration and health, as well as a documentary review according to security, development, trade, human rights, moral/ethical reasonings and global public goods frames identified in the literature. The policy frames identified responded to the challenges these regions currently face. The Association of Southeast Asian Nation’s struggle with re-emerging diseases has led to favouring a securitisation approach to health, the European Union approaches health as a cross-cutting policy issue, the Southern African Development Community presents health as a driver for development, and while the Union of South American Nations emphasises health as a human right and addresses the social determinants of health as an ethical imperative. Overall, these policy frames were useful in analysing the framing of health in foreign policy at the regional level. However, within our analysis, we identified a new frame that approaches health as an intersectoral issue. The impact of regional organisations’ forward will depend on their ability to harness their convening power and speak in a coherent voice on health matters. PMID:26635496

Evolving artificial metalloenzymes via random mutagenesis

Science.gov (United States)

Yang, Hao; Swartz, Alan M.; Park, Hyun June; Srivastava, Poonam; Ellis-Guardiola, Ken; Upp, David M.; Lee, Gihoon; Belsare, Ketaki; Gu, Yifan; Zhang, Chen; Moellering, Raymond E.; Lewis, Jared C.

2018-03-01

Random mutagenesis has the potential to optimize the efficiency and selectivity of protein catalysts without requiring detailed knowledge of protein structure; however, introducing synthetic metal cofactors complicates the expression and screening of enzyme libraries, and activity arising from free cofactor must be eliminated. Here we report an efficient platform to create and screen libraries of artificial metalloenzymes (ArMs) via random mutagenesis, which we use to evolve highly selective dirhodium cyclopropanases. Error-prone PCR and combinatorial codon mutagenesis enabled multiplexed analysis of random mutations, including at sites distal to the putative ArM active site that are difficult to identify using targeted mutagenesis approaches. Variants that exhibited significantly improved selectivity for each of the cyclopropane product enantiomers were identified, and higher activity than previously reported ArM cyclopropanases obtained via targeted mutagenesis was also observed. This improved selectivity carried over to other dirhodium-catalysed transformations, including N-H, S-H and Si-H insertion, demonstrating that ArMs evolved for one reaction can serve as starting points to evolve catalysts for others.

Induced repair and mutagenesis in animal cells

International Nuclear Information System (INIS)

Takimoto, Koichi

1981-01-01

Induced repair and mutagenesis of animal cells against UV were studied in contrast with SOS repair of E. coli primarily by the use of viruses. Since UV-enhanced reactivation is a phenomenon similar to UV-reactivation (mutagenesis) and the presence of lesion bypass synthsis has been suggested, UV-enhanced reactivation has several common aspects with SOS reactivation of E. coli. However, correlation is not necessarily noted between increase in the viral survival rate and mutagenesis, nor do protease blockers exert any effect. Therefore, SOS repair of E. coli may have different mechansms from induced repair and mutagenesis in animal cells. (Ueda, J.)

Initial Alignment for SINS Based on Pseudo-Earth Frame in Polar Regions.

Science.gov (United States)

Gao, Yanbin; Liu, Meng; Li, Guangchun; Guang, Xingxing

2017-06-16

An accurate initial alignment must be required for inertial navigation system (INS). The performance of initial alignment directly affects the following navigation accuracy. However, the rapid convergence of meridians and the small horizontalcomponent of rotation of Earth make the traditional alignment methods ineffective in polar regions. In this paper, from the perspective of global inertial navigation, a novel alignment algorithm based on pseudo-Earth frame and backward process is proposed to implement the initial alignment in polar regions. Considering that an accurate coarse alignment of azimuth is difficult to obtain in polar regions, the dynamic error modeling with large azimuth misalignment angle is designed. At the end of alignment phase, the strapdown attitude matrix relative to local geographic frame is obtained without influence of position errors and cumbersome computation. As a result, it would be more convenient to access the following polar navigation system. Then, it is also expected to unify the polar alignment algorithm as much as possible, thereby further unifying the form of external reference information. Finally, semi-physical static simulation and in-motion tests with large azimuth misalignment angle assisted by unscented Kalman filter (UKF) validate the effectiveness of the proposed method.

The Roles of UmuD in Regulating Mutagenesis

Directory of Open Access Journals (Sweden)

Jaylene N. Ollivierre

2010-01-01

Full Text Available All organisms are subject to DNA damage from both endogenous and environmental sources. DNA damage that is not fully repaired can lead to mutations. Mutagenesis is now understood to be an active process, in part facilitated by lower-fidelity DNA polymerases that replicate DNA in an error-prone manner. Y-family DNA polymerases, found throughout all domains of life, are characterized by their lower fidelity on undamaged DNA and their specialized ability to copy damaged DNA. Two E. coli Y-family DNA polymerases are responsible for copying damaged DNA as well as for mutagenesis. These DNA polymerases interact with different forms of UmuD, a dynamic protein that regulates mutagenesis. The UmuD gene products, regulated by the SOS response, exist in two principal forms: UmuD2, which prevents mutagenesis, and UmuD2′, which facilitates UV-induced mutagenesis. This paper focuses on the multiple conformations of the UmuD gene products and how their protein interactions regulate mutagenesis.

Characterization of Oblique Dual Frame Pairs

DEFF Research Database (Denmark)

Christensen, Ole; Eldar, Yonina

2006-01-01

Given a frame for a subspace W of a Hilbert space H, we consider all possible families of oblique dual frame vectors on an appropriately chosen subspace V. In place of the standard description, which involves computing the pseudoinverse of the frame operator, we develop an alternative characteriz...... for the case of shift-invariant spaces with a single generator. The theory is also adapted to the standard frame setting in which the original and dual frames are defined on the same space. Copyright (C) 2006 Hindawi Publishing Corporation. All rights reserved.......Given a frame for a subspace W of a Hilbert space H, we consider all possible families of oblique dual frame vectors on an appropriately chosen subspace V. In place of the standard description, which involves computing the pseudoinverse of the frame operator, we develop an alternative...

Mutagenesis

International Nuclear Information System (INIS)

Dubinin, N.P.

1986-01-01

Problems on radiation mutagenesis, in particular, data on general factors of genetic radiation effects, dependences of mutation frequencies on radiation dose and threshold in genetic radiation effects, problems of low doses, modification of genetic radiation effects, repauir of injuries of genetic material, photoreactivation, causing structure chromosomal mutations under radiation action, on relative genetic efficiency of different types of radiation are considered besides others

Ambiguities in the deduction of rest frame fluctuation spectrums from spectrums computed in moving frames

International Nuclear Information System (INIS)

Fredericks, R.W.; Coroniti, F.V.

1976-01-01

The problem of interpretation of power spectrums computed by Fourier analysis of data time series taken in frames moving with respect to the medium containing the fluctuations is examined. It is found that no unique connection exists between the rest frame power spectrum as a function of scale length and the derived power spectrum as a function 'frequency' computed from the time series data taken in the moving frame. This caused by a complex Doppler-shifting phenomenon that leads to a basically aliased frequency spectrum in the moving frame. Examples of nonuniqueness are given for various types of rest frame density or wave turbulence that lead to the same frequency dependence of the power spectrum computed in the moving frame. This has implications for the past interpretations of power spectrums of density or magnetic field fluctuations from satellites or interplanetary probes

Reynolds Stress Closure for Inertial Frames and Rotating Frames

Science.gov (United States)

Petty, Charles; Benard, Andre

2017-11-01

In a rotating frame-of-reference, the Coriolis acceleration and the mean vorticity field have a profound impact on the redistribution of kinetic energy among the three components of the fluctuating velocity. Consequently, the normalized Reynolds (NR) stress is not objective. Furthermore, because the Reynolds stress is defined as an ensemble average of a product of fluctuating velocity vector fields, its eigenvalues must be non-negative for all turbulent flows. These fundamental properties (realizability and non-objectivity) of the NR-stress cannot be compromised in computational fluid dynamic (CFD) simulations of turbulent flows in either inertial frames or in rotating frames. The recently developed universal realizable anisotropic prestress (URAPS) closure for the NR-stress depends explicitly on the local mean velocity gradient and the Coriolis operator. The URAPS-closure is a significant paradigm shift from turbulent closure models that assume that dyadic-valued operators associated with turbulent fluctuations are objective.

Marching toward reproductive justice: coalitional (re) framing of the March for Women's Lives.

Science.gov (United States)

Luna, Zakiya T

2010-01-01

This article examines how coalition frames develop and what happens to that frame after the formal coalition ends. To that end, I analyze the frame shift around the 2004 March for Women's Lives (March). The March initially focused on established ideas of reproductive rights around which the four national mainstream co-sponsors previously organized. However, after a newer reproductive justice organization joined the coalition, material and organizing reflected a shift in framing to reproductive justice. How did this change happen? What are the impacts of this event for the women's movement? Through document analysis and interviews, I trace the negotiations that facilitated this framing shift. I argue that this new coalition frame translated into positive lasting changes in organizing for women's reproductive health even as the coalition dissolved and some of the tensions within the larger women's movement remain.

Directional Time-frequency Analysis via Continuous Frames

DEFF Research Database (Denmark)

Christensen, Ole; Forster, Birgitte; Massopust, Peter

2015-01-01

spaces. The first step allows us to apply the theory to several other classes of frames, for example wavelet frames and shift-invariant systems, and the second one significantly extends the class of examples and applications. We consider applications to the Meyer wavelet and complex B...

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.

Highly Efficient ENU Mutagenesis in Zebrafish.

NARCIS (Netherlands)

de Bruijn, E.; Cuppen, E.; Feitsma, H.

2009-01-01

ENU (N-ethyl-N-nitrosourea) mutagenesis is a widely accepted and proven method to introduce random point mutations in the genome. Because there are no targeted knockout strategies available for zebrafish so far, random mutagenesis is currently the preferred method in both forward and reverse genetic

Complementation of a pKM101 derivative that decreases resistance to UV killing but increases susceptibility to mutagenesis

International Nuclear Information System (INIS)

Langer, P.J.; Perry, K.L.; Walker, G.C.

1985-01-01

The drug resistance plasmid pKM101 makes Escherichia coli resistant to the lethal effects of ultraviolet (UV) irradiation and more susceptible to mutagenesis by a variety of agents. The plasmid operon responsible for increasing mutagenesis has been termed mucAB (Mutagenesis, UV and chemical). The authors have isolated a derivative of pKM101 called pGW1975 which makes cells more sensitive to killing by UV but which retains the ability of pKM101 to increase susceptibility to methyl methanesulfonate (MMS) mutagenesis. pGW1975 increases UV mutagenesis less than pKM101 in a uvrA + strain but more than pKM101 in a uvrA - strain. muc - point and insertion mutants of pKM101 and pGW1975 complement to restore the plasmid-mediated: (i) ability to reactivate UV-irradiated phage, (ii) resistance to killing by UV, and (iii) level of susceptibility to UV mutagenesis. They have identified a 2.0 kb region of pKM101 which is responsible for the complementation and which maps counterclockwise of mucAB. (Auth)

Non-targeted mutagenesis of unirradiated lambda phage in Escherichia coli

International Nuclear Information System (INIS)

Wood, R.D.; Hutchinson, F.

1984-01-01

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)

Non-targeted mutagenesis of unirradiated lambda phage in Escherichia coli

Energy Technology Data Exchange (ETDEWEB)

Wood, R.D.; Hutchinson, F. (Yale Univ., New Haven, CT (USA). Dept. of Molecular Biophysics and Biochemistry)

1984-03-05

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/sup +/ 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.

Mutagenesis and carcinogenesis resulting from environment pollution

International Nuclear Information System (INIS)

Dimitrov, B.

2001-01-01

The paper reviews different ways of environmental contamination with natural and artificial harmful substances (chemical and radioactive) and their role in the processes of mutagenesis and carcinogenesis. The recent studies of the mechanism of mutagenesis and carcinogenesis due to environmental pollution are discussed

Direct random insertion mutagenesis of Helicobacter pylori

NARCIS (Netherlands)

de Jonge, Ramon; Bakker, Dennis; van Vliet, Arnoud H. M.; Kuipers, Ernst J.; Vandenbroucke-Grauls, Christina M. J. E.; Kusters, Johannes G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

Direct random insertion mutagenesis of Helicobacter pylori.

NARCIS (Netherlands)

Jonge, de R.; Bakker, D.; Vliet, van AH; Kuipers, E.J.; Vandenbroucke-Grauls, C.M.J.E.; Kusters, J.G.

2003-01-01

Random insertion mutagenesis is a widely used technique for the identification of bacterial virulence genes. Most strategies for random mutagenesis involve cloning in Escherichia coli for passage of plasmids or for phenotypic selection. This can result in biased selection due to restriction or

A Review on Microbial Mutagenesis through Gamma Irradiation for Agricultural Applications

International Nuclear Information System (INIS)

Hoe, P.C.K.; Khairuddin Abdul Rahim

2016-01-01

Gamma irradiation is widely used in sterilization and mutagenesis, especially for plant breeding and crop protection. Microbial mutagenesis through gamma irradiation is mainly applied in fermentation industry. In agriculture, gamma irradiation is mostly applied in crop improvement. Microbial mutagenesis is mainly applied against fungus and spore-forming bacteria, which are resistant to gamma irradiation. Response of microbes to gamma irradiation varies and depends on various factors. Review of previous works on gamma irradiation for microbial mutagenesis in agriculture may provide some information for the use of this method. The general view on gamma irradiation, its application, and mutagenesis are discussed in this paper. Further investigation on microbial mutagenesis should consider molecular changes, information on which is lacking in previous works. Moreover, studies on microbial mutagenesis are still lacking in Malaysia despite having several gamma irradiation facilities. Therefore, further studies on microbial mutagenesis should be conducted. (author)

Radioprotective action of glycerol and cysteamine on inactivation and mutagenesis in Salmonella tester strains after gamma and heavy ion irradiation

International Nuclear Information System (INIS)

Basha, S.G.; Krasavin, E.A.; Kozubek, S.

1991-01-01

Inactivation and mutagenesis were studied in Salmonella tester strains after γ-irradiation and after heavy ion irradiation in the presence of glycerol and cysteamine. Bacterial cells were irradiated at Dubna, JINR. Ions from deuterons to carbon were used with residual energies 2-9 MeV/u. The protective effect of glycerol was found both for γ-radiation and for heavy ions up to 50 keV/μm for both cell inactivation and mutagenesis in Salmonella tester strains with different mutation events. Cell sensitivity slightly increased with LET before falling down. The maximum was shifted in the presence of glycerol to the left and was less pronounced. The radioprotective effect of glycerol diminished gradually with LET from 2.0 for γ-radiation to 1.1 for carbon ions. Mutagenesis increases with LET in TA100 strain; in TA98 strain no marked increase could be detected. 13 refs.; 4 figs.; 5 tabs

Application of a regional hurricane wind risk forecasting model for wood-frame houses.

Science.gov (United States)

Jain, Vineet Kumar; Davidson, Rachel Ann

2007-02-01

Hurricane wind risk in a region changes over time due to changes in the number, type, locations, vulnerability, and value of buildings. A model was developed to quantitatively estimate changes over time in hurricane wind risk to wood-frame houses (defined in terms of potential for direct economic loss), and to estimate how different factors, such as building code changes and population growth, contribute to that change. The model, which is implemented in a simulation, produces a probability distribution of direct economic losses for each census tract in the study region at each time step in the specified time horizon. By changing parameter values and rerunning the analysis, the effects of different changes in the built environment on the hurricane risk trends can be estimated and the relative effectiveness of hypothetical mitigation strategies can be evaluated. Using a case study application for wood-frame houses in selected counties in North Carolina from 2000 to 2020, this article demonstrates how the hurricane wind risk forecasting model can be used: (1) to provide insight into the dynamics of regional hurricane wind risk-the total change in risk over time and the relative contribution of different factors to that change, and (2) to support mitigation planning. Insights from the case study include, for example, that the many factors contributing to hurricane wind risk for wood-frame houses interact in a way that is difficult to predict a priori, and that in the case study, the reduction in hurricane losses due to vulnerability changes (e.g., building code changes) is approximately equal to the increase in losses due to building inventory growth. The potential for the model to support risk communication is also discussed.

Shifting College Students' Epistemological Framing Using Hypothetical Debate Problems

Science.gov (United States)

Hu, Dehui; Rebello, N. Sanjay

2014-01-01

Developing expertise in physics problem solving requires the ability to use mathematics effectively in physical scenarios. Novices and experts often perceive the use of mathematics in physics differently. Students' perceptions and how they frame the use of mathematics in physics play an important role in their physics problem solving. In this…

A frame-shift mutation of PMS2 is a widespread cause of Lynch syndrome.

Science.gov (United States)

Clendenning, M; Senter, L; Hampel, H; Robinson, K Lagerstedt; Sun, S; Buchanan, D; Walsh, M D; Nilbert, M; Green, J; Potter, J; Lindblom, A; de la Chapelle, A

2008-06-01

When compared to the other mismatch repair genes involved in Lynch syndrome, the identification of mutations within PMS2 has been limited (PMS2. This disparity is primarily due to complications in the study of this gene caused by interference from pseudogene sequences. Using a recently developed method for detecting PMS2 specific mutations, we have screened 99 patients who are likely candidates for PMS2 mutations based on immunohistochemical analysis. We have identified a frequently occurring frame-shift mutation (c.736_741del6ins11) in 12 ostensibly unrelated Lynch syndrome patients (20% of patients we have identified with a deleterious mutation in PMS2, n = 61). These individuals all display the rare allele (population frequency 10 000 carriers of this mutation in the USA alone. The identification of both the mutation and the common haplotype in one Swedish control sample (n = 225), along with evidence that Lynch syndrome associated cancers are rarer than expected in the probands' families, would suggest that this is a prevalent mutation with reduced penetrance.

Pseudo-entanglement evaluated in noninertial frames

International Nuclear Information System (INIS)

Mehri-Dehnavi, Hossein; Mirza, Behrouz; Mohammadzadeh, Hosein; Rahimi, Robabeh

2011-01-01

Research highlights: → We study pseudo-entanglement in noninertial frames. → We examine different measures of entanglement and nonclassical correlation for the state. → We find the threshold for entanglement is changed in noninertial frames. → We also describe the behavior of local unitary classes of states in noninertial frames. - Abstract: We study quantum discord, in addition to entanglement, of bipartite pseudo-entanglement in noninertial frames. It is shown that the entanglement degrades from its maximum value in a stationary frame to a minimum value in an infinite accelerating frame. There is a critical region found in which, for particular cases, entanglement of states vanishes for certain accelerations. The quantum discord of pseudo-entanglement decreases by increasing the acceleration. Also, for a physically inaccessible region, entanglement and nonclassical correlation are evaluated and shown to match the corresponding values of the physically accessible region for an infinite acceleration.

Opportunistic Market-Driven Regional Shifts of Cropping Practices Reduce Food Production Capacity of China

Science.gov (United States)

Yuan, Wenping; Liu, Shuguang; Liu, Wei; Zhao, Shuqing; Dong, Wenjie; Tao, Fulu; Chen, Min; Lin, Hui

2018-04-01

China is facing the challenge of feeding a growing population with the declining cropland and increasing shortage of water resources under the changing climate. This study identified that the opportunistic profit-driven shifts of planting areas and crop species composition have strongly reduced the food production capacity of China. First, the regional cultivation patterns of major crops in China have substantially shifted during the past five decades. Southeast and South China, the regions with abundant water resources and fewer natural disasters, have lost large planting areas of cropland in order to pursue industry and commerce. Meanwhile, Northeast and Northwest China, the regions with low water resources and frequent natural disasters, have witnessed increases in planting areas. These macroshifts have reduced the national food production by 1.02% per year. The lost grain production would have been enough to feed 13 million people. Second, the spatial shifts have been accompanied by major changes in crop species composition, with substantial increases in planting area and production of maize, due to its low water consumption and high economic returns. Consequently, the stockpile of maize in China has accounted for more than half of global stockpile, and the stock to use ratio of maize in China has exceeded the reliable level. Market-driven regional shifts of cropping practices have resulted in larger irrigation requirements and aggravated environmental stresses. Our results highlighted the need for Chinese food policies to consider the spatial shifts in cultivation, and the planting crop compositions limited by regional water resources and climate change.

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP) receptor expression and function.

Science.gov (United States)

Bill, Anke; Rosethorne, Elizabeth M; Kent, Toby C; Fawcett, Lindsay; Burchell, Lynn; van Diepen, Michiel T; Marelli, Anthony; Batalov, Sergey; Miraglia, Loren; Orth, Anthony P; Renaud, Nicole A; Charlton, Steven J; Gosling, Martin; Gaither, L Alex; Groot-Kormelink, Paul J

2014-01-01

The human prostacyclin receptor (hIP receptor) is a seven-transmembrane G protein-coupled receptor (GPCR) that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR) mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

High throughput mutagenesis for identification of residues regulating human prostacyclin (hIP receptor expression and function.

Directory of Open Access Journals (Sweden)

Anke Bill

Full Text Available The human prostacyclin receptor (hIP receptor is a seven-transmembrane G protein-coupled receptor (GPCR that plays a critical role in vascular smooth muscle relaxation and platelet aggregation. hIP receptor dysfunction has been implicated in numerous cardiovascular abnormalities, including myocardial infarction, hypertension, thrombosis and atherosclerosis. Genomic sequencing has discovered several genetic variations in the PTGIR gene coding for hIP receptor, however, its structure-function relationship has not been sufficiently explored. Here we set out to investigate the applicability of high throughput random mutagenesis to study the structure-function relationship of hIP receptor. While chemical mutagenesis was not suitable to generate a mutagenesis library with sufficient coverage, our data demonstrate error-prone PCR (epPCR mediated mutagenesis as a valuable method for the unbiased screening of residues regulating hIP receptor function and expression. Here we describe the generation and functional characterization of an epPCR derived mutagenesis library compromising >4000 mutants of the hIP receptor. We introduce next generation sequencing as a useful tool to validate the quality of mutagenesis libraries by providing information about the coverage, mutation rate and mutational bias. We identified 18 mutants of the hIP receptor that were expressed at the cell surface, but demonstrated impaired receptor function. A total of 38 non-synonymous mutations were identified within the coding region of the hIP receptor, mapping to 36 distinct residues, including several mutations previously reported to affect the signaling of the hIP receptor. Thus, our data demonstrates epPCR mediated random mutagenesis as a valuable and practical method to study the structure-function relationship of GPCRs.

Biologically aggressive regions within glioblastoma identified by spin-lock contrast T1 relaxation in the rotating frame (T1ρ MRI

Directory of Open Access Journals (Sweden)

Ramon Francisco Barajas, Jr., MD

2017-12-01

Full Text Available Spin-lattice relaxation in the rotating frame magnetic resonance imaging allows for the quantitative assessment of spin-lock contrast within tissues. We describe the utility of spin-lattice relaxation in the rotating frame metrics in characterizing glioblastoma biological heterogeneity. A 84-year-old man presented to our institution with a right frontal temporal mass. Prior tissue sampling from a peripheral nonenhancing lesion was nondiagnostic. Stereotactic image-guided tissue sampling of the nonenhancing T2-fluid-attenuated inversion recovery hyperintense region involving the anterior cingulate gyrus with elevated spin-lattice relaxation in the rotating frame metrics provided a pathologic diagnosis of glioblastoma. This case illustrates the utility of spin-lattice relaxation in the rotating frame magnetic resonance imaging in identifying biologically aggressive regions within glioblastoma.

Recent advances of microbial breeding via heavy-ion mutagenesis at IMP.

Science.gov (United States)

Hu, W; Li, W; Chen, J

2017-10-01

Nowadays, the value of heavy-ion mutagenesis has been accepted as a novel powerful mutagen technique to generate new microbial mutants due to its high linear energy transfer and high relative biological effectiveness. This paper briefly reviews recent progress in developing a more efficient mutagenesis technique for microbial breeding using heavy-ion mutagenesis, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou. Then, new insights into microbial biotechnology via heavy-ion mutagenesis are also further explored. We hope that our concerns will give deep insight into microbial breeding biotechnology via heavy-ion mutagenesis. We also believe that heavy-ion mutagenesis breeding will greatly contribute to the progress of a comprehensive study industrial strain engineering for bioindustry in the future. There is currently a great interest in developing rapid and diverse microbial mutation tool for strain modification. Heavy-ion mutagenesis has been proved as a powerful technology for microbial breeding due to its broad spectrum of mutation phenotypes with high efficiency. In order to deeply understand heavy-ion mutagenesis technology, this paper briefly reviews recent progress in microbial breeding using heavy-ion mutagenesis at IMP, and also presents the outline of the beam line for microbial breeding in Heavy Ion Research Facility of Lanzhou (HIRFL) as well as new insights into microbial biotechnology via heavy-ion mutagenesis. Thus, this work can provide the guidelines to promote the development of novel microbial biotechnology cross-linking heavy-ion mutagenesis breeding that could make breeding process more efficiently in the future. © 2017 The Society for Applied Microbiology.

Operator Representations of Frames: Boundedness, Duality, and Stability

DEFF Research Database (Denmark)

Christensen, Ole; Hasannasab, Marzieh

2017-01-01

The purpose of the paper is to analyze frames (Formula presented.) having the form (Formula presented.) for some linear operator (Formula presented.). A key result characterizes boundedness of the operator T in terms of shift-invariance of a certain sequence space. One of the consequences is a ch...... in frame theory. Various ways of avoiding this problem will be discussed. Throughout the paper the results will be connected with the operators and function systems appearing in applied harmonic analysis, as well as with general group representations.......The purpose of the paper is to analyze frames (Formula presented.) having the form (Formula presented.) for some linear operator (Formula presented.). A key result characterizes boundedness of the operator T in terms of shift-invariance of a certain sequence space. One of the consequences...... is a characterization of the case where the representation (Formula presented.) can be achieved for an operator T that has an extension to a bounded bijective operator (Formula presented.) In this case we also characterize all the dual frames that are representable in terms of iterations of an operator V; in particular...

The finite section method and problems in frame theory

DEFF Research Database (Denmark)

Christensen, Ole; Strohmer, T.

2005-01-01

solves related computational problems in frame theory. In the case of a frame which is localized w.r.t. an orthonormal basis we are able to estimate the rate of approximation. The results are applied to the reproducing kernel frame appearing in the theory for shift-invariant spaces generated by a Riesz......The finite section method is a convenient tool for approximation of the inverse of certain operators using finite-dimensional matrix techniques. In this paper we demonstrate that the method is very useful in frame theory: it leads to an efficient approximation of the inverse frame operator and also...

Targeted mutagenesis in tetraploid switchgrass (Panicum virgatum L.) using CRISPR/Cas9.

Science.gov (United States)

Liu, Yang; Merrick, Paul; Zhang, Zhengzhi; Ji, Chonghui; Yang, Bing; Fei, Shui-Zhang

2018-02-01

The CRISPR/Cas9 system has become a powerful tool for targeted mutagenesis. Switchgrass (Panicum virgatum L.) is a high yielding perennial grass species that has been designated as a model biomass crop by the U.S. Department of Energy. The self-infertility and high ploidy level make it difficult to study gene function or improve germplasm. To overcome these constraints, we explored the feasibility of using CRISPR/Cas9 for targeted mutagenesis in a tetraploid cultivar 'Alamo' switchgrass. We first developed a transient assay by which a non-functional green-fluorescent protein gene containing a 1-bp frameshift insertion in its 5' coding region was successfully mutated by a Cas9/sgRNA complex resulting in its restored function. Agrobacterium-mediated stable transformation of embryogenic calli derived from mature caryopses averaged a 3.0% transformation efficiency targeting the genes of teosinte branched 1(tb1)a and b and phosphoglycerate mutase (PGM). With a single construct containing two sgRNAs targeting different regions of tb1a and tb1b genes, primary transformants (T0) containing CRISPR/Cas9-induced mutations were obtained at frequencies of 95.5% (tb1a) and 11% (tb1b), respectively, with T0 mutants exhibiting increased tiller production. Meanwhile, a mutation frequency of 13.7% was obtained for the PGM gene with a CRISPR/Cas9 construct containing a single sgRNA. Among the PGM T0 mutants, six are heterozygous and one is homozygous for a 1-bp deletion in the target region with no apparent phenotypical alterations. We show that CRISPR/Cas9 system can generate targeted mutagenesis effectively and obtain targeted homozygous mutants in T0 generation in switchgrass, circumventing the need of inbreeding. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Environmental stress induces trinucleotide repeat mutagenesis in human cells.

Science.gov (United States)

Chatterjee, Nimrat; Lin, Yunfu; Santillan, Beatriz A; Yotnda, Patricia; Wilson, John H

2015-03-24

The dynamic mutability of microsatellite repeats is implicated in the modification of gene function and disease phenotype. Studies of the enhanced instability of long trinucleotide repeats (TNRs)-the cause of multiple human diseases-have revealed a remarkable complexity of mutagenic mechanisms. Here, we show that cold, heat, hypoxic, and oxidative stresses induce mutagenesis of a long CAG repeat tract in human cells. We show that stress-response factors mediate the stress-induced mutagenesis (SIM) of CAG repeats. We show further that SIM of CAG repeats does not involve mismatch repair, nucleotide excision repair, or transcription, processes that are known to promote TNR mutagenesis in other pathways of instability. Instead, we find that these stresses stimulate DNA rereplication, increasing the proportion of cells with >4 C-value (C) DNA content. Knockdown of the replication origin-licensing factor CDT1 eliminates both stress-induced rereplication and CAG repeat mutagenesis. In addition, direct induction of rereplication in the absence of stress also increases the proportion of cells with >4C DNA content and promotes repeat mutagenesis. Thus, environmental stress triggers a unique pathway for TNR mutagenesis that likely is mediated by DNA rereplication. This pathway may impact normal cells as they encounter stresses in their environment or during development or abnormal cells as they evolve metastatic potential.

On frame properties for Fourier-like systems

DEFF Research Database (Denmark)

Christensen, Ole; Osgooei, Elnaz

2013-01-01

Fourier-like systems are formed by multiplying a class of exponentials with a set of window functions. Via the Fourier transform they are equivalent to shift-invariant systems. We present sufficient and easily verifiable conditions for such systems to form a frame with a dual frame having the same...... structure. An attractive class of frames is formed by letting the window functions be trigonometric polynomials, restricted to compact intervals. We prove, under weak conditions, that such systems generate a frame with a dual that is also generated by a trigonometric polynomial. For polynomial windows......, a result of this type does not hold. Throughout the paper the results are related to the well established theory for Gabor systems....

Radioprotective action of glycerol and cysteamine on inactivation and mutagenesis in Salmonella tester strains after γ- and heavy ion irradiation

International Nuclear Information System (INIS)

Basha, S.G.; Krasavin, E.A.; Kozubek, S.

1992-01-01

Inactivation and mutagenesis were studied in Salmonella tester strains after γ-irradiation and after heavy ion irradiation in the presence of glycerol and cysteamine. Ions from deuteron to carbon with residual energies of 2-9 MeV/n were used. Cell sensitivity slightly increased with LET before decreasing. In the presence of glycerol the maximum was shifted to higher values of LET. The radioprotective effect of glycerol for cell killing diminished gradually with increasing LET from 2.0 for γ-radiation to 1.1 for carbon ions. Mutagenic effectiveness increased slightly for deuterium and helium ions. The radioprotective effect of cysteamine on mutagenesis was found to be very small in the case of γ-radiation for the three strains examined. (author). 20 refs.; 4 figs.; 5 tabs

Framing effects in choices between multioutcome life-expectancy lotteries.

Science.gov (United States)

Bernstein, L M; Chapman, G B; Elstein, A S

1999-01-01

To explore framing or editing effects and a method to debias framing in a clinical context. Clinical scenarios using multioutcome life-expectancy lotteries of equal value required choices between two supplementary drugs that either prolonged or shortened life from the 20-year beneficial effect of a baseline drug. The effects of these supplementary drugs were presented in two conditions, using a between-subjects design. In segregated editing (n = 116) the effects were presented separately from the effects of the baseline drug. In integrated editing (n = 100), effects of supplementary and baseline drugs were combined in the lottery presentation. Each subject responded to 30 problems. To explore one method of debiasing, another 100 subjects made choices after viewing both segregated and integrated editings of 20 problems (dual framing). Statistically significant preference reversals between segregated and integrated editing of pure lotteries occurred only when one framing placed outcomes in the gain domain, and the other framing placed them in the loss domain. When both editings resulted in gain-domain outcomes only, there was no framing effect. There was a related relationship of framing-effect shifts from losses to gains in mixed-lottery-choice problems. Responses to the dual framing condition did not consistently coincide with responses to either single framing. In some situations, dual framing eliminated or lessened framing effects. The results support two components of prospect theory, coding outcomes as gains or losses from a reference point, and an s-shaped utility function (concave in gain, convex in loss domains). Presenting both alternative editings of a complex situation prior to choice more fully informs the decision maker and may help to reduce framing effects. Given the extent to which preferences shift in response to alternative presentations, it is unclear which choice represents the subject's "true preferences."

Strategic Framing Study Circles: Toward a Gold Standard of Framing Pedagogy

Science.gov (United States)

Feinberg, Jane

2009-01-01

This article explains how communities of practice have been developed as part of FrameWorks' field-building efforts. Strategic Framing Study Circles, as they are known, have been conducted with four statewide coalitions, one group of national organizations, and an emerging regional coalition. The goal of each community of practice is to build…

Introducing COCOS: codon consequence scanner for annotating reading frame changes induced by stop-lost and frame shift variants.

Science.gov (United States)

Butkiewicz, Mariusz; Haines, Jonathan L; Bush, William S

2017-05-15

Reading frame altering genomic variants can impact gene expression levels and the structure of protein products, thus potentially inducing disease phenotypes. Current annotation approaches report the impact of such variants in the context of altered DNA sequence only; attributes of the resulting transcript, reading frame and translated protein product are not reported. To remedy this shortcoming, we present a new genetic annotation approach termed Codon Consequence Scanner (COCOS). Implemented as an Ensembl variant effect predictor (VEP) plugin, COCOS captures amino acid sequence alterations stemming from variants that produce an altered reading frame, such as stop-lost variants and small insertions and deletions (InDels). To highlight its significance, COCOS was applied to data from the 1000 Genomes Project. Transcripts affected by stop-lost variants introduce a median of 15 amino acids, while InDels have a more extensive impact with a median of 66 amino acids being incorporated. Captured sequence alterations are written out in FASTA format and can be further analyzed for impact on the underlying protein structure. COCOS is available to all users on github: https://github.com/butkiem/COCOS. mariusz.butkiewicz@case.edu. © The Author 2017. Published by Oxford University Press.

Modification of γ-induced mutagenesis in Ames test-strains

International Nuclear Information System (INIS)

Basha, S.G.; Krasavin, E.A.; Kozubek, S.; Amirtaev, K.G.

1990-01-01

Glycerine and cysteamine protective effect on mutagenesis was studied in 3 strains of Salmonella typhimurium under γ-radiation. Glycerine modifying effect was shown to be not similar for various test-strains and depended on DNA injury nature. DNA complex injuries were shown to play significant role in mutagenesis of TA100 and TA102 strains. Absence of cysteamine modifying effect on γ-induced mutagenesis testified to cysteamine effect on enzyme balance. 20 refs.; 2 figs.; 1 tab

Mutagenesis and Teratogenesis Section

International Nuclear Information System (INIS)

Anon.

1976-01-01

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

Fluorescence-Based Reporters for Detection of Mutagenesis in E. coli.

Science.gov (United States)

Standley, Melissa; Allen, Jennifer; Cervantes, Layla; Lilly, Joshua; Camps, Manel

2017-01-01

Mutagenesis in model organisms following exposure to chemicals is used as an indicator of genotoxicity. Mutagenesis assays are also used to study mechanisms of DNA homeostasis. This chapter focuses on detection of mutagenesis in prokaryotes, which boils down to two approaches: reporter inactivation (forward mutation assay) and reversion of an inactivating mutation (reversion mutation assay). Both methods are labor intensive, involving visual screening, quantification of colonies on solid media, or determining a Poisson distribution in liquid culture. Here, we present two reversion reporters for in vivo mutagenesis that produce a quantitative output, and thus have the potential to greatly reduce the amount of test chemical and labor involved in these assays. This output is obtained by coupling a TEM β lactamase-based reversion assay with GFP fluorescence, either by placing the two genes on the same plasmid or by fusing them translationally and interrupting the N-terminus of the chimeric ORF with a stop codon. We also describe a reporter aimed at facilitating the monitoring of continuous mutagenesis in mutator strains. This reporter couples two reversion markers, allowing the temporal separation of mutation events in time, thus providing information about the dynamics of mutagenesis in mutator strains. Here, we describe these reporter systems, provide protocols for use, and demonstrate their key functional features using error-prone Pol I mutagenesis as a source of mutations. © 2017 Elsevier Inc. All rights reserved.

Untargeted viral mutagenesis is not found in X-irradiated monkey cells

International Nuclear Information System (INIS)

Lytle, C.D.; Carney, P.G.; Lee, W.; Bushar, H.F.

1988-01-01

The existence of untargeted viral mutagenesis in X-irradiated cells was investigated in a mammalian virus/cell system, where a low level of such viral mutagenesis can be demonstrated in UV-irradiated cells. In the positive control experiment UV-elicited mutagenesis was shown with cell exposures of 5, 10 and 15 J/m 2 and a delay of 24 h between cell irradiation and infection with unirradiated herpes simplex virus. Although X-ray doses of 1, 3 and 10 Gy elicit enhanced reactivation of UV-irradiated virus, no untargeted mutagenesis for any X-ray dose at post-irradiation infection times of 0, 24 or 72 h was observed in this study. Thus untargeted mutagenesis of herpes simplex virus was not demonstrated in X-irradiated monkey cells, under conditions where X-ray-enhanced reactivation occurs and where untargeted mutagenesis in UV-irradiated cells occurs. (author)

The Yeast Environmental Stress Response Regulates Mutagenesis Induced by Proteotoxic Stress

Science.gov (United States)

Shor, Erika; Fox, Catherine A.; Broach, James R.

2013-01-01

Conditions of chronic stress are associated with genetic instability in many organisms, but the roles of stress responses in mutagenesis have so far been elucidated only in bacteria. Here, we present data demonstrating that the environmental stress response (ESR) in yeast functions in mutagenesis induced by proteotoxic stress. We show that the drug canavanine causes proteotoxic stress, activates the ESR, and induces mutagenesis at several loci in an ESR-dependent manner. Canavanine-induced mutagenesis also involves translesion DNA polymerases Rev1 and Polζ and non-homologous end joining factor Ku. Furthermore, under conditions of chronic sub-lethal canavanine stress, deletions of Rev1, Polζ, and Ku-encoding genes exhibit genetic interactions with ESR mutants indicative of ESR regulating these mutagenic DNA repair processes. Analyses of mutagenesis induced by several different stresses showed that the ESR specifically modulates mutagenesis induced by proteotoxic stress. Together, these results document the first known example of an involvement of a eukaryotic stress response pathway in mutagenesis and have important implications for mechanisms of evolution, carcinogenesis, and emergence of drug-resistant pathogens and chemotherapy-resistant tumors. PMID:23935537

Beyond the Natural Proteome: Nondegenerate Saturation Mutagenesis-Methodologies and Advantages.

Science.gov (United States)

Ferreira Amaral, M M; Frigotto, L; Hine, A V

2017-01-01

Beyond the natural proteome, high-throughput mutagenesis offers the protein engineer an opportunity to "tweak" the wild-type activity of a protein to create a recombinant protein with required attributes. Of the various approaches available, saturation mutagenesis is one of the core techniques employed by protein engineers, and in recent times, nondegenerate saturation mutagenesis is emerging as the approach of choice. This review compares the current methodologies available for conducting nondegenerate saturation mutagenesis with traditional, degenerate saturation and briefly outlines the options available for screening the resulting libraries, to discover a novel protein with the required activity and/or specificity. © 2017 Elsevier Inc. All rights reserved.

FULL ELECTROMAGNETIC FEL SIMULATION VIA THE LORENTZ-BOOSTED FRAME TRANSFORMATION

International Nuclear Information System (INIS)

Fawley, William; Vay, Jean-Luc

2010-01-01

Numerical electromagnetic simulation of some systems containing charged particles with highly relativistic directed motion can by speeded up by orders of magnitude by choice of the proper Lorentz-boosted frame. A particularly good application for calculation in a boosted frame isthat of short wavelength free-electron lasers (FELs) where a high energy electron beam with small fractional energy spread interacts with a static magnetic undulator. In the optimal boost frame (i.e., the ponderomotive rest frame), the red-shifted FEL radiation and blue-shifted undulator field have identical wavelengths and the number of required longitudinal grid cells and time-steps for fully electromagnetic simulation (relative to the laboratory frame) decrease by factors of gamma 2 each. In theory, boosted frame EM codes permit direct study of FEL problems for which the eikonal approximation for propagation of the radiation field and wiggler-period-averaging for the particle-field interaction may be suspect. We have adapted the WARP code to apply this method to several electromagnetic FEL problems including spontaneous emission, strong exponential gain in a seeded, single pass amplifier configuration, and emission from e-beams in undulators with multiple harmonic components. WARP has a standard relativistic macroparticle mover and a fully 3-D electromagnetic field solver. We discuss our boosted frame results and compare with those obtained using the 'standard' eikonal FEL simulation approach.

Photodynamic action of the methylene blue: mutagenesis and sinergism

International Nuclear Information System (INIS)

Capella, M.A.M.

1988-01-01

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.)

Computer Simulation of Mutagenesis.

Science.gov (United States)

North, J. C.; Dent, M. T.

1978-01-01

A FORTRAN program is described which simulates point-substitution mutations in the DNA strands of typical organisms. Its objective is to help students to understand the significance and structure of the genetic code, and the mechanisms and effect of mutagenesis. (Author/BB)

Density of Gabor Frames

DEFF Research Database (Denmark)

Christensen, Ole; Heil, C.; Deng, B.

1997-01-01

A Gabor system is a set of time-frequency shifts$S(g,\\Lambda) = \\{e^{2\\pi i b x} g(x-a)\\}_{(a,b) \\in \\Lambda}$of a function $g \\in L^2({\\bold R}^d)$.We prove that if a finite union of Gabor systems$\\bigcup_{k=1}^r S(g_k,\\Lambda_k)$, with arbitrary sequences $\\Lambda_k$,forms a frame for $L^2({\\bo...

Concepts and Contexts – Argumentative Forms of Framing

DEFF Research Database (Denmark)

Gabrielsen, Jonas; Nørholm Just, Sine; Bengtsson, Mette

2011-01-01

this argument we combine theories of framing with the classical rhetorical theory of the stases, more precisely status definitio and status translatio. Our focus is primarily theoretical, but we illustrate our points by means of examples taken from public debates on the value of real estate.......The notion of framing has become central in the field of argumentation. The question is, however, what we gain from studying the process of argumentation through framing, since framing is itself a broad concept in need of specification. Different traditions understand the term differently......, and it is necessary to determine what argumentative forms the concept of framing actually covers. In this paper we argue that framing refers to at least two different argumentative forms. One is an internal definition of the concepts in question; the other is an external shift in the context of the case. In making...

A neuroimaging investigation of attribute framing and individual differences

Science.gov (United States)

Murch, Kevin B.

2014-01-01

Functional magnetic resonance imaging was used to evaluate the neural basis of framing effects. We tested the reflexive and reflective systems model of social cognition as it relates to framing. We also examined the relationships among frame susceptibility, intelligence and personality measures. Participants evaluated whether personal attributes applied to themselves from multiple perspectives and in positive and negative frames. Participants rated whether each statement was descriptive or not and endorsed positive frames more than negative frames. Individual differences on frame decisions enabled us to form high and low frame susceptibility groups. Endorsement of frame-consistent attributes was associated with personality factors, cognitive reflection and intelligence. Reflexive brain regions were associated with positive frames while reflective areas were associated with negative frames. Region of Interest analyses showed that frame-inconsistent responses were associated with increased activation within reflective cognitive control regions including the left dorsolateral prefrontal cortex (PFC), dorsomedial PFC and left ventrolateral PFC. Frame-consistent responses were associated with increased activation in the right orbitofrontal cortex. These results demonstrate that individual differences in frame susceptibility influence personal attribute evaluations. Overall, this study clarifies the neural correlates of the reflective and reflexive systems of social cognition as applied to decisions about social attributions. PMID:23988759

Empirical complexities in the genetic foundations of lethal mutagenesis.

Science.gov (United States)

Bull, James J; Joyce, Paul; Gladstone, Eric; Molineux, Ian J

2013-10-01

From population genetics theory, elevating the mutation rate of a large population should progressively reduce average fitness. If the fitness decline is large enough, the population will go extinct in a process known as lethal mutagenesis. Lethal mutagenesis has been endorsed in the virology literature as a promising approach to viral treatment, and several in vitro studies have forced viral extinction with high doses of mutagenic drugs. Yet only one empirical study has tested the genetic models underlying lethal mutagenesis, and the theory failed on even a qualitative level. Here we provide a new level of analysis of lethal mutagenesis by developing and evaluating models specifically tailored to empirical systems that may be used to test the theory. We first quantify a bias in the estimation of a critical parameter and consider whether that bias underlies the previously observed lack of concordance between theory and experiment. We then consider a seemingly ideal protocol that avoids this bias-mutagenesis of virions-but find that it is hampered by other problems. Finally, results that reveal difficulties in the mere interpretation of mutations assayed from double-strand genomes are derived. Our analyses expose unanticipated complexities in testing the theory. Nevertheless, the previous failure of the theory to predict experimental outcomes appears to reside in evolutionary mechanisms neglected by the theory (e.g., beneficial mutations) rather than from a mismatch between the empirical setup and model assumptions. This interpretation raises the specter that naive attempts at lethal mutagenesis may augment adaptation rather than retard it.

Compactly supported frames for decomposition spaces

DEFF Research Database (Denmark)

Nielsen, Morten; Rasmussen, Kenneth Niemann

2012-01-01

In this article we study a construction of compactly supported frame expansions for decomposition spaces of Triebel-Lizorkin type and for the associated modulation spaces. This is done by showing that finite linear combinations of shifts and dilates of a single function with sufficient decay in b...

Shifting frames : Conditional indirect effects of contested issues on perceived effectiveness through multiple emotions

NARCIS (Netherlands)

Feinholdt, A.; Schuck, A.R.T.; Lecheler, S.K.; de Vreese, C.H.

2017-01-01

Prior research has found that exposure to news frames can cause emotional responses to political issues. Yet, little is known about how different combinations of news frames and issues relate to discrete emotions and whether these emotions, in turn, affect issue perceptions. The present study

Analytical Assessment of Structural Shifts in the Economy of the Volgograd Region in Conditions of Development of Convergent Technologies

Directory of Open Access Journals (Sweden)

Irina Aleksandrovna Elkhina

2016-06-01

Full Text Available The article presents the results of the assessment of the structural shifts in the economy of the Volgograd region due to the development of convergent technologies, innovation and technology. The development of convergent technologies is one of the factors for the transition of the economy to a new technological order. Industry structure undergoes quantitative and qualitative changes under the influence of scientific and technological progress, the development of cyclical economy and other factors. Such changes ultimately lead to structural shifts. The results of assessments of structural shifts in the economy of the Volgograd region in terms of gross value added, employment of economically active population and investment in fixed assets by economic activity are presented for the time period from 2005 to 2014. To count structural shifts in economy the author uses the index of Ryabtsev, as it has a scale of structural differences. Based on the findings, the author makes conclusions about the structural development of the region in time and as compared to the other regions in the Southern Russia. The smallest structural shifts have been obtained in terms of employment, the largest – in terms of investment in fixed assets. However, application of this index does not let to assess the degree of influence of the technological base on the development of economic system. Therefore, the author proposes to supplement the research of structural shifts by the author’s characteristic such as impulse of structural shifts, which serves as a measure of resource supply process of initiating structural shifts. Approbation of methodology for calculating impulse of structural shifts made on the basis of the Southern Russian regions with the rating on the author’s sample indicators, reflecting the state of infrastructure, innovation, human resources security, efficiency and the promotion of scientific development, amount of the costs of innovation

Frames and semi-frames

International Nuclear Information System (INIS)

Antoine, Jean-Pierre; Balazs, Peter

2011-01-01

Loosely speaking, a semi-frame is a generalized frame for which one of the frame bounds is absent. More precisely, given a total sequence in a Hilbert space, we speak of an upper (resp. lower) semi-frame if only the upper (resp. lower) frame bound is valid. Equivalently, for an upper semi-frame, the frame operator is bounded, but has an unbounded inverse, whereas a lower semi-frame has an unbounded frame operator, with a bounded inverse. We study mostly upper semi-frames, both in the continuous and discrete case, and give some remarks for the dual situation. In particular, we show that reconstruction is still possible in certain cases.

Favipiravir elicits antiviral mutagenesis during virus replication in vivo.

Science.gov (United States)

Arias, Armando; Thorne, Lucy; Goodfellow, Ian

2014-10-21

Lethal mutagenesis has emerged as a novel potential therapeutic approach to treat viral infections. Several studies have demonstrated that increases in the high mutation rates inherent to RNA viruses lead to viral extinction in cell culture, but evidence during infections in vivo is limited. In this study, we show that the broad-range antiviral nucleoside favipiravir reduces viral load in vivo by exerting antiviral mutagenesis in a mouse model for norovirus infection. Increased mutation frequencies were observed in samples from treated mice and were accompanied with lower or in some cases undetectable levels of infectious virus in faeces and tissues. Viral RNA isolated from treated animals showed reduced infectivity, a feature of populations approaching extinction during antiviral mutagenesis. These results suggest that favipiravir can induce norovirus mutagenesis in vivo, which in some cases leads to virus extinction, providing a proof-of-principle for the use of favipiravir derivatives or mutagenic nucleosides in the clinical treatment of noroviruses.

A neuroimaging investigation of attribute framing and individual differences.

Science.gov (United States)

Murch, Kevin B; Krawczyk, Daniel C

2014-10-01

Functional magnetic resonance imaging was used to evaluate the neural basis of framing effects. We tested the reflexive and reflective systems model of social cognition as it relates to framing. We also examined the relationships among frame susceptibility, intelligence and personality measures. Participants evaluated whether personal attributes applied to themselves from multiple perspectives and in positive and negative frames. Participants rated whether each statement was descriptive or not and endorsed positive frames more than negative frames. Individual differences on frame decisions enabled us to form high and low frame susceptibility groups. Endorsement of frame-consistent attributes was associated with personality factors, cognitive reflection and intelligence. Reflexive brain regions were associated with positive frames while reflective areas were associated with negative frames. Region of Interest analyses showed that frame-inconsistent responses were associated with increased activation within reflective cognitive control regions including the left dorsolateral prefrontal cortex (PFC), dorsomedial PFC and left ventrolateral PFC. Frame-consistent responses were associated with increased activation in the right orbitofrontal cortex. These results demonstrate that individual differences in frame susceptibility influence personal attribute evaluations. Overall, this study clarifies the neural correlates of the reflective and reflexive systems of social cognition as applied to decisions about social attributions. © The Author (2013). Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Measurement of in-plane strain with dual beam spatial phase-shift digital shearography

International Nuclear Information System (INIS)

Xie, Xin; Chen, Xu; Li, Junrui; Yang, Lianxiang; Wang, Yonghong

2015-01-01

Full-field in-plane strain measurement under dynamic loading by digital shearography remains a big challenge in practice. A phase measurement for in-plane strain information within one time frame has to be achieved to solve this problem. This paper presents a dual beam spatial phase-shift digital shearography system with the capacity to measure phase distribution corresponding to in-plane strain information within a single time frame. Two laser beams with different wavelengths are symmetrically arranged to illuminate the object under test, and two cameras with corresponding filters, which enable simultaneous recording of two shearograms, are utilized for data acquisition. The phase information from the recorded shearograms, which corresponds to the in-plane strain, is evaluated by the spatial phase-shift method. The spatial phase-shift shearography system realizes a measurement of the in-plane strain through the introduction of the spatial phase-shift technique, using one frame after the loading and one frame before loading. This paper presents the theory of the spatial phase-shift digital shearography for in-plane strain measurement and its derivation, experimental results, and the technique’s potential. (paper)

Mechanism of SOS-induced targeted and untargeted mutagenesis in E. coli

International Nuclear Information System (INIS)

Maenhaut-Michel, G.

1985-01-01

This paper retraces the evolution of hypotheses concerning mechanisms of SOS induced mutagenesis. Moreover, it reports some recent data which support a new model for the mechanism of targeted and untargeted mutagenesis in E. coli. In summary, the SOS mutator effect, which is responsible for untargeted mutagenesis and perhaps for the misincorporation step in targeted mutagenesis, is believed to involve a fidelity function associated with DNA polymerase III and does not require the umuC gene product. umuC and umuD gene products are probably required specifically for elongation of DNA synthesis past blocking lesions, i.e. to allow mutagenic replication of damaged DNA

Plasmid (pKM101)-mediated enhancement of repair and mutagenesis: dependence on chromosomal genes in 'Escherichia coli' K-12

International Nuclear Information System (INIS)

Walker, G.C.

1977-01-01

The drug resistance plasmid pKM101 plays a major role in the Ames Salmonella/microsome carcinogen detecting system by enhancing chemical mutagenesis. It is shown that in Escherichia coli K-12 the plasmid pKM101 enhances both spontaneous and methyl methanesulfonate-caused reversion of an ochre mutation, bacterial survival after ultaviolet irradiation, and reactivation of ultraviolet-irradiated lambda in unirradiated cells. All these effects are shown to be dependent on the recA + lexA + genotype but not on the recB + recC + or recF + genotypes. The recA lexA-dependence of the plasmid-mediated repair and mutagenesis suggests an interaction with the cell's inducible error-prone repair system. The presence of pKM101 is shown to cause an additional increase in methyl methanesulfonate mutagenesis in a tif mutant beyond that caused by growth at 42 0 . The presence of the plasmid raises the level of the Weigle-reactivation curve for the reactivation of ultraviolet-irradiated lambda in E. coli and causes a shift of the maximum to a higher UV fluence. These observations suggest that pKM101 does not exert its effects by altering the regulation of the cell's error-prone repair system but rather by supplying a mechanistic component or components. (orig.) [de

Random mutagenesis by error-prone pol plasmid replication in Escherichia coli.

Science.gov (United States)

Alexander, David L; Lilly, Joshua; Hernandez, Jaime; Romsdahl, Jillian; Troll, Christopher J; Camps, Manel

2014-01-01

Directed evolution is an approach that mimics natural evolution in the laboratory with the goal of modifying existing enzymatic activities or of generating new ones. The identification of mutants with desired properties involves the generation of genetic diversity coupled with a functional selection or screen. Genetic diversity can be generated using PCR or using in vivo methods such as chemical mutagenesis or error-prone replication of the desired sequence in a mutator strain. In vivo mutagenesis methods facilitate iterative selection because they do not require cloning, but generally produce a low mutation density with mutations not restricted to specific genes or areas within a gene. For this reason, this approach is typically used to generate new biochemical properties when large numbers of mutants can be screened or selected. Here we describe protocols for an advanced in vivo mutagenesis method that is based on error-prone replication of a ColE1 plasmid bearing the gene of interest. Compared to other in vivo mutagenesis methods, this plasmid-targeted approach allows increased mutation loads and facilitates iterative selection approaches. We also describe the mutation spectrum for this mutagenesis methodology in detail, and, using cycle 3 GFP as a target for mutagenesis, we illustrate the phenotypic diversity that can be generated using our method. In sum, error-prone Pol I replication is a mutagenesis method that is ideally suited for the evolution of new biochemical activities when a functional selection is available.

Regional wall thickening in gated myocardial perfusion SPECT in a Japanese population: effect of sex, radiotracer, rotation angles and frame rates

Energy Technology Data Exchange (ETDEWEB)

Akhter, Nasima; Nakajima, Kenichi; Okuda, Koichi; Matsuo, Shinro; Yoneyama, Tatsuya; Taki, Junichi; Kinuya, Seigo [Kanazawa University Hospital, Department of Nuclear Medicine, Kanazawa, Ishikawa (Japan)

2008-09-15

Gated single-photon emission computed tomography (SPECT) imaging of myocardium by {sup 99m}Tc and {sup 201}Tl is used extensively to measure quantitative cardiac functional parameters. However, factors affecting normal values for myocardial functional parameters and population-specific standards have not yet been established. The aim of the study was to determine the effect of sex, radiotracer, rotation angles and frame rates on resting myocardial wall thickening (WT) and to develop a Japanese standard of normal values for WT. Data from a total of 202 patients with low possibility of having cardiac problems were collected from nine hospitals throughout Japan. Patients were divided into five groups according to study protocol, and WT was evaluated according to the 17-segment and four-region (basal, mid and apical regions and the apex) polar map distribution. WT was generally higher in women than in men irrespective of the use of radiotracers, rotation angles or frame rates, and the difference was highly significant in the mid and apical regions. In any protocol used, resting myocardial thickening in the apex was higher than in the mid and apical regions, and thickening was lowest in the basal region, suggesting heterogeneous regional myocardial thickening (%) in normal subjects. Different rotation angles showed no significant change on WT, but different frame rates and tracers showed significant WT change in both sexes. Percent thickening of the myocardium was significantly higher in imaging by {sup 99m}Tc-labelled tracers than in {sup 201}Tl. Sex, radiotracers and frame rates had a significant effect on myocardial thickening, and the importance of population-specific standards should be emphasized. A normal database can serve as a standard for gated SPECT evaluation of myocardial thickening in a Japanese population and might be applicable to Asian populations having a similar physique. (orig.)

Signatures of global warming and regional climate shift in the Arabian Sea

Digital Repository Service at National Institute of Oceanography (India)

PrasannaKumar, S.; Roshin, R.P.; Narvekar, J.; DineshKumar, P.K.; Vivekanandan, E.

phytoplankton biomass during fall and winter is attributed to the iron-fertilization driven by enhanced dust-delivery under this regional climate shift. Finally, it is shown that the increased fish (oil-sardine) catch in the eastern and western Arabian Sea after...

Comments on mutagenesis risk estimation

International Nuclear Information System (INIS)

Russell, W.L.

1976-01-01

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

Phenotypic heterogeneity in a bacteriophage population only appears as stress-induced mutagenesis.

Science.gov (United States)

Yosef, Ido; Edgar, Rotem; Qimron, Udi

2016-11-01

Stress-induced mutagenesis has been studied in cancer cells, yeast, bacteria, and archaea, but not in viruses. In a recent publication, we present a bacteriophage model showing an apparent stress-induced mutagenesis. We show that the stress does not drive the mutagenesis, but only selects the fittest mutants. The mechanism underlying the observed phenomenon is a phenotypic heterogeneity that resembles persistence of the viral population. The new findings, the background for the ongoing debate on stress-induced mutagenesis, and the phenotypic heterogeneity underlying a novel phage infection strategy are discussed in this short manuscript.

Multiplex conditional mutagenesis in zebrafish using the CRISPR/Cas system.

Science.gov (United States)

Yin, L; Maddison, L A; Chen, W

2016-01-01

The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein (Cas) system is a powerful tool for genome editing in numerous organisms. However, the system is typically used for gene editing throughout the entire organism. Tissue and temporal specific mutagenesis is often desirable to determine gene function in a specific stage or tissue and to bypass undesired consequences of global mutations. We have developed the CRISPR/Cas system for conditional mutagenesis in transgenic zebrafish using tissue-specific and/or inducible expression of Cas9 and U6-driven expression of sgRNA. To allow mutagenesis of multiple targets, we have isolated four distinct U6 promoters and designed Golden Gate vectors to easily assemble transgenes with multiple sgRNAs. We provide experimental details on the reagents and applications for multiplex conditional mutagenesis in zebrafish. Copyright © 2016 Elsevier Inc. All rights reserved.

Optogenetic Random Mutagenesis Using Histone-miniSOG in C. elegans.

Science.gov (United States)

Noma, Kentaro; Jin, Yishi

2016-11-14

Forward genetic screening in model organisms is the workhorse to discover functionally important genes and pathways in many biological processes. In most mutagenesis-based screens, researchers have relied on the use of toxic chemicals, carcinogens, or irradiation, which requires designated equipment, safety setup, and/or disposal of hazardous materials. We have developed a simple approach to induce heritable mutations in C. elegans using germline-expressed histone-miniSOG, a light-inducible potent generator of reactive oxygen species. This mutagenesis method is free of toxic chemicals and requires minimal laboratory safety and waste management. The induced DNA modifications include single-nucleotide changes and small deletions, and complement those caused by classical chemical mutagenesis. This methodology can also be used to induce integration of extrachromosomal transgenes. Here, we provide the details of the LED setup and protocols for standard mutagenesis and transgene integration.

Development of potent in vivo mutagenesis plasmids with broad mutational spectra.

Science.gov (United States)

Badran, Ahmed H; Liu, David R

2015-10-07

Methods to enhance random mutagenesis in cells offer advantages over in vitro mutagenesis, but current in vivo methods suffer from a lack of control, genomic instability, low efficiency and narrow mutational spectra. Using a mechanism-driven approach, we created a potent, inducible, broad-spectrum and vector-based mutagenesis system in E. coli that enhances mutation 322,000-fold over basal levels, surpassing the mutational efficiency and spectra of widely used in vivo and in vitro methods. We demonstrate that this system can be used to evolve antibiotic resistance in wild-type E. coli in mutagenesis of chromosomes, episomes and viruses in vivo, and are applicable to both bacterial and bacteriophage-mediated laboratory evolution platforms.

Heat shock and herpes virus: enhanced reactivation without untargeted mutagenesis

International Nuclear Information System (INIS)

Lytle, C.D.; Carney, P.G.

1988-01-01

Enhanced reactivation of Ultraviolet-irradiated virus has been reported to occur in heat-shocked host cells. Since enhanced virus reactivation is often accompanied by untargeted mutagenesis, we investigated whether such mutagenesis would occur for herpes simplex virus (HSV) in CV-1 monkey kidney cells subjected to heat shock. In addition to expressing enhanced reactivation, the treated cells were transiently more susceptible to infection by unirradiated HSV. No mutagenesis of unirradiated HSV was found whether infection occurred at the time of increased susceptibility to infection or during expression of enhanced viral reactivation

Framing Effects: Dynamics and Task Domains

Science.gov (United States)

Wang

1996-11-01

The author examines the mechanisms and dynamics of framing effects in risky choices across three distinct task domains (i.e., life-death, public property, and personal money). The choice outcomes of the problems presented in each of the three task domains had a binary structure of a sure thing vs a gamble of equal expected value; the outcomes differed in their framing conditions and the expected values, raging from 6000, 600, 60, to 6, numerically. It was hypothesized that subjects would become more risk seeking, if the sure outcome was below their aspiration level (the minimum requirement). As predicted, more subjects preferred the gamble when facing the life-death choice problems than facing the counterpart problems presented in the other two task domains. Subjects' risk preference varied categorically along the group size dimension in the life-death domain but changed more linearly over the expected value dimension in the monetary domain. Framing effects were observed in 7 of 13 pairs of problems, showing a positive frame-risk aversion and negative frame-risk seeking relationship. In addition, two types of framing effects were theoretically defined and empirically identified. A bidirectional framing effect involves a reversal in risk preference, and occurs when a decision maker's risk preference is ambiguous or weak. Four bidirectional effects were observed; in each case a majority of subjects preferred the sure outcome under a positive frame but the gamble under a negative frame. In contrast, a unidirectional framing effect refers to a preference shift due to the framing of choice outcomes: A majority of subjects preferred one choice outcome (either the sure thing or the gamble) under both framing conditions, with positive frame augmented the preference for the sure thing and negative frame augmented the preference for the gamble. These findings revealed some dynamic regularities of framing effects and posed implications for developing predictive and testable

MMS exposure promotes increased MtDNA mutagenesis in the presence of replication-defective disease-associated DNA polymerase γ variants.

Science.gov (United States)

Stumpf, Jeffrey D; Copeland, William C

2014-10-01

Mitochondrial DNA (mtDNA) encodes proteins essential for ATP production. Mutant variants of the mtDNA polymerase cause mutagenesis that contributes to aging, genetic diseases, and sensitivity to environmental agents. We interrogated mtDNA replication in Saccharomyces cerevisiae strains with disease-associated mutations affecting conserved regions of the mtDNA polymerase, Mip1, in the presence of the wild type Mip1. Mutant frequency arising from mtDNA base substitutions that confer erythromycin resistance and deletions between 21-nucleotide direct repeats was determined. Previously, increased mutagenesis was observed in strains encoding mutant variants that were insufficient to maintain mtDNA and that were not expected to reduce polymerase fidelity or exonuclease proofreading. Increased mutagenesis could be explained by mutant variants stalling the replication fork, thereby predisposing the template DNA to irreparable damage that is bypassed with poor fidelity. This hypothesis suggests that the exogenous base-alkylating agent, methyl methanesulfonate (MMS), would further increase mtDNA mutagenesis. Mitochondrial mutagenesis associated with MMS exposure was increased up to 30-fold in mip1 mutants containing disease-associated alterations that affect polymerase activity. Disrupting exonuclease activity of mutant variants was not associated with increased spontaneous mutagenesis compared with exonuclease-proficient alleles, suggesting that most or all of the mtDNA was replicated by wild type Mip1. A novel subset of C to G transversions was responsible for about half of the mutants arising after MMS exposure implicating error-prone bypass of methylated cytosines as the predominant mutational mechanism. Exposure to MMS does not disrupt exonuclease activity that suppresses deletions between 21-nucleotide direct repeats, suggesting the MMS-induce mutagenesis is not explained by inactivated exonuclease activity. Further, trace amounts of CdCl2 inhibit mtDNA replication but

Tachyons, Lamb Shifts and Superluminal Chaos

CERN Document Server

Tomaschitz, R

2000-01-01

An elementary account on the origins of cosmic chaos in an open and multiply connected universe is given; there is a finite region in the open 3-space in which the world-lines of galaxies are chaotic, and the mixing taking place in this chaotic nucleus of the universe provides a mechanism to create equidistribution. The galaxy background defines a distinguished frame of reference and a unique cosmic time order; in this context superluminal signal transfer is studied. Tachyons are described by a real Proca field with negative mass square, coupled to a current of subluminal matter. Estimates on tachyon mixing in the geometric optics limit are derived. The potential of a static point source in this field theory is a damped periodic function. We treat this tachyon potential as a perturbation of the Coulomb potential, and study its effects on energy levels in hydrogenic systems. By comparing the induced level shifts to high-precision Lamb shift measurements and QED calculations, we suggest a tachyon mass of 2.1 ke...

Defect of Fe-S cluster binding by DNA polymerase δ in yeast suppresses UV-induced mutagenesis, but enhances DNA polymerase ζ - dependent spontaneous mutagenesis.

Science.gov (United States)

Stepchenkova, E I; Tarakhovskaya, E R; Siebler, H M; Pavlov, Y I

2017-01-01

Eukaryotic genomes are duplicated by a complex machinery, utilizing high fidelity replicative B-family DNA polymerases (pols) α, δ and ε. Specialized error-prone pol ζ, the fourth B-family member, is recruited when DNA synthesis by the accurate trio is impeded by replication stress or DNA damage. The damage tolerance mechanism dependent on pol ζ prevents DNA/genome instability and cell death at the expense of increased mutation rates. The pol switches occurring during this specialized replication are not fully understood. The loss of pol ζ results in the absence of induced mutagenesis and suppression of spontaneous mutagenesis. Disruption of the Fe-S cluster motif that abolish the interaction of the C-terminal domain (CTD) of the catalytic subunit of pol ζ with its accessory subunits, which are shared with pol δ, leads to a similar defect in induced mutagenesis. Intriguingly, the pol3-13 mutation that affects the Fe-S cluster in the CTD of the catalytic subunit of pol δ also leads to defective induced mutagenesis, suggesting the possibility that Fe-S clusters are essential for the pol switches during replication of damaged DNA. We confirmed that yeast strains with the pol3-13 mutation are UV-sensitive and defective in UV-induced mutagenesis. However, they have increased spontaneous mutation rates. We found that this increase is dependent on functional pol ζ. In the pol3-13 mutant strain with defective pol δ, there is a sharp increase in transversions and complex mutations, which require functional pol ζ, and an increase in the occurrence of large deletions, whose size is controlled by pol ζ. Therefore, the pol3-13 mutation abrogates pol ζ-dependent induced mutagenesis, but allows for pol ζ recruitment for the generation of spontaneous mutations and prevention of larger deletions. These results reveal differential control of the two major types of pol ζ-dependent mutagenesis by the Fe-S cluster present in replicative pol δ. Copyright © 2016

Frame properties of wave packet systes in L^2 (R^d)

DEFF Research Database (Denmark)

Christensen, Ole; Rahimi, Asghar

2008-01-01

Extending work by Hernandez, Labate and Weiss, we present a sufficent condition for a generalized shift-invariant system to be a Bessel sequence or even a frame forL(2)(R-d). In particular, this leads to a sufficient condition for a wave packet system to form a frame. On the other hand, we show...

Materiality, magic and belief: framing the countryside in fantastical live-action roleplay games

OpenAIRE

Mitchell, L

2015-01-01

This account of a UK live-action roleplay (LARP) event highlights complex shifts between different interpretive frames, foregrounding the role of the physical setting as well as non-players and locals in providing symbolic resources that inhibit or support the breaking of interpretive frames. The conception of framing used here draws upon Goffman’s (1974) definition of a frame as part of the organization of activity that specifies meaning and expectations of involvement. In looking at the set...

Revised Mechanism and Improved Efficiency of the QuikChange Site-Directed Mutagenesis Method.

Science.gov (United States)

Xia, Yongzhen; Xun, Luying

2017-01-01

Site-directed mutagenesis has been widely used for the substitution, addition or deletion of nucleotide residues in a defined DNA sequence. QuikChange™ site-directed mutagenesis and its related protocols have been widely used for this purpose because of convenience and efficiency. We have recently demonstrated that the mechanism of the QuikChange™ site-directed mutagenesis process is different from that being proposed. The new mechanism promotes the use of partially overlapping primers and commercial PCR enzymes for efficient PCR and mutagenesis.

Recovery during radiation and chemical mutagenesis

International Nuclear Information System (INIS)

Deen, D.F.

1975-01-01

These investigations were directed toward the study of recovery in radiation and chemical mutagenesis in cultured mammalian cells. A mutagenesis system was established in which mutation of V79-17lb Chinese hamster cells to 8-azaguanine resistance was tested. The effects of split dose and postirradiation treatments upon both x-ray and EMS induced mutagenesis were determined. Increasing the cell inoculum by a factor of 5 (from 10 5 to 5 x 10 5 ) decreased both the spontaneous and x-ray induced mutation frequencies by two orders of magnitude. The x-ray induced mutation frequency was found to be higher for those cells allowed to attach for 5 hours before irradiation, in comparison to those allowed to attach for 2 hours. The uv spectrum of 8-azaguanine changes as a function of storage time at low temperature, but not when diluted to either 10 μg/ml or 30 μg/ml and maintained at 37 0 C. The optimal expression time required after irradiation is dose dependent and can be determined from the relationship: E.T. = 1.93(10 -2 )D + 15.5. (E.T. = hours; D = rads). The duration of the optimal expression time can be estimated by summing the cell cycle time and the radiation induced lag time

Theory of misrepair mutagenesis

International Nuclear Information System (INIS)

Bresler, S.E.

1975-01-01

On the basis of experimental data, a model of induced mutagenesis is proposed that takes into account the repair of DNA damage by the Rec system. The peculiar feature of the Rec system is the cleavage and resynthesis of long sequences near the recognized DNA damage. Up to 1000-2000 nucleotides are replaced in one act. Therefore a definite probability exists of finding a damaged point on the second strand serving as template. It is believed that at this point no requirements of complementarity exist and that a random substitution can take place. This is the origin of a point mutation (transversion or frameshift). From this model, a general formula for the dose-response curve of mutagenesis is deduced which also takes into account the possibility of simultaneously initiated repair on both complementary strands of DNA. The latter leads to a lethal event when the points are situated proximally. This formula fits the observations in different cases studied. Some fundamental observations such as the absence of mutants from predominant single-strand breaks of DNA chains are readily explained

Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs.

Science.gov (United States)

Yin, Linlin; Maddison, Lisette A; Li, Mingyu; Kara, Nergis; LaFave, Matthew C; Varshney, Gaurav K; Burgess, Shawn M; Patton, James G; Chen, Wenbiao

2015-06-01

Determining the mechanism of gene function is greatly enhanced using conditional mutagenesis. However, generating engineered conditional alleles is inefficient and has only been widely used in mice. Importantly, multiplex conditional mutagenesis requires extensive breeding. Here we demonstrate a system for one-generation multiplex conditional mutagenesis in zebrafish (Danio rerio) using transgenic expression of both cas9 and multiple single guide RNAs (sgRNAs). We describe five distinct zebrafish U6 promoters for sgRNA expression and demonstrate efficient multiplex biallelic inactivation of tyrosinase and insulin receptor a and b, resulting in defects in pigmentation and glucose homeostasis. Furthermore, we demonstrate temporal and tissue-specific mutagenesis using transgenic expression of Cas9. Heat-shock-inducible expression of cas9 allows temporal control of tyr mutagenesis. Liver-specific expression of cas9 disrupts insulin receptor a and b, causing fasting hypoglycemia and postprandial hyperglycemia. We also show that delivery of sgRNAs targeting ascl1a into the eye leads to impaired damage-induced photoreceptor regeneration. Our findings suggest that CRISPR/Cas9-based conditional mutagenesis in zebrafish is not only feasible but rapid and straightforward. Copyright © 2015 by the Genetics Society of America.

Regional Distribution Shifts Help Explain Local Changes in Wintering Raptor Abundance: Implications for Interpreting Population Trends

Science.gov (United States)

Paprocki, Neil; Heath, Julie A.; Novak, Stephen J.

2014-01-01

Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975–2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs) were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus) and Golden Eagles (Aquila chrysaetos) showed the fastest rate of change, with 8.41 km yr−1 and 7.74 km yr−1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally change as

Regional distribution shifts help explain local changes in wintering raptor abundance: implications for interpreting population trends.

Directory of Open Access Journals (Sweden)

Neil Paprocki

Full Text Available Studies of multiple taxa across broad-scales suggest that species distributions are shifting poleward in response to global climate change. Recognizing the influence of distribution shifts on population indices will be an important part of interpreting trends within management units because current practice often assumes that changes in local populations reflect local habitat conditions. However, the individual- and population-level processes that drive distribution shifts may occur across a large, regional scale and have little to do with the habitats within the management unit. We examined the latitudinal center of abundance for the winter distributions of six western North America raptor species using Christmas Bird Counts from 1975-2011. Also, we considered whether population indices within western North America Bird Conservation Regions (BCRs were explained by distribution shifts. All six raptors had significant poleward shifts in their wintering distributions over time. Rough-legged Hawks (Buteo lagopus and Golden Eagles (Aquila chrysaetos showed the fastest rate of change, with 8.41 km yr(-1 and 7.74 km yr(-1 shifts, respectively. Raptors may be particularly responsive to warming winters because of variable migration tendencies, intraspecific competition for nesting sites that drives males to winter farther north, or both. Overall, 40% of BCR population trend models were improved by incorporating information about wintering distributions; however, support for the effect of distribution on BCR indices varied by species with Rough-legged Hawks showing the most evidence. These results emphasize the importance of understanding how regional distribution shifts influence local-scale population indices. If global climate change is altering distribution patterns, then trends within some management units may not reflect changes in local habitat conditions. The methods used to monitor and manage bird populations within local BCRs will fundamentally

Identification of virulence determinants for endocarditis in Streptococcus sanguinis by signature-tagged mutagenesis.

Science.gov (United States)

Paik, Sehmi; Senty, Lauren; Das, Sankar; Noe, Jody C; Munro, Cindy L; Kitten, Todd

2005-09-01

Streptococcus sanguinis is a gram-positive, facultative anaerobe and a normal inhabitant of the human oral cavity. It is also one of the most common agents of infective endocarditis, a serious endovascular infection. To identify virulence factors for infective endocarditis, signature-tagged mutagenesis (STM) was applied to the SK36 strain of S. sanguinis, whose genome is being sequenced. STM allows the large-scale creation, in vivo screening, and recovery of a series of mutants with altered virulence. Screening of 800 mutants by STM identified 38 putative avirulent and 5 putative hypervirulent mutants. Subsequent molecular analysis of a subset of these mutants identified genes encoding undecaprenol kinase, homoserine kinase, anaerobic ribonucleotide reductase, adenylosuccinate lyase, and a hypothetical protein. Virulence reductions ranging from 2-to 150-fold were confirmed by competitive index assays. One putatively hypervirulent strain with a transposon insertion in an intergenic region was identified, though increased virulence was not confirmed in competitive index assays. All mutants grew comparably to SK36 in aerobic broth culture except for the homoserine kinase mutant. Growth of this mutant was restored by the addition of threonine to the medium. Mutants containing an insertion or in-frame deletion in the anaerobic ribonucleotide reductase gene failed to grow under strictly anaerobic conditions. The results suggest that housekeeping functions such as cell wall synthesis, amino acid and nucleic acid synthesis, and the ability to survive under anaerobic conditions are important virulence factors in S. sanguinis endocarditis.

The Framing of Decisions and the Psychology of Choice.

Science.gov (United States)

Tversky, Amos; Kahneman, Daniel

1981-01-01

Presents evidence that the psychological principles that govern the perception of decision problems and evaluation of probabilities and outcomes produce predictable shifts of preference when the same problem is framed in different ways. (Author/SK)

ENU mutagenesis to generate genetically modified rat models.

Science.gov (United States)

van Boxtel, Ruben; Gould, Michael N; Cuppen, Edwin; Smits, Bart M G

2010-01-01

The rat is one of the most preferred model organisms in biomedical research and has been extremely useful for linking physiology and pathology to the genome. However, approaches to genetically modify specific genes in the rat germ line remain relatively scarce. To date, the most efficient approach for generating genetically modified rats has been the target-selected N-ethyl-N-nitrosourea (ENU) mutagenesis-based technology. Here, we describe the detailed protocols for ENU mutagenesis and mutant retrieval in the rat model organism.

Energy-Efficient Region Shift Scheme to Support Mobile Sink Group in Wireless Sensor Networks.

Science.gov (United States)

Yim, Yongbin; Kim, Kyong Hoon; Aldwairi, Monther; Kim, Ki-Il

2017-12-30

Mobile sink groups play crucial roles to perform their own missions in many wireless sensor network (WSN) applications. In order to support mobility of such sink groups, it is important to design a mechanism for effective discovery of the group in motion. However, earlier studies obtain group region information by periodic query. For that reason, the mechanism leads to significant signaling overhead due to frequent flooding for the query regardless of the group movement. Furthermore, the mechanism worsens the problem by the flooding in the whole expected area. To deal with this problem, we propose a novel mobile sink group support scheme with low communication cost, called Region-Shift-based Mobile Geocasting Protocol (RSMGP). In this study, we utilize the group mobility feature for which members of a group have joint motion patterns. Thus, we could trace group movement by shifting the region as much as partial members move out of the previous region. Furthermore, the region acquisition is only performed at the moment by just deviated members without collaboration of all members. Experimental results validate the improved signaling overhead of our study compared to the previous studies.

Radiation-induced base substitution mutagenesis in single-stranded DNA phage M13

International Nuclear Information System (INIS)

Brandenburger, A.; Godson, G.N.; Glickman, B.W.; Sluis, C.A. van

1981-01-01

To elucidate the relative contributions of targeted and untargeted mutations to γ and UV radiation mutagenesis, the DNA sequences of 174 M13 revertant phages isolated from stocks of irradiated or unirradiated amber mutants grown in irradiated (SOS-induced) or unirradiated (non-induced) host bacteria, have been determined. Differences in the spectra of base change mutations induced in the various conditions were apparent, but no obvious specificity of mutagenesis was detected. In particular, under the present conditions, pyrimidine dimers did not seem to be the principal sites of UV-induced base substitution mutagenesis, suggesting that such mutagenesis occurs at the sites of lesions other than pyrimidine dimers, or is untargeted. (U.K.)

Genetic modifications of established varieties of potato through mutagenesis

International Nuclear Information System (INIS)

Brown, C.R.

1984-01-01

Owing to the high intercrossability of improved clones with primitive cultivars and many wild species there is little justification for use of induced mutations in potato to increase variability per se. Modification of certain traits while leaving the genotype basically intact is a promising use of mutagenesis in potato. The successful curing of defects in clones will depend on the establishment a priori of three principles. First, the clones undergoing mutagenesis should be well established varieties tolerant or resistant to the major biotic and abiotic stresses in the area of cultivation. The yield and culinary quality should also be considered high. Second, there should exist some indication that the variation desired is induceable, either through reports of natural intra-clone variation or previous mutagenesis studies. Third, initial screening should be done in virus-free materials

Step-By-Step In Vitro Mutagenesis: Lessons From Fucose-Binding Lectin PA-IIL.

Science.gov (United States)

Mrázková, Jana; Malinovská, Lenka; Wimmerová, Michaela

2017-01-01

Site-directed mutagenesis is a powerful technique which is used to understand the basis of interactions between proteins and their binding partners, as well as to modify these interactions. Methods of rational design that are based on detailed knowledge of the structure of a protein of interest are often used for preliminary investigations of the possible outcomes which can result from the practical application of site-directed mutagenesis. Also, random mutagenesis can be used in tandem with site-directed mutagenesis for an examination of amino acid "hotspots."Lectins are sugar-binding proteins which, among other functions, mediate the recognition of host cells by a pathogen and its adhesion to the host cell surface. Hence, lectins and their binding properties are studied and engineered using site-directed mutagenesis.In this chapter, we describe a site-directed mutagenesis method used for investigating the sugar binding pattern of the PA-IIL lectin from the pathogenic bacterium Pseudomonas aeruginosa. Moreover, procedures for the production and purification of PA-IIL mutants are described, and several basic methods for characterizing the mutants are discussed.

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging

OpenAIRE

Soreq, Lilach; Rose, Jamie; Soreq, Eyal; Hardy, John; Trabzuni, Daniah; Cookson, Mark R.; Smith, Colin; Ryten, Mina; Patani, Rickie; Ule, Jernej

2017-01-01

Summary Gene expression studies suggest that aging of the human brain is determined by a complex interplay of molecular events, although both its region- and cell-type-specific consequences remain poorly understood. Here, we extensively characterized aging-altered gene expression changes across ten human brain regions from 480 individuals ranging in?age from 16 to 106 years. We show that astrocyte-?and oligodendrocyte-specific genes, but not neuron-specific genes, shift their regional express...

Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides

DEFF Research Database (Denmark)

Bonde, Mads; Kosuri, Sriram; Genee, Hans Jasper

2015-01-01

Multiplex Automated Genome Engineering (MAGE) allows simultaneous mutagenesis of multiple target sites in bacterial genomes using short oligonucleotides. However, large-scale mutagenesis requires hundreds to thousands of unique oligos, which are costly to synthesize and impossible to scale-up by ...

A Simple Combinatorial Codon Mutagenesis Method for Targeted Protein Engineering.

Science.gov (United States)

Belsare, Ketaki D; Andorfer, Mary C; Cardenas, Frida S; Chael, Julia R; Park, Hyun June; Lewis, Jared C

2017-03-17

Directed evolution is a powerful tool for optimizing enzymes, and mutagenesis methods that improve enzyme library quality can significantly expedite the evolution process. Here, we report a simple method for targeted combinatorial codon mutagenesis (CCM). To demonstrate the utility of this method for protein engineering, CCM libraries were constructed for cytochrome P450 BM3 , pfu prolyl oligopeptidase, and the flavin-dependent halogenase RebH; 10-26 sites were targeted for codon mutagenesis in each of these enzymes, and libraries with a tunable average of 1-7 codon mutations per gene were generated. Each of these libraries provided improved enzymes for their respective transformations, which highlights the generality, simplicity, and tunability of CCM for targeted protein engineering.

CRISPR/Cas9 mediates efficient conditional mutagenesis in Drosophila.

Science.gov (United States)

Xue, Zhaoyu; Wu, Menghua; Wen, Kejia; Ren, Menda; Long, Li; Zhang, Xuedi; Gao, Guanjun

2014-09-05

Existing transgenic RNA interference (RNAi) methods greatly facilitate functional genome studies via controlled silencing of targeted mRNA in Drosophila. Although the RNAi approach is extremely powerful, concerns still linger about its low efficiency. Here, we developed a CRISPR/Cas9-mediated conditional mutagenesis system by combining tissue-specific expression of Cas9 driven by the Gal4/upstream activating site system with various ubiquitously expressed guide RNA transgenes to effectively inactivate gene expression in a temporally and spatially controlled manner. Furthermore, by including multiple guide RNAs in a transgenic vector to target a single gene, we achieved a high degree of gene mutagenesis in specific tissues. The CRISPR/Cas9-mediated conditional mutagenesis system provides a simple and effective tool for gene function analysis, and complements the existing RNAi approach. Copyright © 2014 Xue et al.

Mechanisms of mutagenesis of E. coli by ultraviolet light

International Nuclear Information System (INIS)

Hutchinson, F.; Wood, R.D.

1986-01-01

This summary shows that uv mutagenesis involves several processes and several types of mutations. It is important to know, if some step or event affects, say, uv-induced reversion of a his mutant, what kinds of mutation cause the reversion. More, if reversion of the mutant is not affected, it is essential to know what kinds of mutation are involved, because statements can only be made about these mutations, and not about uv mutagenesis in general. It is also clear that the spectrum of mutations will depend on dose. Thus, extrapolation from experimental data at high dose to low dose situations involve considerations both of numbers and of kinds of mutations. Extrapolation of these results to other organisms may be particularly difficult because the SOS functions play such a large role in uv mutagenesis of E. coli. 34 refs., 1 tab

2012 Gordon Research Conference on Mutagenesis - Formal Schedule and Speaker/Poster Program

Energy Technology Data Exchange (ETDEWEB)

Demple, Bruce [Stony Brook Univ., NY (United States). School of Medicine

2012-08-24

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.

Effective lethal mutagenesis of influenza virus by three nucleoside analogs.

Science.gov (United States)

Pauly, Matthew D; Lauring, Adam S

2015-04-01

Lethal mutagenesis is a broad-spectrum antiviral strategy that exploits the high mutation rate and low mutational tolerance of many RNA viruses. This approach uses mutagenic drugs to increase viral mutation rates and burden viral populations with mutations that reduce the number of infectious progeny. We investigated the effectiveness of lethal mutagenesis as a strategy against influenza virus using three nucleoside analogs, ribavirin, 5-azacytidine, and 5-fluorouracil. All three drugs were active against a panel of seasonal H3N2 and laboratory-adapted H1N1 strains. We found that each drug increased the frequency of mutations in influenza virus populations and decreased the virus' specific infectivity, indicating a mutagenic mode of action. We were able to drive viral populations to extinction by passaging influenza virus in the presence of each drug, indicating that complete lethal mutagenesis of influenza virus populations can be achieved when a sufficient mutational burden is applied. Population-wide resistance to these mutagenic agents did not arise after serial passage of influenza virus populations in sublethal concentrations of drug. Sequencing of these drug-passaged viral populations revealed genome-wide accumulation of mutations at low frequency. The replicative capacity of drug-passaged populations was reduced at higher multiplicities of infection, suggesting the presence of defective interfering particles and a possible barrier to the evolution of resistance. Together, our data suggest that lethal mutagenesis may be a particularly effective therapeutic approach with a high genetic barrier to resistance for influenza virus. Influenza virus is an RNA virus that causes significant morbidity and mortality during annual epidemics. Novel therapies for RNA viruses are needed due to the ease with which these viruses evolve resistance to existing therapeutics. Lethal mutagenesis is a broad-spectrum strategy that exploits the high mutation rate and the low

The relationship between survival and mutagenesis in Escherichia coli after fractionated ultraviolet irradiation

International Nuclear Information System (INIS)

Dzidic, S.; Salaj-Smic, E.; Trgovcevic, Z.

1986-01-01

The relationship between survival and mutagenesis in Escherichia coli after fractionated ultraviolet (UV) irradiation was studied. The cells were incubated either in buffer or nutrient media. Regardless of incubation conditions, greater survival is observed after fractionated irradiation than after acute irradiation. When the cells are incubated in buffer, UV mutagenesis decreases with an increase in the number of dose fractions. However, when the cells are cultivated in nutrient media, the increased survival is coupled with the enhanced capacity for UV mutagenesis. The authors, therefore, assume that during incubation in nutrient media, fractionated irradiation leads to full and prolonged expression of all UV inducible (SOS) genes, including those required for mutagenesis. (Auth.)

Does having the right visitor mix do the job? Applying an econometric shift-share model to regional tourism developments

OpenAIRE

Firgo, Matthias; Fritz, Oliver

2016-01-01

This paper is the first to apply an econometric shift-share model to tourism. The approach allows us to isolate the growth contributions of changes in regional touristic attractiveness from those induced by the structure of visitors, but does not share the caveats of the conventional shift-share approach. Our application to regional tourism in Austria reveals important results: First, differences in long-run performance between regions are mostly related to idiosyncratic changes in the touris...

Back to the future: revisiting HIV-1 lethal mutagenesis

Science.gov (United States)

Dapp, Michael J.; Patterson, Steven E.; Mansky, Louis M.

2012-01-01

The concept of eliminating HIV-1 infectivity by elevating the viral mutation rate was first proposed over a decade ago, even though the general concept had been conceived earlier for RNA viruses. Lethal mutagenesis was originally viewed as a novel chemotherapeutic approach for treating HIV-1 infection in which use of a viral mutagen would over multiple rounds of replication lead to the lethal accumulation of mutations, rendering the virus population non infectious – known as the slow mutation accumulation model. There have been limitations in obtaining good efficacy data with drug leads, leaving some doubt into clinical translation. More recent studies of the APOBEC3 proteins as well as new progress in the use of nucleoside analogs for inducing lethal mutagenesis have helped to refocus attention on rapid induction of HIV-1 lethal mutagenesis in a single or limited number of replication cycles leading to a rapid mutation accumulation model. PMID:23195922

The framing of decisions and the psychology of choice.

Science.gov (United States)

Tversky, A; Kahneman, D

1981-01-30

The psychological principles that govern the perception of decision problems and the evaluation of probabilities and outcomes produce predictable shifts of preference when the same problem is framed in different ways. Reversals of preference are demonstrated in choices regarding monetary outcomes, both hypothetical and real, and in questions pertaining to the loss of human lives. The effects of frames on preferences are compared to the effects of perspectives on perceptual appearance. The dependence of preferences on the formulation of decision problems is a significant concern for the theory of rational choice.

Complex epidemiological approach to human mutagenesis

International Nuclear Information System (INIS)

Czeizel, A.

1980-01-01

The main characteristics of the epidemiological approach are summarised and the criteria discussed for the adoption of this approach for the detection of human mutagenesis. Mutation monitoring systems are described and results of epidemiological studies of higher risk populations are presented. (C.F.)

Genetic improvement of soybean through induced mutagenesis

International Nuclear Information System (INIS)

Manjaya, J.G.; Nandanwar, R.S.; Thengane, R.J.; Muthiah, A.R.

2009-01-01

Soybean (Glycine max (L.) Merril) is one of the important oilseed crops of India. The country produces more than 9.00 million tonnes of soybean per annum and has acquired first place amongst oilseed crops grown in India. Narrow genetic base of cultivated varieties in soybean is of global concern. Efficient mutant production systems, through physical or chemical mutagenesis, have been well established in soybean. A vast amount of genetic variability, of both quantitative and qualitative traits, has been generated through experimental mutagenesis. Two soybean varieties TAMS-38 and TAMS 98-21 have been developed and released for commercial cultivation by Bhabha Atomic Research Centre (BARC). In this paper the role of mutation breeding in soybean improvement has been discussed. (author)

Suitability of the echo-time-shift method as laboratory standard for thermal ultrasound dosimetry

Science.gov (United States)

Fuhrmann, Tina; Georg, Olga; Haller, Julian; Jenderka, Klaus-Vitold

2017-03-01

Ultrasound therapy is a promising, non-invasive application with potential to significantly improve cancer therapies like surgery, viro- or immunotherapy. This therapy needs faster, cheaper and more easy-to-handle quality assurance tools for therapy devices as well as possibilities to verify treatment plans and for dosimetry. This limits comparability and safety of treatments. Accurate spatial and temporal temperature maps could be used to overcome these shortcomings. In this contribution first results of suitability and accuracy investigations of the echo-time-shift method for two-dimensional temperature mapping during and after sonication are presented. The analysis methods used to calculate time-shifts were a discrete frame-to-frame and a discrete frame-to-base-frame algorithm as well as a sigmoid fit for temperature calculation. In the future accuracy could be significantly enhanced by using continuous methods for time-shift calculation. Further improvements can be achieved by improving filtering algorithms and interpolation of sampled diagnostic ultrasound data. It might be a comparatively accurate, fast and affordable method for laboratory and clinical quality control.

Framing the frame

Directory of Open Access Journals (Sweden)

Todd McElroy

2007-08-01

Full Text Available We examined how the goal of a decision task influences the perceived positive, negative valence of the alternatives and thereby the likelihood and direction of framing effects. In Study 1 we manipulated the goal to increase, decrease or maintain the commodity in question and found that when the goal of the task was to increase the commodity, a framing effect consistent with those typically observed in the literature was found. When the goal was to decrease, a framing effect opposite to the typical findings was observed whereas when the goal was to maintain, no framing effect was found. When we examined the decisions of the entire population, we did not observe a framing effect. In Study 2, we provided participants with a similar decision task except in this situation the goal was ambiguous, allowing us to observe participants' self-imposed goals and how they influenced choice preferences. The findings from Study 2 demonstrated individual variability in imposed goal and provided a conceptual replication of Study 1. %need keywords

Deletion of Dystrophin In-Frame Exon 5 Leads to a Severe Phenotype: Guidance for Exon Skipping Strategies.

Directory of Open Access Journals (Sweden)

Zhi Yon Charles Toh

Full Text Available Duchenne and Becker muscular dystrophy severity depends upon the nature and location of the DMD gene lesion and generally correlates with the dystrophin open reading frame. However, there are striking exceptions where an in-frame genomic deletion leads to severe pathology or protein-truncating mutations (nonsense or frame-shifting indels manifest as mild disease. Exceptions to the dystrophin reading frame rule are usually resolved after molecular diagnosis on muscle RNA. We report a moderate/severe Becker muscular dystrophy patient with an in-frame genomic deletion of DMD exon 5. This mutation has been reported by others as resulting in Duchenne or Intermediate muscular dystrophy, and the loss of this in-frame exon in one patient led to multiple splicing events, including omission of exon 6, that disrupts the open reading frame and is consistent with a severe phenotype. The patient described has a deletion of dystrophin exon 5 that does not compromise recognition of exon 6, and although the deletion does not disrupt the reading frame, his clinical presentation is more severe than would be expected for classical Becker muscular dystrophy. We suggest that the dystrophin isoform lacking the actin-binding sequence encoded by exon 5 is compromised, reflected by the phenotype resulting from induction of this dystrophin isoform in mouse muscle in vivo. Hence, exon skipping to address DMD-causing mutations within DMD exon 5 may not yield an isoform that confers marked clinical benefit. Additional studies will be required to determine whether multi-exon skipping strategies could yield more functional dystrophin isoforms, since some BMD patients with larger in-frame deletions in this region have been reported with mild phenotypes.

The Structure of Urease Activation Complexes Examined by Flexibility Analysis, Mutagenesis, and Small-angle X-ray Scattering Approaches

International Nuclear Information System (INIS)

Quiroz, Soledad; Sukuru, Sai Chetan K.; Hausinger, Robert P.; Kuhn, Leslie A.; Heller, William T

2008-01-01

Conformational changes of Klebsiella aerogenes urease apoprotein (UreABC) 3 induced upon binding of the UreD and UreF accessory proteins were examined by a combination of flexibility analysis, mutagenesis, and small-angle X-ray scattering (SAXS). ProFlex analysis of urease provided evidence that the major domain of UreB can move in a hinge-like motion to account for prior chemical cross-linking results. Rigidification of the UreB hinge region, accomplished through a G11P mutation, reduced the extent of urease activation, in part by decreasing the nickel content of the mutant enzyme, and by sequestering a portion of the urease apoprotein in a novel activation complex that includes all of the accessory proteins. SAXS analyses of urease, (UreABC-UreD) 3 , and (UreABC-UreDF) 3 confirm that UreD and UreF bind near UreB at the periphery of the (UreAC) 3 structure. This study supports an activation model in which a domain-shifted UreB conformation in (UreABC-UreDF) 3 allows CO 2 and nickel ions to gain access to the nascent active site

Lethal mutagenesis: targeting the mutator phenotype in cancer.

Science.gov (United States)

Fox, Edward J; Loeb, Lawrence A

2010-10-01

The evolution of cancer and RNA viruses share many similarities. Both exploit high levels of genotypic diversity to enable extensive phenotypic plasticity and thereby facilitate rapid adaptation. In order to accumulate large numbers of mutations, we have proposed that cancers express a mutator phenotype. Similar to cancer cells, many viral populations, by replicating their genomes with low fidelity, carry a substantial mutational load. As high levels of mutation are potentially deleterious, the viral mutation frequency is thresholded at a level below which viral populations equilibrate in a traditional mutation-selection balance, and above which the population is no longer viable, i.e., the population undergoes an error catastrophe. Because their mutation frequencies are fine-tuned just below this error threshold, viral populations are susceptible to further increases in mutational load and, recently this phenomenon has been exploited therapeutically by a concept that has been termed lethal mutagenesis. Here we review the application of lethal mutagenesis to the treatment of HIV and discuss how lethal mutagenesis may represent a novel therapeutic approach for the treatment of solid cancers. Copyright © 2010 Elsevier Ltd. All rights reserved.

A framework of region-based dynamic image fusion

Institute of Scientific and Technical Information of China (English)

WANG Zhong-hua; QIN Zheng; LIU Yu

2007-01-01

A new framework of region-based dynamic image fusion is proposed. First, the technique of target detection is applied to dynamic images (image sequences) to segment images into different targets and background regions. Then different fusion rules are employed in different regions so that the target information is preserved as much as possible. In addition, steerable non-separable wavelet frame transform is used in the process of multi-resolution analysis, so the system achieves favorable characters of orientation and invariant shift. Compared with other image fusion methods, experimental results showed that the proposed method has better capabilities of target recognition and preserves clear background information.

Antimutation effect of an E. coli membrane fraction on UV-mutagenesis

International Nuclear Information System (INIS)

Harper, D.; Kristoff, S.; Bockrath, R.; Indiana Univ., Indianapolis; Indiana Univ., Indianapolis

1980-01-01

The depression of mutagenesis that occurs when irradiated E. coli are plated at high densities is studied. The number of mutant colonies indicated increases linearly with increasing plate density to about 10 8 bacteria per plate. At higher plate densities, suppressor mutations are very sensitive to crowding depression of mutagenesis and backmutations are somewhat sensitive. (orig./AJ)

Framing the frame

OpenAIRE

Todd McElroy; John J. Seta

2007-01-01

We examined how the goal of a decision task influences the perceived positive, negative valence of the alternatives and thereby the likelihood and direction of framing effects. In Study 1 we manipulated the goal to increase, decrease or maintain the commodity in question and found that when the goal of the task was to increase the commodity, a framing effect consistent with those typically observed in the literature was found. When the goal was to decrease, a framing effect opposite to the ty...

A function of mutagenesis on rhodotorula RY strain irradiated by heavy ion

International Nuclear Information System (INIS)

Li Hongyu; Li Chenghua; Ding Xinchun; Wang Jufang; Zhou Guangming; Xie Hongmei; Li Qiang; Dang bingrong; Wen Xiaoqiong; Li Wenjian; Wei Zengquan

2004-01-01

In this paper, red yeast (Rhodotorula RY Strain) that produces carotene is irradiated by 50 MeV/u 12 C 6+ heavy ion from Heavy Ion Accelerator in IMP. Fermentation tests show that 50 MeV/u 12 C 6+ heavy ion has a mutagenesis effect on the red yeast. Some strains of red yeast with changed production of carotene were found by screening. Meanwhile, by RFLP and RAPD analysis, authors have a further evidence that heavy ion can cause mutagenesis in Rhodotorula RY Strain. This presents a new prospect for the mutagenesis breeding by heavy ion in industry

Mutagenesis of Trichoderma Viride by Ultraviolet and Plasma

International Nuclear Information System (INIS)

Yao Risheng; Li Manman; Deng Shengsong; Hu Huajia; Wang Huai; Li Fenghe

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.

Mutagenesis of Trichoderma Viride by Ultraviolet and Plasma

Science.gov (United States)

Yao, Risheng; Li, Manman; Deng, Shengsong; Hu, Huajia; Wang, Huai; Li, Fenghe

2012-04-01

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.

Multiple pathways for SOS-induced mutagenesis in Escherichia coli: An overexpression of dinB/dinP results in strongly enhancing mutagenesis in the absence of any exogenous treatment to damage DNA

Science.gov (United States)

Kim, Su-Ryang; Maenhaut-Michel, Geneviéve; Yamada, Masami; Yamamoto, Yoshihiro; Matsui, Keiko; Sofuni, Toshio; Nohmi, Takehiko; Ohmori, Haruo

1997-01-01

dinP is an Escherichia coli gene recently identified at 5.5 min of the genetic map, whose product shows a similarity in amino acid sequence to the E. coli UmuC protein involved in DNA damage-induced mutagenesis. In this paper we show that the gene is identical to dinB, an SOS gene previously localized near the lac locus at 8 min, the function of which was shown to be required for mutagenesis of nonirradiated λ phage infecting UV-preirradiated bacterial cells (termed λUTM for λ untargeted mutagenesis). A newly constructed dinP null mutant exhibited the same defect for λUTM as observed previously with a dinB::Mu mutant, and the defect was complemented by plasmids carrying dinP as the only intact bacterial gene. Furthermore, merely increasing the dinP gene expression, without UV irradiation or any other DNA-damaging treatment, resulted in a strong enhancement of mutagenesis in F′lac plasmids; at most, 800-fold increase in the G6-to-G5 change. The enhanced mutagenesis did not depend on recA, uvrA, or umuDC. Thus, our results establish that E. coli has at least two distinct pathways for SOS-induced mutagenesis: one dependent on umuDC and the other on dinB/P. PMID:9391106

Long-term regional shifts in plant community composition are largely explained by local deer impact experiments.

Directory of Open Access Journals (Sweden)

Katie Frerker

Full Text Available The fact that herbivores and predators exert top-down effects to alter community composition and dynamics at lower trophic levels is no longer controversial, yet we still lack evidence of the full nature, extent, and longer-term effects of these impacts. Here, we use results from a set of replicated experiments on the local impacts of white-tailed deer to evaluate the extent to which such impacts could account for half-century shifts in forest plant communities across the upper Midwest, USA. We measured species' responses to deer at four sites using 10-20 year-old deer exclosures. Among common species, eight were more abundant outside the exclosures, seven were commoner inside, and 16 had similar abundances in- and outside. Deer herbivory greatly increased the abundance of ferns and graminoids and doubled the abundance of exotic plants. In contrast, deer greatly reduced tree regeneration, shrub cover (100-200 fold in two species, plant height, plant reproduction, and the abundance of forbs. None of 36 focal species increased in reproduction or grew taller in the presence of deer, contrary to expectations. We compared these results to data on 50-year regional shifts in species abundances across 62 sites. The effects of herbivory by white-tailed deer accurately account for many of the long-term regional shifts observed in species' abundances (R2 = 0.41. These results support the conjecture that deer impacts have driven many of the regional shifts in forest understory cover and composition observed in recent decades. Our ability to link results from shorter-term, local experiments to regional long-term studies of ecological change strengthens the inferences we can draw from both approaches.

Shifting problems and shifting policies to reduce student drop-out

DEFF Research Database (Denmark)

Jørgensen, Christian Helms

2016-01-01

, as well as the policies that have been implemented in pursuit of improving student retention. The review identifies two pervasive ways in which the drop-out problem has been framed in both policy and research. The first locates the drop-out problem with individual students, while the second locates...... finds that the rate of student drop-out has been a cause for ongoing concern among policy makers for more than a century, and that the framing of the problem has shifted considerably over time. The problem has variously been placed with the individual apprentice, the basic structure of vocational......Education policy generally places a premium on raising the level of education attained by the young generation ultimately heading towards the labour market. While the rate of enrolment in post-compulsory education has risen in most countries, so too has the rate of drop-out, in particular from...

Gabor frames on locally compact abelian groups and related topics

DEFF Research Database (Denmark)

Jakobsen, Mads Sielemann

This thesis consists of four papers. The first one introduces generalized translation invariant systems and considers their frame properties, the second and third paper give new results on the theory of Gabor frames, and the fourth is a review paper with proofs and new results on the Feichtinger......- and shearlet-type and for (generalized) shift-invariant systems and their continuous formulations. This thesis advances the theory of both separable and non-separable, discrete, semicontinuous and continuous Gabor systems. In particular, the well established structure theory for separable lattice Gabor frames...... and Gabor Riesz bases. The theory of GTI systems and Gabor frames in this thesis is developed and presented in the setting of locally compact abelian groups, however, even in the euclidean setting the results given here improve the existing theory. Finally, the thesis contains a review paper with proofs...

Ribozyme Mediated gRNA Generation for In Vitro and In Vivo CRISPR/Cas9 Mutagenesis.

Science.gov (United States)

Lee, Raymond Teck Ho; Ng, Ashley Shu Mei; Ingham, Philip W

2016-01-01

CRISPR/Cas9 is now regularly used for targeted mutagenesis in a wide variety of systems. Here we report the use of ribozymes for the generation of gRNAs both in vitro and in zebrafish embryos. We show that incorporation of ribozymes increases the types of promoters and number of target sites available for mutagenesis without compromising mutagenesis efficiency. We have tested this by comparing the efficiency of mutagenesis of gRNA constructs with and without ribozymes and also generated a transgenic zebrafish expressing gRNA using a heat shock promoter (RNA polymerase II-dependent promoter) that was able to induce mutagenesis of its target. Our method provides a streamlined approach to test gRNA efficiency as well as increasing the versatility of conditional gene knock out in zebrafish.

Pilot study of large-scale production of mutant pigs by ENU mutagenesis.

Science.gov (United States)

Hai, Tang; Cao, Chunwei; Shang, Haitao; Guo, Weiwei; Mu, Yanshuang; Yang, Shulin; Zhang, Ying; Zheng, Qiantao; Zhang, Tao; Wang, Xianlong; Liu, Yu; Kong, Qingran; Li, Kui; Wang, Dayu; Qi, Meng; Hong, Qianlong; Zhang, Rui; Wang, Xiupeng; Jia, Qitao; Wang, Xiao; Qin, Guosong; Li, Yongshun; Luo, Ailing; Jin, Weiwu; Yao, Jing; Huang, Jiaojiao; Zhang, Hongyong; Li, Menghua; Xie, Xiangmo; Zheng, Xuejuan; Guo, Kenan; Wang, Qinghua; Zhang, Shibin; Li, Liang; Xie, Fei; Zhang, Yu; Weng, Xiaogang; Yin, Zhi; Hu, Kui; Cong, Yimei; Zheng, Peng; Zou, Hailong; Xin, Leilei; Xia, Jihan; Ruan, Jinxue; Li, Hegang; Zhao, Weiming; Yuan, Jing; Liu, Zizhan; Gu, Weiwang; Li, Ming; Wang, Yong; Wang, Hongmei; Yang, Shiming; Liu, Zhonghua; Wei, Hong; Zhao, Jianguo; Zhou, Qi; Meng, Anming

2017-06-22

N-ethyl-N-nitrosourea (ENU) mutagenesis is a powerful tool to generate mutants on a large scale efficiently, and to discover genes with novel functions at the whole-genome level in Caenorhabditis elegans, flies, zebrafish and mice, but it has never been tried in large model animals. We describe a successful systematic three-generation ENU mutagenesis screening in pigs with the establishment of the Chinese Swine Mutagenesis Consortium. A total of 6,770 G1 and 6,800 G3 pigs were screened, 36 dominant and 91 recessive novel pig families with various phenotypes were established. The causative mutations in 10 mutant families were further mapped. As examples, the mutation of SOX10 (R109W) in pig causes inner ear malfunctions and mimics human Mondini dysplasia, and upregulated expression of FBXO32 is associated with congenital splay legs. This study demonstrates the feasibility of artificial random mutagenesis in pigs and opens an avenue for generating a reservoir of mutants for agricultural production and biomedical research.

Isotope shift studies in the spectra of gadolinium in UV region and term shifts of high even levels of Gd I

International Nuclear Information System (INIS)

Afzal, S.M.; Venugopalan, A.; Ahmad, S.A.

1997-01-01

Isotope shift Δσ( 156 Gd- 160 Gd) is reported in 70 spectral lines of neutral gadolinium atom (Gd I) in the 3290-3920 A region providing isotope shift data in UV lines of Gd I spectrum for the first time. The measurements were carried out on a photoelectric recording Fabry-Perot Spectrometer using highly enriched isotopic samples of gadolinium. Term isotope shifts ΔT( 156 Gd- 160 Gd) have been evaluated for 48 high lying even parity energy levels of Gd I using this data; new ΔT values have been obtained for 24 levels. Electronic configurations 4f 7 5d6s6p, 4f 7 5d 2 6p and 4f 8 5d6s assigned earlier to these even levels have been either confirmed or configuration mixing pointed out in some of these levels. Probable assignment of 4f 8 5d6s configuration to 8 even levels between 32930 and 35500 cm -1 have been confirmed. (orig.)

Frames of Mind in Intertemporal Choice

OpenAIRE

George F. Loewenstein

1988-01-01

Recent research has demonstrated that choices between gambles are systematically influenced by the way they are expressed. Kahneman and Tversky's Prospect Theory (Kahneman, D., A. Tversky. 1979. Prospect theory: An analysis of decision under risk. Econometrica 47(2) 363--391.) explains many of these "framing" effects as shifts in the point of reference from which prospects are evaluated. This paper demonstrates the applicability of the reference point concept to intertemporal choice. Three ex...

Novel Random Mutagenesis Method for Directed Evolution.

Science.gov (United States)

Feng, Hong; Wang, Hai-Yan; Zhao, Hong-Yan

2017-01-01

Directed evolution is a powerful strategy for gene mutagenesis, and has been used for protein engineering both in scientific research and in the biotechnology industry. The routine method for directed evolution was developed by Stemmer in 1994 (Stemmer, Proc Natl Acad Sci USA 91, 10747-10751, 1994; Stemmer, Nature 370, 389-391, 1994). Since then, various methods have been introduced, each of which has advantages and limitations depending upon the targeted genes and procedure. In this chapter, a novel alternative directed evolution method which combines mutagenesis PCR with dITP and fragmentation by endonuclease V is described. The kanamycin resistance gene is used as a reporter gene to verify the novel method for directed evolution. This method for directed evolution has been demonstrated to be efficient, reproducible, and easy to manipulate in practice.

Joint variable frame rate and length analysis for speech recognition under adverse conditions

DEFF Research Database (Denmark)

Tan, Zheng-Hua; Kraljevski, Ivan

2014-01-01

This paper presents a method that combines variable frame length and rate analysis for speech recognition in noisy environments, together with an investigation of the effect of different frame lengths on speech recognition performance. The method adopts frame selection using an a posteriori signal......-to-noise (SNR) ratio weighted energy distance and increases the length of the selected frames, according to the number of non-selected preceding frames. It assigns a higher frame rate and a normal frame length to a rapidly changing and high SNR region of a speech signal, and a lower frame rate and an increased...... frame length to a steady or low SNR region. The speech recognition results show that the proposed variable frame rate and length method outperforms fixed frame rate and length analysis, as well as standalone variable frame rate analysis in terms of noise-robustness....

Evidence for a climate-induced ecohydrological state shift in wetland ecosystems of the southern Prairie Pothole Region

Science.gov (United States)

McKenna, Owen; Mushet, David M.; Rosenberry, Donald O.; LaBaugh, James W.

2017-01-01

Changing magnitude, frequency, and timing of precipitation can influence aquatic-system hydrological, geochemical, and biological processes, in some cases resulting in system-wide shifts to an alternate state. Since the early 1990s, the southern Prairie Pothole Region has been subjected to an extended period of increased wetness resulting in marked changes to aquatic systems defining this region. We explored numerous lines of evidence to identify: (1) how the recent wet period compared to historical variability, (2) hydrological, geochemical, and biological responses, and (3) how these responses might represent a state shift in the region’s wetland ecosystems. We analyzed long-term climate records and compared how different hydrological variables responded in this wet period compared to decades before the observed shift. Additionally, we used multi-decadal records of waterfowl population and subsurface tile drain records to explore wildlife and human responses to a shifting climate. Since 1993, a novel precipitation regime corresponded with increased pond numbers, ponded-water depths, lake levels, stream flows, groundwater heights, soil-moisture, waterfowl populations, and installation of subsurface tile drains in agricultural fields. These observed changes reflect an alteration in water storage and movement across the landscape that in turn has altered solute sources and concentrations of prairie-pothole wetlands and has increased pond permanence. Combined, these changes represent significant evidence for a state shift in the ecohydrological functioning of the region’s wetland ecosystems, a shift that may require a significant refinement of the previously developed “wetland continuum” concept.

Target-selected mutagenesis of the rat

NARCIS (Netherlands)

Smits, B.M.; Mudde, J.B.; Plasterk, R.; Cuppen, E.

2004-01-01

The rat is one of the most extensively studied model organisms, and with its genome being sequenced, tools to manipulate gene function in vivo have become increasingly important. We here report proof of principle for target-selected mutagenesis as a reverse genetic or knockout approach for the rat.

DNA MUTAGENESIS IN PANAX GINSENG CELL CULTURES

Directory of Open Access Journals (Sweden)

Kiselev K.V.

2012-08-01

Full Text Available At the present time, it is well documented that plant tissue culture induces a number of mutations and chromosome rearrangements termed “somaclonal variations”. However, little is known about the nature and the molecular mechanisms of the tissue culture-induced mutagenesis and the effects of long-term subculturing on the rate and specific features of the mutagenesis. The aim of the present study was to investigate and compare DNA mutagenesis in different genes of Panax ginseng callus cultures of different age. It has previously been shown that the nucleotide sequences of the Agrobacterium rhizogenes rolC locus and the selective marker nptII developed mutations during long-term cultivation of transgenic cell cultures of P. ginseng. In the present work, we analyzed nucleotide sequences of selected plant gene families in a 2-year-old and 20-year-old P. ginseng 1c cell culture and in leaves of cultivated P. ginseng plants. We analysed sequence variability between the Actin genes, which are a family of house-keeping genes; the phenylalanine ammonia-lyase (PAL and dammarenediol synthase (DDS genes, which actively participate in the biosynthesis of ginsenosides; and the somatic embryogenesis receptor kinase (SERK genes, which control plant development. The frequency of point mutations in the Actin, PAL, DDS, and SERK genes in the 2-year-old callus culture was markedly higher than that in cultivated plants but lower than that in the 20-year-old callus culture of P. ginseng. Most of the mutations in the 2- and 20-year-old P. ginseng calli were A↔G and T↔C transitions. The number of nonsynonymous mutations was higher in the 2- and 20-year-old callus cultures than the number of nonsynonymous mutations in the cultivated plants of P. ginseng. Interestingly, the total number of N→G or N→C substitutions in the analyzed genes was 1.6 times higher than the total number of N→A or N→T substitutions. Using methylation-sensitive DNA fragmentation

Gene discovery by chemical mutagenesis and whole-genome sequencing in Dictyostelium.

Science.gov (United States)

Li, Cheng-Lin Frank; Santhanam, Balaji; Webb, Amanda Nicole; Zupan, Blaž; Shaulsky, Gad

2016-09-01

Whole-genome sequencing is a useful approach for identification of chemical-induced lesions, but previous applications involved tedious genetic mapping to pinpoint the causative mutations. We propose that saturation mutagenesis under low mutagenic loads, followed by whole-genome sequencing, should allow direct implication of genes by identifying multiple independent alleles of each relevant gene. We tested the hypothesis by performing three genetic screens with chemical mutagenesis in the social soil amoeba Dictyostelium discoideum Through genome sequencing, we successfully identified mutant genes with multiple alleles in near-saturation screens, including resistance to intense illumination and strong suppressors of defects in an allorecognition pathway. We tested the causality of the mutations by comparison to published data and by direct complementation tests, finding both dominant and recessive causative mutations. Therefore, our strategy provides a cost- and time-efficient approach to gene discovery by integrating chemical mutagenesis and whole-genome sequencing. The method should be applicable to many microbial systems, and it is expected to revolutionize the field of functional genomics in Dictyostelium by greatly expanding the mutation spectrum relative to other common mutagenesis methods. © 2016 Li et al.; Published by Cold Spring Harbor Laboratory Press.

Suppression and Narrative Time Shifts in Adults with Right-Hemisphere Brain Damage

Science.gov (United States)

Scharp, Victoria L.; Tompkins, Connie A.

2013-01-01

Purpose: This study examined the functioning of a central comprehension mechanism, suppression, in adults with right-hemisphere damage (RHD) while they processed narratives that cued a shift in time frame. In normal language comprehension, mental activation of concepts from a prior time frame is suppressed. The (re)activation of information…

The use of plant tissue culture system in the mutagenesis of Secale cereale L

International Nuclear Information System (INIS)

Rybczynski, J.J.; KozIowska, W.; Turzynski, D.

1990-01-01

Full text: Among cereals, Secale cereale L. is the worst species for 'in vitro' mutagenesis. In the case of seed mutagenesis of rye each seed is expected to be a different genotype and only somatic embryogenesis assures propagation towards numerous individuals possessing the same genotype. Therefore, another system of in-vitro mutagenesis is explored. Immature embryos were isolated from spikes of field growing plants. The established cultures were irradiated with 0.5; 1.0 and 1.5 kR gamma rays on the first day of the culture and after 6 weeks in culture. After irradiation all cultures were subcultured. For mutagenesis in general uniformity of the original material is very important. Therefore, in rye, irradiation of regenerated somatic embryos may be a good approach. (author)

Nelson`s syndrome associated with a somatic frame shift mutation in the glucocorticoid recepter gene

Energy Technology Data Exchange (ETDEWEB)

Karl, M.; Stratakis, C.A.; Chrousos, G.P.; Katz, D.A.; Ali, I.U.; Oldfield, E.H. [National Inst. of Neurological Disorders and Stroke, Bethesda, MD (United States)] [and others

1996-01-01

Nelson`s syndrome is the appearance and/or progression of ACTH-secreting pituitary macroadenomas in patients who had previously undergone bilateral adrenalectomy for Cushing`s disease. Extremely high plasma ACTH levels and aggressive neoplastic growth might be explained by the lack of appropriate glucocorticoid negative feedback due to defective glucocorticoid signal transduction. To study the glucocorticoid receptor (GR) gene in Nelson`s syndrome, DNA was extracted from pituitary adenomas and leukocytes of four patients with this condition and amplified by PCR for direct sequence analysis. In one of the tumors, a heterozygous mutation, consisting of an insertion of a thymine between complementary DNA nucleotides 1188 and 1189, was found in exon 2. This frame-shift mutation led to premature termination at amino acid residue 366 of the world-type coding sequence, excluding the expression of a functioning receptor protein from the defective allele. The mutation was not detected in the sequence of the GR gene in the patient`s leukocyte DNA, indicating a somatic origin. By lowering the receptor number in tumorous cells, this defect might have caused local resistance to negative glucocorticoid feedback similar to that caused by the presence of a null allele in a kindred with the generalized glucocorticoid resistance syndrome. P53 protein accumulation, previously reported in 60% of corticotropinomas, could not be detected in any of the four pituitary tumors examined by immunohistochemistry. We suggest that a somatic GR defect might have played a pathophysiological role in the tumorigenesis of the corticotropinoma bearing this mutation. 35 refs., 3 figs., 1 tab.

Genome-wide maps of alkylation damage, repair, and mutagenesis in yeast reveal mechanisms of mutational heterogeneity.

Science.gov (United States)

Mao, Peng; Brown, Alexander J; Malc, Ewa P; Mieczkowski, Piotr A; Smerdon, Michael J; Roberts, Steven A; Wyrick, John J

2017-10-01

DNA base damage is an important contributor to genome instability, but how the formation and repair of these lesions is affected by the genomic landscape and contributes to mutagenesis is unknown. Here, we describe genome-wide maps of DNA base damage, repair, and mutagenesis at single nucleotide resolution in yeast treated with the alkylating agent methyl methanesulfonate (MMS). Analysis of these maps revealed that base excision repair (BER) of alkylation damage is significantly modulated by chromatin, with faster repair in nucleosome-depleted regions, and slower repair and higher mutation density within strongly positioned nucleosomes. Both the translational and rotational settings of lesions within nucleosomes significantly influence BER efficiency; moreover, this effect is asymmetric relative to the nucleosome dyad axis and is regulated by histone modifications. Our data also indicate that MMS-induced mutations at adenine nucleotides are significantly enriched on the nontranscribed strand (NTS) of yeast genes, particularly in BER-deficient strains, due to higher damage formation on the NTS and transcription-coupled repair of the transcribed strand (TS). These findings reveal the influence of chromatin on repair and mutagenesis of base lesions on a genome-wide scale and suggest a novel mechanism for transcription-associated mutation asymmetry, which is frequently observed in human cancers. © 2017 Mao et al.; Published by Cold Spring Harbor Laboratory Press.

Dynamic response and stability of semi-rigid frames

Science.gov (United States)

Abu-Yasein, Omar Ali

This dissertation presents a method to determine the load capacity as well as end member forces and deformations of frames with partial rigid joint connections by using the direct stiffness method. The connections are modeled as rotational springs attached at the ends of framed members. The lumped mass method, which is an approximate method, and the distributed mass method, which is an exact method, are also presented to compute the natural frequency of frames. The effects of the axial forces and the flexibility of joint connections are both included. Furthermore, the time-dependent response of semi-rigid frames subjected to periodic axial forces is formulated. The harmonic function is approximated by dividing the periodic function into n intervals and the periodic axial forces are evaluated at each time interval as constant forces using 'piecewise approximation'. The regions of instability of frames with different joint stiffness were determined using the characteristic equation method. The time-dependent part of the differential equation for free vibration of a framed member subjected to a harmonic force can be written in the form of the Mathieu-Hill equation where all characteristics of the Mathieu-Hill equation solutions can be used to determine the boundaries of instability regions.

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

International Nuclear Information System (INIS)

Wood, R.D.; Stein, J.

1986-01-01

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.)

Symposium on molecular and cellular mechanisms of mutagenesis

International Nuclear Information System (INIS)

1981-01-01

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

State Dementia Plans and the Alzheimer's Disease Movement: Framing Diagnosis, Prognosis, and Motivation.

Science.gov (United States)

Arbogast, Charlotte E; Welleford, E Ayn; Netting, F Ellen

2017-07-01

An interpretive analysis of 38 state dementia plans compares similarities and differences in diagnostic framing (problem identification/trends/issues), prognosis framing (addressing the problem), and motivational framing (calls for action) across plans. In framing diagnosis, only 6 plans used dementia alone in their titles. In framing prognosis and the subsequent call to action, state plans were consistent in their dire prognostications about the progressive and fatal consequences of the disease with a primary focus on the cost. Motivational language mirrored that of the Alzheimer's Disease (AD) Movement, from raising awareness to using inflammatory words to incite action. The language used set up the frame for clinical interventions that may not distinguish between types of dementia and could undercut the provision of person-centered care, shifts the victimization focus from persons with AD to caregivers and ultimately the state, and may subintentionally reflect cultural biases.

Seed mutagenesis in Portulaca grandiflora (Hook)

International Nuclear Information System (INIS)

Bennani, F.; Rossi-Hassani, B.D.

2001-01-01

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

Some relationship between G-frames and frames

Directory of Open Access Journals (Sweden)

Mehdi Rashidi-Kouchi

2015-06-01

Full Text Available In this paper we proved that every g-Riesz basis for Hilbert space $H$ with respect to $K$ by adding a condition is a Riesz basis for Hilbert $B(K$-module $B(H,K$. This is an extension of [A. Askarizadeh,M. A. Dehghan, {em G-frames as special frames}, Turk. J. Math., 35, (2011 1-11]. Also, we derived similar results for g-orthonormal and orthogonal bases. Some relationships between dual frame, dual g-frame and exact frame and exact g-frame are presented too.

A frame-critical policy analysis of Canada's response to the World Food Summit 1998-2008.

Science.gov (United States)

Mah, Catherine L; Hamill, Catherine; Rondeau, Krista; McIntyre, Lynn

2014-01-01

The 2012 visit to Canada of Olivier De Schutter, the United Nations Special Rapporteur on the Right to Food, led to a public rebuff by Canadian governmental officials. This paper adapts the frame-critical policy analysis of Schön and Rein (1994), to explore the rhetorical basis for this conflict. This examination is offered as an illustrative example of how food insecurity is framed as a public policy problem in a high-income nation and how this framing has changed over time. We analyze Canada's decade of sequential responses to the 1996 World Food Summit, spanning 1998-2008, in the form of Canada's Action Plan on Food Security, and its subsequent Progress Reports. We conducted a qualitative policy analysis, adapting the frame-critical approach first delineated by Schön and Rein (1994). This analysis uses a social constructionist approach to map out the relationships between tacit understanding of policy by particular actors, explicit rhetoric in the public domain, and action in this policy area over time. We identify three key ways in which competing rhetorical frames arise over time: frame shifts (e.g., a shift away from language highlighting the right to food and health); frame blending (e.g., discussion about poverty becomes obscured by complexity discourse); and within-frame incongruence (e.g., monitoring for health indicators that are unrelated to policy solutions). Together, these frames illustrate how the conflict embodied in the UN Special Rapporteur's visit has been deeply woven into the policy discourse on food insecurity in Canada over time. Frame-critical analysis is instructive for exposing and also predicting tensions that impede forward progress on difficult policy issues. Accordingly, such analyses may be helpful in not only dissecting how policy can become 'stuck' in the process of change but in active reframing towards new policy solutions.

DinB Upregulation Is the Sole Role of the SOS Response in Stress-Induced Mutagenesis in Escherichia coli

Science.gov (United States)

Galhardo, Rodrigo S.; Do, Robert; Yamada, Masami; Friedberg, Errol C.; Hastings, P. J.; Nohmi, Takehiko; Rosenberg, Susan M.

2009-01-01

Stress-induced mutagenesis is a collection of mechanisms observed in bacterial, yeast, and human cells in which adverse conditions provoke mutagenesis, often under the control of stress responses. Control of mutagenesis by stress responses may accelerate evolution specifically when cells are maladapted to their environments, i.e., are stressed. It is therefore important to understand how stress responses increase mutagenesis. In the Escherichia coli Lac assay, stress-induced point mutagenesis requires induction of at least two stress responses: the RpoS-controlled general/starvation stress response and the SOS DNA-damage response, both of which upregulate DinB error-prone DNA polymerase, among other genes required for Lac mutagenesis. We show that upregulation of DinB is the only aspect of the SOS response needed for stress-induced mutagenesis. We constructed two dinB(oc) (operator-constitutive) mutants. Both produce SOS-induced levels of DinB constitutively. We find that both dinB(oc) alleles fully suppress the phenotype of constitutively SOS-“off” lexA(Ind−) mutant cells, restoring normal levels of stress-induced mutagenesis. Thus, dinB is the only SOS gene required at induced levels for stress-induced point mutagenesis. Furthermore, although spontaneous SOS induction has been observed to occur in only a small fraction of cells, upregulation of dinB by the dinB(oc) alleles in all cells does not promote a further increase in mutagenesis, implying that SOS induction of DinB, although necessary, is insufficient to differentiate cells into a hypermutable condition. PMID:19270270

Symposium on molecular and cellular mechanisms of mutagenesis

Energy Technology Data Exchange (ETDEWEB)

1981-01-01

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. (ERB)

The neural bases of framing effects in social dilemmas

DEFF Research Database (Denmark)

Macoveanu, Julian; Ramsøy, Thomas Z.; Skov, Martin

2016-01-01

findings provide the first insight into the mechanisms underlying framing of behavior in social dilemmas, indicating increased engagement of the hippocampus and neocortical areas involved in memory, social reasoning, and mentalizing when participants make decisions that conform to the imposed social frame.......Human behavior in social dilemmas is strongly framed by the social context, but the mechanisms underlying this framing effect remain poorly understood. To identify the behavioral and neural responses mediating framing of social interactions, participants underwent functional MRI while playing...... a prisoner’s dilemma game. In separate neuroimaging sessions, the game was either framed as a cooperation game or a competition game. The framing of social decisions engaged the hippocampal formation, precuneus, dorsomedial prefrontal cortex, and lateral temporal gyrus. Among these regions, the engagement...

Self-organized architectures from assorted DNA-framed nanoparticles

Science.gov (United States)

Liu, Wenyan; Halverson, Jonathan; Tian, Ye; Tkachenko, Alexei V.; Gang, Oleg

2016-09-01

The science of self-assembly has undergone a radical shift from asking questions about why individual components self-organize into ordered structures, to manipulating the resultant order. However, the quest for far-reaching nanomanufacturing requires addressing an even more challenging question: how to form nanoparticle (NP) structures with designed architectures without explicitly prescribing particle positions. Here we report an assembly concept in which building instructions are embedded into NPs via DNA frames. The integration of NPs and DNA origami frames enables the fabrication of NPs with designed anisotropic and selective interactions. Using a pre-defined set of different DNA-framed NPs, we show it is possible to design diverse planar architectures, which include periodic structures and shaped meso-objects that spontaneously emerge on mixing of the different topological types of NP. Even objects of non-trivial shapes, such as a nanoscale model of Leonardo da Vinci's Vitruvian Man, can be self-assembled successfully.

[Influence of diethyl sulfate (DES) mutagenesis on growth properties and pigment secondary metabolites of Phellinus igniarius].

Science.gov (United States)

Wang, Jing; Wu, Xin-yuan; Ma, Wei; Chen, Jing; Liu, Cheng; Wu, Xiu-li

2015-06-01

The diethyl sulfate (DES) mutagenesis was chosen for the mutagenic treatment to Phellinus igniarius, and the relationship of mutagenesis time and death rate was investigated with 0.5% DES. The differences of mycelial growth speed, liquid fermentation mycelia biomass, morphology and pigment classes of secondary metabolites production speed and antioxidant activities of metabolite products were discussed. The study displayed that DES mutagenesis could change mycelial morphology without obvious effect on mycelium growth, and the DES mutagenesis improved antioxidant activities of the active ingredients of P. igniarius and had more antioxidant activity of hypoxia/sugar PC12 nerve cells than that of P. igniarius.

A pronounced evolutionary shift of the pseudoautosomal region boundary in house mice.

Science.gov (United States)

White, Michael A; Ikeda, Akihiro; Payseur, Bret A

2012-08-01

The pseudoautosomal region (PAR) is essential for the accurate pairing and segregation of the X and Y chromosomes during meiosis. Despite its functional significance, the PAR shows substantial evolutionary divergence in structure and sequence between mammalian species. An instructive example of PAR evolution is the house mouse Mus musculus domesticus (represented by the C57BL/6J strain), which has the smallest PAR among those that have been mapped. In C57BL/6J, the PAR boundary is located just ~700 kb from the distal end of the X chromosome, whereas the boundary is found at a more proximal position in Mus spretus, a species that diverged from house mice 2-4 million years ago. In this study we used a combination of genetic and physical mapping to document a pronounced shift in the PAR boundary in a second house mouse subspecies, Mus musculus castaneus (represented by the CAST/EiJ strain), ~430 kb proximal of the M. m. domesticus boundary. We demonstrate molecular evolutionary consequences of this shift, including a marked lineage-specific increase in sequence divergence within Mid1, a gene that resides entirely within the M. m. castaneus PAR but straddles the boundary in other subspecies. Our results extend observations of structural divergence in the PAR to closely related subspecies, pointing to major evolutionary changes in this functionally important genomic region over a short time period.

Towards controlled mutagenesis with transposons Ac and Tam3

Energy Technology Data Exchange (ETDEWEB)

Haring, M; Veken, J; Windrich, R; Kneppers, T; Rommens, C; Nijkamp, H J.J.; Hille, J [Department of Genetics, Free University, Amsterdam (Netherlands)

1990-01-01

Full text: The discovery of mobile genetic elements in plants has permitted the use of these transposons for insertional mutagenesis. This applies so far only to Zea mays and Antirrhinum majus, because other plant transposable elements have not been characterised so thoroughly at the genetic and the molecular level. To establish whether transposons (Ac from maize and Tam3 from Antirrhinum) remain mobile in heterologous hosts, either in somatic tissue or after meiosis, a phenotypic assay system for transposition was developed. The separation of the two transposition functions will allow controlled mutagenesis of plant genes. Our results indicate that both transposable elements remain active in heterologous hosts. (author)

Tissue culture regeneration and radiation induced mutagenesis in banana

International Nuclear Information System (INIS)

Kulkarni, V.M.; Ganapathi, T.R.

2009-01-01

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)

The framing of two major flood episodes in the Irish print news media: Implications for societal adaptation to living with flood risk.

Science.gov (United States)

Devitt, Catherine; O'Neill, Eoin

2017-10-01

Societal adaptation to flooding is a critical component of contemporary flood policy. Using content analysis, this article identifies how two major flooding episodes (2009 and 2014) are framed in the Irish broadsheet news media. The article considers the extent to which these frames reflect shifts in contemporary flood policy away from protection towards risk management, and the possible implications for adaptation to living with flood risk. Frames help us make sense of the social world, and within the media, framing is an essential tool for communication. Five frames were identified: flood resistance and structural defences, politicisation of flood risk, citizen as risk manager, citizen as victim and emerging trade-offs. These frames suggest that public debates on flood management do not fully reflect shifts in contemporary flood policy, with negative implications for the direction of societal adaptation. Greater discussion is required on the influence of the media on achieving policy objectives.

Genetic and physiological factors affecting repair and mutagenesis in yeast

International Nuclear Information System (INIS)

Lemontt, J.F.

1979-01-01

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

Genetic and physiological factors affecting repair and mutagenesis in yeast

International Nuclear Information System (INIS)

Lemontt, J.F.

1979-01-01

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

Genetic and physiological factors affecting repair and mutagenesis in yeast

Energy Technology Data Exchange (ETDEWEB)

Lemontt, J F

1979-01-01

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.

Genetic and physiological factors affecting repair and mutagenesis in yeast

Energy Technology Data Exchange (ETDEWEB)

Lemontt, J F

1979-01-01

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.

Canceling the momentum in a phase-shifting algorithm to eliminate spatially uniform errors.

Science.gov (United States)

Hibino, Kenichi; Kim, Yangjin

2016-08-10

In phase-shifting interferometry, phase modulation nonlinearity causes both spatially uniform and nonuniform errors in the measured phase. Conventional linear-detuning error-compensating algorithms only eliminate the spatially variable error component. The uniform error is proportional to the inertial momentum of the data-sampling weight of a phase-shifting algorithm. This paper proposes a design approach to cancel the momentum by using characteristic polynomials in the Z-transform space and shows that an arbitrary M-frame algorithm can be modified to a new (M+2)-frame algorithm that acquires new symmetry to eliminate the uniform error.

Effects of competing news media frames of weight on antifat stigma, beliefs about weight and support for obesity-related public policies.

Science.gov (United States)

Frederick, D A; Saguy, A C; Sandhu, G; Mann, T

2016-03-01

In the popular news media, public health officials routinely emphasize the health risks of obesity and portray weight as under personal control. These messages may increase support for policies designed to reduce rates of obesity, but can also increase antifat stigma. Less often, the media cover 'Health at Every Size' or 'Fat Rights' perspectives that may have the opposite effects. We investigated how exposure to different 'fat frames' shifts attitudes about weight and support for obesity policies. Across four experiments (n=2187), people read constructed news articles framing fatness as negative (unhealthy, controllable, acceptable to stigmatize) or positive (healthy, uncontrollable, unacceptable to stigmatize). Compared with people who read fat-positive frames, people who read fat-negative frames expressed more: belief in the health risks of being fat (d=0.95-1.22), belief weight is controllable (d=0.38-0.55), support for charging obese people more for health insurance (d=0.26-0.77), antifat prejudice (in three out of four experiments, d=0.28-0.39), willingness to discriminate against fat people (d=0.39-0.71) and less willingness to celebrate body size diversity (d=0.37-0.64). They were also less willing to say that women at the lower end of the obese range could be healthy at their weights. Effects on support for public policies, however, were generally small and/or nonsignificant. Compared with a control condition, exposure to fat-positive frames generally shifted attitudes more than fat-negative frames. In experiment 4, adding a message about the unacceptability of weight-based discrimination to unhealthy/controllable news articles only reduced antifat stigma on one of three measures compared with articles adding a discrimination-acceptable message. Exposure to different news frames of fat can shift beliefs about weight-related health risks and weight-based stigma. Shifting policy attitudes, however, is more challenging.

Do Scale Frames Matter? Scale Frame Mismatches in the Decision Making Process of a "Mega Farm" in a Small Dutch Village

Directory of Open Access Journals (Sweden)

Maartje van. Lieshout

2011-03-01

Full Text Available Scale issues are an increasingly important feature of complex sustainability issues, but they are mostly taken for granted in policy processes. However, the scale at which a problem is defined as well as the scale at which it should be solved are potentially contentious issues. The framing of a problem as a local, regional, or global problem is not without consequences and influences processes of inclusion and exclusion. Little is known about the ways actors frame scales and the effect of different scale frames on decision making processes. This paper addresses the questions that different scale frames actors use and what the implications of scale frames are for policy processes. It does so by analyzing the scale frames deployed by different actors on the establishment of a so-called new mixed company or mega farm and the related decision making process in a Dutch municipality. We find that actors deploy different and conflicting scale frames, leading to scale frame mismatches. We conclude that scale frame mismatches play an important role in the stagnation of the decision making process.

Quantitative evaluation of DNA damage and mutation rate by atmospheric and room-temperature plasma (ARTP) and conventional mutagenesis.

Science.gov (United States)

Zhang, Xue; Zhang, Chong; Zhou, Qian-Qian; Zhang, Xiao-Fei; Wang, Li-Yan; Chang, Hai-Bo; Li, He-Ping; Oda, Yoshimitsu; Xing, Xin-Hui

2015-07-01

DNA damage is the dominant source of mutation, which is the driving force of evolution. Therefore, it is important to quantitatively analyze the DNA damage caused by different mutagenesis methods, the subsequent mutation rates, and their relationship. Atmospheric and room temperature plasma (ARTP) mutagenesis has been used for the mutation breeding of more than 40 microorganisms. However, ARTP mutagenesis has not been quantitatively compared with conventional mutation methods. In this study, the umu test using a flow-cytometric analysis was developed to quantify the DNA damage in individual viable cells using Salmonella typhimurium NM2009 as the model strain and to determine the mutation rate. The newly developed method was used to evaluate four different mutagenesis systems: a new ARTP tool, ultraviolet radiation, 4-nitroquinoline-1-oxide (4-NQO), and N-methyl-N'-nitro-N-nitrosoguanidine (MNNG) mutagenesis. The mutation rate was proportional to the corresponding SOS response induced by DNA damage. ARTP caused greater DNA damage to individual living cells than the other conventional mutagenesis methods, and the mutation rate was also higher. By quantitatively comparing the DNA damage and consequent mutation rate after different types of mutagenesis, we have shown that ARTP is a potentially powerful mutagenesis tool with which to improve the characteristics of microbial cell factories.

Natural selection underlies apparent stress-induced mutagenesis in a bacteriophage infection model.

Science.gov (United States)

Yosef, Ido; Edgar, Rotem; Levy, Asaf; Amitai, Gil; Sorek, Rotem; Munitz, Ariel; Qimron, Udi

2016-04-18

The emergence of mutations following growth-limiting conditions underlies bacterial drug resistance, viral escape from the immune system and fundamental evolution-driven events. Intriguingly, whether mutations are induced by growth limitation conditions or are randomly generated during growth and then selected by growth limitation conditions remains an open question(1). Here, we show that bacteriophage T7 undergoes apparent stress-induced mutagenesis when selected for improved recognition of its host's receptor. In our unique experimental set-up, the growth limitation condition is physically and temporally separated from mutagenesis: growth limitation occurs while phage DNA is outside the host, and spontaneous mutations occur during phage DNA replication inside the host. We show that the selected beneficial mutations are not pre-existing and that the initial slow phage growth is enabled by the phage particle's low-efficiency DNA injection into the host. Thus, the phage particle allows phage populations to initially extend their host range without mutagenesis by virtue of residual recognition of the host receptor. Mutations appear during non-selective intracellular replication, and the frequency of mutant phages increases by natural selection acting on free phages, which are not capable of mutagenesis.

On transforms between Gabor frames and wavelet frames

DEFF Research Database (Denmark)

Christensen, Ole; Goh, Say Song

2013-01-01

We describe a procedure that enables us to construct dual pairs of wavelet frames from certain dual pairs of Gabor frames. Applying the construction to Gabor frames generated by appropriate exponential Bsplines gives wavelet frames generated by functions whose Fourier transforms are compactly...... supported splines with geometrically distributed knot sequences. There is also a reverse transform, which yields pairs of dual Gabor frames when applied to certain wavelet frames....

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

Science.gov (United States)

Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

2015-08-01

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 in rice using different Cas9 and/or gRNA expression cassettes under standardized experimental conditions. We introduced Cas9 and gRNA expression cassettes separately or sequentially into rice calli, and assessed the frequency of mutagenesis at the same endogenous targeted sequences. Mutation frequencies differed significantly depending on the Cas9 expression cassette used. In addition, a gRNA driven by the OsU6 promoter was superior to one driven by the OsU3 promoter. Using an all-in-one expression vector harboring the best combined Cas9/gRNA expression cassette resulted in a much improved frequency of targeted mutagenesis in rice calli, and bi-allelic mutant plants were produced in the T0 generation. The approach presented here could be adapted to optimize the construction of Cas9/gRNA cassettes for genome editing in a variety of plants.

Targeted mutagenesis in sea urchin embryos using TALENs.

Science.gov (United States)

Hosoi, Sayaka; Sakuma, Tetsushi; Sakamoto, Naoaki; Yamamoto, Takashi

2014-01-01

Genome editing with engineered nucleases such as zinc-finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs) has been reported in various animals. We previously described ZFN-mediated targeted mutagenesis and insertion of reporter genes in sea urchin embryos. In this study, we demonstrate that TALENs can induce mutagenesis at specific genomic loci of sea urchin embryos. Injection of TALEN mRNAs targeting the HpEts transcription factor into fertilized eggs resulted in the impairment of skeletogenesis. Sequence analyses of the mutations showed that deletions and/or insertions occurred at the HpEts target site in the TALEN mRNAs-injected embryos. The results suggest that targeted gene disruption using TALENs is feasible in sea urchin embryos. © 2013 The Authors Development, Growth & Differentiation © 2013 Japanese Society of Developmental Biologists.

Quantitative Missense Variant Effect Prediction Using Large-Scale Mutagenesis Data.

Science.gov (United States)

Gray, Vanessa E; Hause, Ronald J; Luebeck, Jens; Shendure, Jay; Fowler, Douglas M

2018-01-24

Large datasets describing the quantitative effects of mutations on protein function are becoming increasingly available. Here, we leverage these datasets to develop Envision, which predicts the magnitude of a missense variant's molecular effect. Envision combines 21,026 variant effect measurements from nine large-scale experimental mutagenesis datasets, a hitherto untapped training resource, with a supervised, stochastic gradient boosting learning algorithm. Envision outperforms other missense variant effect predictors both on large-scale mutagenesis data and on an independent test dataset comprising 2,312 TP53 variants whose effects were measured using a low-throughput approach. This dataset was never used for hyperparameter tuning or model training and thus serves as an independent validation set. Envision prediction accuracy is also more consistent across amino acids than other predictors. Finally, we demonstrate that Envision's performance improves as more large-scale mutagenesis data are incorporated. We precompute Envision predictions for every possible single amino acid variant in human, mouse, frog, zebrafish, fruit fly, worm, and yeast proteomes (https://envision.gs.washington.edu/). Copyright © 2017 Elsevier Inc. All rights reserved.

Measurement of multiplicity and momentum spectra in the current fragmentation region of the Breit frame at HERA

International Nuclear Information System (INIS)

Derrick, M.; Krakauer, D.; Magill, S.

1995-01-01

Charged particle production has been measured in Deep Inelastic Scattering (DIS) events using the ZEUS detector over a large range of Q 2 from 10 to 1280 GeV 2 . The evolution with Q of the charged multiplicity and scaled momentum has been investigated in the current fragmentation region of the Breit frame. The data are used to study QCD coherence effects in DIS and are compared with corresponding e + e - data in order to test the universality of quark fragmentation. (orig.)

Proton nuclear magnetic resonance studies on bulge-containing DNA oligonucleotides from a mutational hot-spot sequence

International Nuclear Information System (INIS)

Woodson, S.A.; Crothers, D.M.

1987-01-01

A series of bulge-containing and normal double-helical synthetic oligodeoxyribonucleotides, of sequence corresponding to a frame-shift mutational hot spot in the λ C/sub I/ gene, are compared by proton magnetic resonance spectroscopy at 500 MHz. The imino proton resonances are assigned by one-dimensional nuclear Overhauser effect spectroscopy. Nonselective T 1 inversion-recovery experiments are used to determine exchangeable proton lifetimes and to compare helix stability and dynamics of the three duplexes. An extra adenosine flanking the internal G-C base pairs has a strongly localized effect on helix stability, but the destabilizing effect of an extra cytidine in a C tract is delocalized over the entire G-C run. These data lead to the conclusion that the position of the bulge migrates along the run in the fast-exchange limit on the NMR time scale. Rapid migration of the bulge defect in homopolymeric sequences may help rationalize both frame-shift mutagenesis and translational frame shifting. The authors estimate that the unfavorable free energy of a localized bulge defect is 2.9-3.2 kcal/mol, in good agreement with earlier estimates for RNA helices

Misrepair of overlapping daughter strand gaps as a possible mechanism for UV induced mutagenesis in uvr strains of Escherichia coli: a general model for induced mutagenesis by misrepair (SOS repair) of closely spaced DNA lesions

International Nuclear Information System (INIS)

Sedgwick, S.G.

1976-01-01

It has been previously reported that an inducible form of post-replication repair appeared to be required for UV induced mutagenesis in an uvrA strain of Escherichia coli. It is shown here that the numbers of daughter strand gaps requiring inducible repair were similar to the numbers calculated to be overlapping one another in opposite daughter chromosomes. An estimation of survival with no repair of these gaps resembled the survival predicted with mutagenesis. It is thus proposed that inducible post-replication repair causes mutagenesis by the repair of overlapping daughter strand gaps. A general model for induced mutagenesis is presented. It is proposed that (a) some DNA lesions introduced by any DNA damaging agent may be close enough to interfere with constitutive repair replication of each other, (b) these lesions induce a repair system (SOS repair) which involves the recA + . lexA + and polC + genes (c) repair, and noncomitant mutagenesis occurs during repair replication by the insertion of mismatched bases oppposite the noncoding DNA lesions

One-Tube-Only Standardized Site-Directed Mutagenesis: An Alternative Approach to Generate Amino Acid Substitution Collections.

Directory of Open Access Journals (Sweden)

Janire Mingo

Full Text Available Site-directed mutagenesis (SDM is a powerful tool to create defined collections of protein variants for experimental and clinical purposes, but effectiveness is compromised when a large number of mutations is required. We present here a one-tube-only standardized SDM approach that generates comprehensive collections of amino acid substitution variants, including scanning- and single site-multiple mutations. The approach combines unified mutagenic primer design with the mixing of multiple distinct primer pairs and/or plasmid templates to increase the yield of a single inverse-PCR mutagenesis reaction. Also, a user-friendly program for automatic design of standardized primers for Ala-scanning mutagenesis is made available. Experimental results were compared with a modeling approach together with stochastic simulation data. For single site-multiple mutagenesis purposes and for simultaneous mutagenesis in different plasmid backgrounds, combination of primer sets and/or plasmid templates in a single reaction tube yielded the distinct mutations in a stochastic fashion. For scanning mutagenesis, we found that a combination of overlapping primer sets in a single PCR reaction allowed the yield of different individual mutations, although this yield did not necessarily follow a stochastic trend. Double mutants were generated when the overlap of primer pairs was below 60%. Our results illustrate that one-tube-only SDM effectively reduces the number of reactions required in large-scale mutagenesis strategies, facilitating the generation of comprehensive collections of protein variants suitable for functional analysis.

News Media Framing of New York City's Sugar-Sweetened Beverage Portion-Size Cap.

Science.gov (United States)

Donaldson, Elisabeth A; Cohen, Joanna E; Truant, Patricia L; Rutkow, Lainie; Kanarek, Norma F; Barry, Colleen L

2015-11-01

We assessed news media framing of New York City's proposed regulation to prohibit the sale of sugar-sweetened beverages greater than 16 ounces. We conducted a quantitative content analysis of print and television news from within and outside New York City media markets. We examined support for and opposition to the portion-size cap in the news coverage from its May 31, 2012, proposal through the appellate court ruling on July 31, 2013. News coverage corresponded to key events in the policy's evolution. Although most stories mentioned obesity as a problem, a larger proportion used opposing frames (84%) than pro-policy frames (36%). Mention of pro-policy frames shifted toward the policy's effect on special populations. The debate's most prominent frame was the opposing frame that the policy was beyond the government's role (69%). News coverage within and outside the New York City media market was more likely to mention arguments in opposition to than in support of the portion-size cap. Understanding how the news media framed this issue provides important insights for advocates interested in advancing similar measures in other jurisdictions.

In vivo site-specific mutagenesis and gene collage using the delitto perfetto system in yeast Saccharomyces cerevisiae.

Science.gov (United States)

Stuckey, Samantha; Mukherjee, Kuntal; Storici, Francesca

2011-01-01

Delitto perfetto is a site-specific in vivo mutagenesis system that has been developed to generate changes at will in the genome of the yeast Saccharomyces cerevisiae. Using this technique, it is possible to rapidly and efficiently engineer yeast strains without requiring several intermediate steps as it functions in only two steps, both of which rely on homologous recombination to drive the changes to the target DNA region. The first step involves the insertion of a cassette containing two markers at or near the locus to be altered. The second step involves complete removal of this cassette with oligonucleotides and/or other genetic material and transfer of the expected genetic modification(s) to the chosen DNA locus. Here we provide a detailed protocol of the delitto perfetto approach and present examples of the most common and useful applications for in vivo mutagenesis to generate base substitutions, deletions, insertions, as well as for precise in vivo assembly and integration of multiple genetic elements, or gene collage.

A Modernized National Spatial Reference System in 2022: Focus on the Caribbean Terrestrial Reference Frame

Science.gov (United States)

Roman, D. R.

2017-12-01

In 2022, the National Geodetic Survey will replace all three NAD 83 reference frames the four new terrestrial reference frames. Each frame will be named after a tectonic plate (North American, Pacific, Caribbean and Mariana) and each will be related to the IGS frame through three Euler Pole parameters (EPPs). This talk will focus on practical application in the Caribbean region. A working group is being re-established for development of the North American region and will likely also result in analysis of the Pacific region as well. Both of these regions are adequately covered with existing CORS sites to model the EPPs. The Mariana region currently lacks sufficient coverage, but a separate project is underway to collect additional information to help in defining EPPs for that region at a later date. The Caribbean region has existing robust coverage through UNAVCO's COCONet and other data sets, but these require further analysis. This discussion will focus on practical examination of Caribbean sites to establish candidates for determining the Caribbean frame EPPs as well as an examination of any remaining velocities that might inform a model of the remaining velocities within that frame (Intra-Frame Velocity Model). NGS has a vested interest in defining such a model to meet obligations to U.S. citizens in Puerto Rico and the U.S. Virgin Islands. Beyond this, NGS aims to collaborate with other countries in the region through efforts with SIRGAS and UN-GGIM-Americas for a more acceptable regional model to serve everyone's needs.

Primer Extension Mutagenesis Powered by Selective Rolling Circle Amplification

Science.gov (United States)

Huovinen, Tuomas; Brockmann, Eeva-Christine; Akter, Sultana; Perez-Gamarra, Susan; Ylä-Pelto, Jani; Liu, Yuan; Lamminmäki, Urpo

2012-01-01

Primer extension mutagenesis is a popular tool to create libraries for in vitro evolution experiments. Here we describe a further improvement of the method described by T.A. Kunkel using uracil-containing single-stranded DNA as the template for the primer extension by additional uracil-DNA glycosylase treatment and rolling circle amplification (RCA) steps. It is shown that removal of uracil bases from the template leads to selective amplification of the nascently synthesized circular DNA strand carrying the desired mutations by phi29 DNA polymerase. Selective RCA (sRCA) of the DNA heteroduplex formed in Kunkel's mutagenesis increases the mutagenesis efficiency from 50% close to 100% and the number of transformants 300-fold without notable diversity bias. We also observed that both the mutated and the wild-type DNA were present in at least one third of the cells transformed directly with Kunkel's heteroduplex. In contrast, the cells transformed with sRCA product contained only mutated DNA. In sRCA, the complex cell-based selection for the mutant strand is replaced with the more controllable enzyme-based selection and less DNA is needed for library creation. Construction of a gene library of ten billion members is demonstrated with the described method with 240 nanograms of DNA as starting material. PMID:22355397

Hue-shifted monomeric variants of Clavularia cyan fluorescent protein: identification of the molecular determinants of color and applications in fluorescence imaging

Directory of Open Access Journals (Sweden)

Davidson Michael W

2008-03-01

Full Text Available Abstract Background In the 15 years that have passed since the cloning of Aequorea victoria green fluorescent protein (avGFP, the expanding set of fluorescent protein (FP variants has become entrenched as an indispensable toolkit for cell biology research. One of the latest additions to the toolkit is monomeric teal FP (mTFP1, a bright and photostable FP derived from Clavularia cyan FP. To gain insight into the molecular basis for the blue-shifted fluorescence emission we undertook a mutagenesis-based study of residues in the immediate environment of the chromophore. We also employed site-directed and random mutagenesis in combination with library screening to create new hues of mTFP1-derived variants with wavelength-shifted excitation and emission spectra. Results Our results demonstrate that the protein-chromophore interactions responsible for blue-shifting the absorbance and emission maxima of mTFP1 operate independently of the chromophore structure. This conclusion is supported by the observation that the Tyr67Trp and Tyr67His mutants of mTFP1 retain a blue-shifted fluorescence emission relative to their avGFP counterparts (that is, Tyr66Trp and Tyr66His. Based on previous work with close homologs, His197 and His163 are likely to be the residues with the greatest contribution towards blue-shifting the fluorescence emission. Indeed we have identified the substitutions His163Met and Thr73Ala that abolish or disrupt the interactions of these residues with the chromophore. The mTFP1-Thr73Ala/His163Met double mutant has an emission peak that is 23 nm red-shifted from that of mTFP1 itself. Directed evolution of this double mutant resulted in the development of mWasabi, a new green fluorescing protein that offers certain advantages over enhanced avGFP (EGFP. To assess the usefulness of mTFP1 and mWasabi in live cell imaging applications, we constructed and imaged more than 20 different fusion proteins. Conclusion Based on the results of our

Supplier-induced demand as strategic framing

OpenAIRE

De Jaegher, K.J.M.

2010-01-01

This paper develops a model of supplier-induced demand as strategic framing where the patient has reference-dependent references, and the physician can persuade the patient to buy a treatment by affecting the patient’s reference point. In the main result, the patient is assumed to have a constant rate of risk aversion (lovingness) in the gain (loss) region. Two scenarios are treated. In the cure scenario, the physician wants to frame the patient’s decision problem such that he prefers to buy ...

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

Phage transposon mutagenesis.

Science.gov (United States)

Siegrist, M Sloan; Rubin, Eric J

2009-01-01

Phage transduction is an attractive method of genetic manipulation in mycobacteria. PhiMycoMarT7 is well suited for transposon mutagenesis as it is temperature sensitive for replication and contains T7 promoters that promote transcription, a highly active transposase gene, and an Escherichia coli oriR6 K origin of replication. Mycobacterial transposon mutant libraries produced by PhiMycoMarT7 transduction are amenable to both forward and reverse genetic studies. In this protocol, we detail the preparation of PhiMycoMarT7, including a description of the phage, reconstitution of the phage, purification of plaques, preparation of phage stock, and titering of phage stock. We then describe the transduction procedure and finally outline the isolation of individual transposon mutants.

Study of UV-induced mutagenesis in Bacillus subtilis

International Nuclear Information System (INIS)

Filippov, V.D.; Lotareva, O.V.

1978-01-01

The mechanism of UV-induced mutagenesis was studied in Bacillus subtilis departing from the assumption that a lower yield of UV-induced mutations should be found in mutants deficient in the recombination if production of mutations is coupled with the recombination process. Three recombination-deficient strains were used: two (recA and recF) with defects in different recombination pathways and the third (recB) has a block at a stage common for both of them. UV light induced reversions to prototrophy in recB cells and did not in recA and recF strains. Direct mutations, which confer to the cell additional growth requirements, were induced by UV light in recA and recF mutants. It is concluded that UV-induced mutagenesis in B subtilis is independent of the two known recombination mechanisms

Molecular techniques as complementary tools in orchid mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Mohd Nazir Basiran; Sakinah Ariffin [Malaysian Institute for Nuclear Technology Research (MINT), Bangi (Malaysia)

2002-02-01

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)

A high-throughput shotgun mutagenesis approach to mapping B-cell antibody epitopes.

Science.gov (United States)

Davidson, Edgar; Doranz, Benjamin J

2014-09-01

Characterizing the binding sites of monoclonal antibodies (mAbs) on protein targets, their 'epitopes', can aid in the discovery and development of new therapeutics, diagnostics and vaccines. However, the speed of epitope mapping techniques has not kept pace with the increasingly large numbers of mAbs being isolated. Obtaining detailed epitope maps for functionally relevant antibodies can be challenging, particularly for conformational epitopes on structurally complex proteins. To enable rapid epitope mapping, we developed a high-throughput strategy, shotgun mutagenesis, that enables the identification of both linear and conformational epitopes in a fraction of the time required by conventional approaches. Shotgun mutagenesis epitope mapping is based on large-scale mutagenesis and rapid cellular testing of natively folded proteins. Hundreds of mutant plasmids are individually cloned, arrayed in 384-well microplates, expressed within human cells, and tested for mAb reactivity. Residues are identified as a component of a mAb epitope if their mutation (e.g. to alanine) does not support candidate mAb binding but does support that of other conformational mAbs or allows full protein function. Shotgun mutagenesis is particularly suited for studying structurally complex proteins because targets are expressed in their native form directly within human cells. Shotgun mutagenesis has been used to delineate hundreds of epitopes on a variety of proteins, including G protein-coupled receptor and viral envelope proteins. The epitopes mapped on dengue virus prM/E represent one of the largest collections of epitope information for any viral protein, and results are being used to design better vaccines and drugs. © 2014 John Wiley & Sons Ltd.

Novel Escherichia coli umuD′ Mutants: Structure-Function Insights into SOS Mutagenesis

Science.gov (United States)

McLenigan, Mary; Peat, Thomas S.; Frank, Ekaterina G.; McDonald, John P.; Gonzalez, Martín; Levine, Arthur S.; Hendrickson, Wayne A.; Woodgate, Roger

1998-01-01

Although it has been 10 years since the discovery that the Escherichia coli UmuD protein undergoes a RecA-mediated cleavage reaction to generate mutagenically active UmuD′, the function of UmuD′ has yet to be determined. In an attempt to elucidate the role of UmuD′ in SOS mutagenesis, we have utilized a colorimetric papillation assay to screen for mutants of a hydroxylamine-treated, low-copy-number umuD′ plasmid that are unable to promote SOS-dependent spontaneous mutagenesis. Using such an approach, we have identified 14 independent umuD′ mutants. Analysis of these mutants revealed that two resulted from promoter changes which reduced the expression of wild-type UmuD′, three were nonsense mutations that resulted in a truncated UmuD′ protein, and the remaining nine were missense alterations. In addition to the hydroxylamine-generated mutants, we have subcloned the mutations found in three chromosomal umuD1, umuD44, and umuD77 alleles into umuD′. All 17 umuD′ mutants resulted in lower levels of SOS-dependent spontaneous mutagenesis but varied in the extent to which they promoted methyl methanesulfonate-induced mutagenesis. We have attempted to correlate these phenotypes with the potential effect of each mutation on the recently described structure of UmuD′. PMID:9721309

Framing effects in group investment decision making: role of group polarization.

Science.gov (United States)

Cheng, Pi-Yueh; Chiou, Wen-Bin

2008-02-01

Prospect theory proposes that framing effects result in a preference for risk-averse choices in gain situations and risk-seeking choices in loss situations. However, in group polarization situations, groups show a pronounced tendency to shift toward more extreme positions than those they initially held. Whether framing effects in group decision making are more prominent as a result of the group-polarization effect was examined. Purposive sampling of 120 college students (57 men, 63 women; M age = 20.1 yr., SD = 0.9) allowed assessment of relative preference between cautious and risky choices in individual and group decisions. Findings indicated that both group polarization and framing effects occur in investment decisions. More importantly, group decisions in a gain situation appear to be more cautious, i.e., risk averse, than individual decisions, whereas group decisions in the loss situation appear to be more risky than individual decisions. Thus, group decision making may expand framing effects when it comes to investment choices through group polarization.

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.

Attribute Framing and Goal Framing Effects in Health Decisions.

Science.gov (United States)

Krishnamurthy, Parthasarathy; Carter, Patrick; Blair, Edward

2001-07-01

Levin, Schneider, and Gaeth (LSG, 1998) have distinguished among three types of framing-risky choice, attribute, and goal framing-to reconcile conflicting findings in the literature. In the research reported here, we focus on attribute and goal framing. LSG propose that positive frames should be more effective than negative frames in the context of attribute framing, and negative frames should be more effective than positive frames in the context of goal framing. We test this framework by manipulating frame valence (positive vs negative) and frame type (attribute vs goal) in a unified context with common procedures. We also argue that the nature of effects in a goal-framing context may depend on the extent to which the research topic has "intrinsic self-relevance" to the population. In the context of medical decision making, we operationalize low intrinsic self-relevance by using student subjects and high intrinsic self-relevance by using patients. As expected, we find complete support for the LSG framework under low intrinsic self-relevance and modified support for the LSG framework under high intrinsic self-relevance. Overall, our research appears to confirm and extend the LSG framework. Copyright 2001 Academic Press.

Transcription coupled repair deficiency protects against human mutagenesis and carcinogenesis: Personal Reflections on the 50th anniversary of the discovery of xeroderma pigmentosum.

Science.gov (United States)

Cleaver, James E

2017-10-01

Xeroderma pigmentosum (XP) patients who lack the main damage recognition protein for global genome repair (GGR), XPC, have greatly increased skin cancer rates and elevated mutation frequencies originating from unrepaired ultraviolet photoproducts in the nontranscribed regions of the genome and in nontranscribed strands of expressed genes. But they show no increased mutations in transcribed strands. In contrast, cancer is absent from Cockayne syndrome (CS) patients that have defective transcription coupled repair (TCR) despite severe photosensitivity, CS patients remarkably show no elevation of UV induced mutagenesis implying that defective TCR may be protective against mutagenesis and carcinogenesis. Mutation avoidance in CS is postulated to occur through arrested transcription that generates a tripled stranded R loop consisting of DNA double strands and a nascent mRNA strand. R loops result in S phase apoptosis or activation of ATM kinase that causes a delay in DNA replication until TCR, or transcript cleavage by TFIIS or RNAaseH, relieves the transcription block. Resumption of replication then occurs on repaired DNA without concomitant mutagenesis. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

Low-Complexity Variable Frame Rate Analysis for Speech Recognition and Voice Activity Detection

DEFF Research Database (Denmark)

Tan, Zheng-Hua; Lindberg, Børge

2010-01-01

present a low-complexity and effective frame selection approach based on a posteriori signal-to-noise ratio (SNR) weighted energy distance: The use of an energy distance, instead of e.g. a standard cepstral distance, makes the approach computationally efficient and enables fine granularity search......Frame based speech processing inherently assumes a stationary behavior of speech signals in a short period of time. Over a long time, the characteristics of the signals can change significantly and frames are not equally important, underscoring the need for frame selection. In this paper, we......, and the use of a posteriori SNR weighting emphasizes the reliable regions in noisy speech signals. It is experimentally found that the approach is able to assign a higher frame rate to fast changing events such as consonants, a lower frame rate to steady regions like vowels and no frames to silence, even...

Solid-state framing camera with multiple time frames

Energy Technology Data Exchange (ETDEWEB)

Baker, K. L.; Stewart, R. E.; Steele, P. T.; Vernon, S. P.; Hsing, W. W.; Remington, B. A. [Lawrence Livermore National Laboratory, Livermore, California 94550 (United States)

2013-10-07

A high speed solid-state framing camera has been developed which can operate over a wide range of photon energies. This camera measures the two-dimensional spatial profile of the flux incident on a cadmium selenide semiconductor at multiple times. This multi-frame camera has been tested at 3.1 eV and 4.5 keV. The framing camera currently records two frames with a temporal separation between the frames of 5 ps but this separation can be varied between hundreds of femtoseconds up to nanoseconds and the number of frames can be increased by angularly multiplexing the probe beam onto the cadmium selenide semiconductor.

Fear and Anger have Opposite Effects on Risk Seeking in the Gain Frame

Directory of Open Access Journals (Sweden)

Marianne eHabib

2015-03-01

Full Text Available Emotions strongly influence our decisions, particularly those made under risk. A classic example of the effect of emotion on decision making under risk is the framing effect, which involves predictable shifts in preferences when the same problem is formulated in different ways. According to dual process theories, this bias could stem from an affective heuristic belonging to an intuitive type of reasoning. In this study, we examined whether specific incidental negative emotions (i.e., fear and anger influence framing susceptibility and risk-taking identically. In each trial, participants received an initial amount of money, and pictures of angry or fearful faces were presented to them. Finally, participants chose between a sure option and a gamble option of equally expected value in a gain or loss frame. Risk-taking was modulated by emotional context: fear and anger influenced risk-taking specifically in the gain frame and had opposite effects. Fear increased risk-averse choices, whereas anger decreased risk-averse choices, leading to a suppression of the framing effect. These results confirm that emotions play a key role in framing susceptibility.

Fear and anger have opposite effects on risk seeking in the gain frame.

Science.gov (United States)

Habib, Marianne; Cassotti, Mathieu; Moutier, Sylvain; Houdé, Olivier; Borst, Grégoire

2015-01-01

Emotions strongly influence our decisions, particularly those made under risk. A classic example of the effect of emotion on decision making under risk is the "framing effect," which involves predictable shifts in preferences when the same problem is formulated in different ways. According to dual process theories, this bias could stem from an affective heuristic belonging to an intuitive type of reasoning. In this study, we examined whether specific incidental negative emotions (i.e., fear and anger) influence framing susceptibility and risk-taking identically. In each trial, participants received an initial amount of money, and pictures of angry or fearful faces were presented to them. Finally, participants chose between a sure option and a gamble option of equally expected value in a gain or loss frame. Risk-taking was modulated by emotional context: fear and anger influenced risk-taking specifically in the gain frame and had opposite effects. Fear increased risk-averse choices, whereas anger decreased risk-averse choices, leading to a suppression of the framing effect. These results confirm that emotions play a key role in framing susceptibility.

The relation between repair of DNA and radiation and chemical mutagenesis in Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Prakash, L.

1976-01-01

The effect of various genes involved in DNA repair functions on radiation and chemical mutagenesis in Escherichia coli is discussed and compared to similar studies done in yeast. Results of the effect of various genes conferring radiation-sensitivty on mutation induction in yeast are presented and related to current ideas of mutagenesis

Nonmonotonic belief state frames and reasoning frames

NARCIS (Netherlands)

Engelfriet, J.; Herre, H.; Treur, J.

1995-01-01

In this paper five levels of specification of nonmonotonic reasoning are distinguished. The notions of semantical frame, belief state frame and reasoning frame are introduced and used as a semantical basis for the first three levels. Moreover, the semantical connections between the levels are

Excision repair and mutagenesis in Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Kilbey, Brian

1987-01-01

This and succeeding letters discuss the James and Kilbey (1977 and 1978) model for the initiation of u.v. mutagenesis in Saccharomyces cerevisiae and its application to include a number of chemical mutagens. The Baranowska et al (1987) results indicating the role of DNA replication, the differing mechanisms in Escherichia coli, are all discussed. (UK)

Facile Site-Directed Mutagenesis of Large Constructs Using Gibson Isothermal DNA Assembly.

Science.gov (United States)

Yonemoto, Isaac T; Weyman, Philip D

2017-01-01

Site-directed mutagenesis is a commonly used molecular biology technique to manipulate biological sequences, and is especially useful for studying sequence determinants of enzyme function or designing proteins with improved activity. We describe a strategy using Gibson Isothermal DNA Assembly to perform site-directed mutagenesis on large (>~20 kbp) constructs that are outside the effective range of standard techniques such as QuikChange II (Agilent Technologies), but more reliable than traditional cloning using restriction enzymes and ligation.

Mutagenesis and phenotyping resources in zebrafish for studying development and human disease

Science.gov (United States)

Varshney, Gaurav Kumar

2014-01-01

The zebrafish (Danio rerio) is an important model organism for studying development and human disease. The zebrafish has an excellent reference genome and the functions of hundreds of genes have been tested using both forward and reverse genetic approaches. Recent years have seen an increasing number of large-scale mutagenesis projects and the number of mutants or gene knockouts in zebrafish has increased rapidly, including for the first time conditional knockout technologies. In addition, targeted mutagenesis techniques such as zinc finger nucleases, transcription activator-like effector nucleases and clustered regularly interspaced short sequences (CRISPR) or CRISPR-associated (Cas), have all been shown to effectively target zebrafish genes as well as the first reported germline homologous recombination, further expanding the utility and power of zebrafish genetics. Given this explosion of mutagenesis resources, it is now possible to perform systematic, high-throughput phenotype analysis of all zebrafish gene knockouts. PMID:24162064

Ordinal Regression Based Subpixel Shift Estimation for Video Super-Resolution

Directory of Open Access Journals (Sweden)

Petrovic Nemanja

2007-01-01

Full Text Available We present a supervised learning-based approach for subpixel motion estimation which is then used to perform video super-resolution. The novelty of this work is the formulation of the problem of subpixel motion estimation in a ranking framework. The ranking formulation is a variant of classification and regression formulation, in which the ordering present in class labels namely, the shift between patches is explicitly taken into account. Finally, we demonstrate the applicability of our approach on superresolving synthetically generated images with global subpixel shifts and enhancing real video frames by accounting for both local integer and subpixel shifts.

Effect of SOS-induced levels of imuABC on spontaneous and damage-induced mutagenesis in Caulobacter crescentus.

Science.gov (United States)

Alves, Ingrid R; Lima-Noronha, Marco A; Silva, Larissa G; Fernández-Silva, Frank S; Freitas, Aline Luiza D; Marques, Marilis V; Galhardo, Rodrigo S

2017-11-01

imuABC (imuAB dnaE2) genes are responsible for SOS-mutagenesis in Caulobacter crescentus and other bacterial species devoid of umuDC. In this work, we have constructed operator-constitutive mutants of the imuABC operon. We used this genetic tool to investigate the effect of SOS-induced levels of these genes upon both spontaneous and damage-induced mutagenesis. We showed that constitutive expression of imuABC does not increase spontaneous or damage-induced mutagenesis, nor increases cellular resistance to DNA-damaging agents. Nevertheless, the presence of the operator-constitutive mutation rescues mutagenesis in a recA background, indicating that imuABC are the only genes required at SOS-induced levels for translesion synthesis (TLS) in C. crescentus. Furthermore, these data also show that TLS mediated by ImuABC does not require RecA, unlike umuDC-dependent mutagenesis in E. coli. Copyright © 2017 Elsevier B.V. All rights reserved.

Genome-wide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus

DEFF Research Database (Denmark)

Urbanski, Dorian Fabian; Malolepszy, Anna; Stougaard, Jens

2012-01-01

Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis and insert......Insertion mutants facilitate functional analysis of genes, but for most plant species it has been difficult to identify a suitable mutagen and to establish large populations for reverse genetics. The main challenge is developing efficient high-throughput procedures for both mutagenesis...... plants. The identified insertions showed that the endogenous LORE1 retrotransposon is well suited for insertion mutagenesis due to its homogenous gene targeting and exonic insertion preference. Since LORE1 transposition occurs in the germline, harvesting seeds from a single founder line and cultivating...... progeny generates a complete mutant population. This ease of LORE1 mutagenesis combined with the efficient FSTpoolit protocol, which exploits 2D pooling, Illumina sequencing, and automated data analysis, allows highly cost-efficient development of a comprehensive reverse genetic resource....

Mutagenesis breeding research of Lactobacillus brevis of nitrite reduction

Directory of Open Access Journals (Sweden)

LI Zeli

2015-10-01

Full Text Available The pollution of nitrite in food became one of the focus of food safety issues,the use of biotechnology methods degrading nitrite became hotspot.The primitive strain was Lactobacillus brevis C2,preserved in our laboratory,had the ability to degrade nitrite,through composite mutagenesis of 15 W,254 nm,20 cm ultraviolet mutagenesis (UV for 120 s and 0.8% diethyl sulfate(DES in 37℃ mutation for 40 min,after screening,we successfully obtained high efficient strain of nitrite degradation,named UV6-DS2,relative to the starting strain,under the condition of 400 mg/L nitrite,after 12 h degradation,nitrite degradation rate increased from 92.8% to 97.8%,to explore its application in food was able to effectively reduce concentration of nitrite in food.

Ultraviolet mutagenesis and the SOS response in Escherichia coli: A personal perspective

International Nuclear Information System (INIS)

Witkin, E.M.

1989-01-01

The study of ultraviolet (UV) mutagenesis in Escherichia coli began with the assumption that genes were likely to be changed at the instant of photon absorption. Over many decades, it became clear that postirradiation cellular activities, including enzymatic DNA repair of UV photo products and error-prone modes of tolerating unrepaired DNA lesions can exert profound influences on the mutagenic outcome of irradiation. Current study focusses on the molecular details of radiation-induced translesion DNA replication as the final event in UV mutagenesis

The role of upstream sequences in selecting the reading frame on tmRNA

Directory of Open Access Journals (Sweden)

Dewey Jonathan D

2008-06-01

Full Text Available Abstract Background tmRNA acts first as a tRNA and then as an mRNA to rescue stalled ribosomes in eubacteria. Two unanswered questions about tmRNA function remain: how does tmRNA, lacking an anticodon, bypass the decoding machinery and enter the ribosome? Secondly, how does the ribosome choose the proper codon to resume translation on tmRNA? According to the -1 triplet hypothesis, the answer to both questions lies in the unique properties of the three nucleotides upstream of the first tmRNA codon. These nucleotides assume an A-form conformation that mimics the codon-anticodon interaction, leading to recognition by the decoding center and choice of the reading frame. The -1 triplet hypothesis is important because it is the most credible model in which direct binding and recognition by the ribosome sets the reading frame on tmRNA. Results Conformational analysis predicts that 18 triplets cannot form the correct structure to function as the -1 triplet of tmRNA. We tested the tmRNA activity of all possible -1 triplet mutants using a genetic assay in Escherichia coli. While many mutants displayed reduced activity, our findings do not match the predictions of this model. Additional mutagenesis identified sequences further upstream that are required for tmRNA function. An immunoblot assay for translation of the tmRNA tag revealed that certain mutations in U85, A86, and the -1 triplet sequence result in improper selection of the first codon and translation in the wrong frame (-1 or +1 in vivo. Conclusion Our findings disprove the -1 triplet hypothesis. The -1 triplet is not required for accommodation of tmRNA into the ribosome, although it plays a minor role in frame selection. Our results strongly disfavor direct ribosomal recognition of the upstream sequence, instead supporting a model in which the binding of a separate ligand to A86 is primarily responsible for frame selection.

β-lactam antibiotics promote bacterial mutagenesis via an RpoS-mediated reduction in replication fidelity

Science.gov (United States)

Gutierrez, A.; Laureti, L.; Crussard, S.; Abida, H.; Rodríguez-Rojas, A.; Blázquez, J.; Baharoglu, Z.; Mazel, D.; Darfeuille, F.; Vogel, J.; Matic, I.

2013-01-01

Regardless of their targets and modes of action, subinhibitory concentrations of antibiotics can have an impact on cell physiology and trigger a large variety of cellular responses in different bacterial species. Subinhibitory concentrations of β-lactam antibiotics cause reactive oxygen species production and induce PolIV-dependent mutagenesis in Escherichia coli. Here we show that subinhibitory concentrations of β-lactam antibiotics induce the RpoS regulon. RpoS-regulon induction is required for PolIV-dependent mutagenesis because it diminishes the control of DNA-replication fidelity by depleting MutS in E. coli, Vibrio cholerae and Pseudomonas aeruginosa. We also show that in E. coli, the reduction in mismatch-repair activity is mediated by SdsR, the RpoS-controlled small RNA. In summary, we show that mutagenesis induced by subinhibitory concentrations of antibiotics is a genetically controlled process. Because this mutagenesis can generate mutations conferring antibiotic resistance, it should be taken into consideration for the development of more efficient antimicrobial therapeutic strategies. PMID:23511474

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging

Directory of Open Access Journals (Sweden)

Lilach Soreq

2017-01-01

Full Text Available Gene expression studies suggest that aging of the human brain is determined by a complex interplay of molecular events, although both its region- and cell-type-specific consequences remain poorly understood. Here, we extensively characterized aging-altered gene expression changes across ten human brain regions from 480 individuals ranging in age from 16 to 106 years. We show that astrocyte- and oligodendrocyte-specific genes, but not neuron-specific genes, shift their regional expression patterns upon aging, particularly in the hippocampus and substantia nigra, while the expression of microglia- and endothelial-specific genes increase in all brain regions. In line with these changes, high-resolution immunohistochemistry demonstrated decreased numbers of oligodendrocytes and of neuronal subpopulations in the aging brain cortex. Finally, glial-specific genes predict age with greater precision than neuron-specific genes, thus highlighting the need for greater mechanistic understanding of neuron-glia interactions in aging and late-life diseases.

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging.

Science.gov (United States)

Soreq, Lilach; Rose, Jamie; Soreq, Eyal; Hardy, John; Trabzuni, Daniah; Cookson, Mark R; Smith, Colin; Ryten, Mina; Patani, Rickie; Ule, Jernej

2017-01-10

Gene expression studies suggest that aging of the human brain is determined by a complex interplay of molecular events, although both its region- and cell-type-specific consequences remain poorly understood. Here, we extensively characterized aging-altered gene expression changes across ten human brain regions from 480 individuals ranging in age from 16 to 106 years. We show that astrocyte- and oligodendrocyte-specific genes, but not neuron-specific genes, shift their regional expression patterns upon aging, particularly in the hippocampus and substantia nigra, while the expression of microglia- and endothelial-specific genes increase in all brain regions. In line with these changes, high-resolution immunohistochemistry demonstrated decreased numbers of oligodendrocytes and of neuronal subpopulations in the aging brain cortex. Finally, glial-specific genes predict age with greater precision than neuron-specific genes, thus highlighting the need for greater mechanistic understanding of neuron-glia interactions in aging and late-life diseases. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Combined mutagenesis of Rhodosporidium toruloides for improved production of carotenoids and lipids.

Science.gov (United States)

Zhang, Chaolei; Shen, Hongwei; Zhang, Xibin; Yu, Xue; Wang, Han; Xiao, Shan; Wang, Jihui; Zhao, Zongbao K

2016-10-01

To improve production of lipids and carotenoids by the oleaginous yeast Rhodosporidium toruloides by screening mutant strains. Upon physical mutagenesis of the haploid strain R. toruloides np11 with an atmospheric and room temperature plasma method followed by chemical mutagenesis with nitrosoguanidine, a mutant strain, R. toruloides XR-2, formed dark-red colonies on a screening plate. When cultivated in nitrogen-limited media, XR-2 cells grew slower but accumulated 0.23 g lipids/g cell dry wt and 0.75 mg carotenoids/g CDW. To improve its production capacity, different amino acids and vitamins were supplemented. p-Aminobenzoic acid and tryptophan had beneficial effects on cell growth. When cultivated in nitrogen-limited media in the presence of selected vitamins, XR-2 accumulated 0.41 g lipids/g CDW and 0.69 mg carotenoids/g CDW. A mutant R. toruloides strain with improved production profiles for lipids and carotenoids was obtained, indicating its potential to use combined mutagenesis for a more productive phenotype.

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.

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...

The European dimension for the mouse genome mutagenesis

Czech Academy of Sciences Publication Activity Database

Auwerx, J.; Avner, P.; Baldock, R.; Ballabio, A.; Balling, R.; Barbacid, M.; Berns, A.; Bradley, A.; Brown, S.; Carmeliet, P.; Chambon, P.; Cox, R.; Davidson, D.; Davies, K.; Duboule, D.; Forejt, Jiří; Granucci, F.; Hastie, N.; Angelis, M. H. de; Jackson, I.; Kioussis, D.; Kollias, G.; Lathrop, M.; Lendahl, U.; Malumbres, M.; von Melchner, H.; Müller, W.; Partanen, J.; Ricciardi-Castagnoli, P.; Rigby, P.; Rosen, B.; Rosenthal, N.; Skarnes, B.; Stewart, A. F.; Thornton, J.; Tocchini-Valentini, G.; Wagner, E.; Wahli, W.; Wurst, W.

2004-01-01

Roč. 16, - (2004), s. 925-927 ISSN 1061-4036 R&D Projects: GA MŠk(CZ) LN00A079 Institutional research plan: CEZ:AV0Z5052915 Keywords : The European Mouse Mutagenesis Consortium Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 24.695, year: 2004

Hybrid parallel computing architecture for multiview phase shifting

Science.gov (United States)

Zhong, Kai; Li, Zhongwei; Zhou, Xiaohui; Shi, Yusheng; Wang, Congjun

2014-11-01

The multiview phase-shifting method shows its powerful capability in achieving high resolution three-dimensional (3-D) shape measurement. Unfortunately, this ability results in very high computation costs and 3-D computations have to be processed offline. To realize real-time 3-D shape measurement, a hybrid parallel computing architecture is proposed for multiview phase shifting. In this architecture, the central processing unit can co-operate with the graphic processing unit (GPU) to achieve hybrid parallel computing. The high computation cost procedures, including lens distortion rectification, phase computation, correspondence, and 3-D reconstruction, are implemented in GPU, and a three-layer kernel function model is designed to simultaneously realize coarse-grained and fine-grained paralleling computing. Experimental results verify that the developed system can perform 50 fps (frame per second) real-time 3-D measurement with 260 K 3-D points per frame. A speedup of up to 180 times is obtained for the performance of the proposed technique using a NVIDIA GT560Ti graphics card rather than a sequential C in a 3.4 GHZ Inter Core i7 3770.

Framing Confusion: Dementia, Society, and History.

Science.gov (United States)

Ballenger, Jesse F

2017-07-01

This essay will briefly sketch historical changes in the framing of dementia since the late nineteenth century. In broad terms, this period has seen a shift from viewing dementia as a pathological variant of normal aging to viewing it as a distinct disease. Although this broad reframing of dementia was clearly positive in raising awareness and funding for research, it had some negative aspects that should be considered. Caregiving came to seem less important than research aimed at a cure, and the stigma surrounding dementia has, if anything, increased. © 2017 American Medical Association. All Rights Reserved.

Himar1 Transposon for Efficient Random Mutagenesis in Aggregatibacter actinomycetemcomitans

Directory of Open Access Journals (Sweden)

Qinfeng Ding

2017-09-01

Full Text Available Aggregatibacter actinomycetemcomitans is the primary etiological agent of aggressive periodontal disease. Identification of novel virulence factors at the genome-wide level is hindered by lack of efficient genetic tools to perform mutagenesis in this organism. The Himar1 mariner transposon is known to yield a random distribution of insertions in an organism’s genome with requirement for only a TA dinucleotide target and is independent of host-specific factors. However, the utility of this system in A. actinomycetemcomitans is unknown. In this study, we found that Himar1 transposon mutagenesis occurs at a high frequency (×10-4, and can be universally applied to wild-type A. actinomycetemcomitans strains of serotypes a, b, and c. The Himar1 transposon inserts were stably inherited in A. actinomycetemcomitans transconjugants in the absence of antibiotics. A library of 16,000 mutant colonies of A. actinomycetemcomitans was screened for reduced biofilm formation. Mutants with transposon inserts in genes encoding pilus, putative ion transporters, multidrug resistant proteins, transcription regulators and enzymes involved in the synthesis of extracellular polymeric substance, bacterial metabolism and stress response were discovered in this screen. Our results demonstrated the utility of the Himar1 mutagenesis system as a novel genetic tool for functional genomic analysis in A. actinomycetemcomitans.

Mismatch repair deficiency does not enhance ENU mutagenesis in the zebrafish germ line.

Science.gov (United States)

Feitsma, Harma; de Bruijn, Ewart; van de Belt, Jose; Nijman, Isaac J; Cuppen, Edwin

2008-07-01

S(N)1-type alkylating agents such as N-ethyl-N-nitrosourea (ENU) are very potent mutagens. They act by transferring their alkyl group to DNA bases, which, upon mispairing during replication, can cause single base pair mutations in the next replication cycle. As DNA mismatch repair (MMR) proteins are involved in the recognition of alkylation damage, we hypothesized that ENU-induced mutation rates could be increased in a MMR-deficient background, which would be beneficial for mutagenesis approaches. We applied a standard ENU mutagenesis protocol to adult zebrafish deficient in the MMR gene msh6 and heterozygous controls to study the effect of MMR on ENU-induced DNA damage. Dose-dependent lethality was found to be similar for homozygous and heterozygous mutants, indicating that there is no difference in ENU resistance. Mutation discovery by high-throughput dideoxy resequencing of genomic targets in outcrossed progeny of the mutagenized fish did also not reveal any differences in germ line mutation frequency. These results may indicate that the maximum mutation load for zebrafish has been reached with the currently used, highly optimized ENU mutagenesis protocol. Alternatively, the MMR system in the zebrafish germ line may be saturated very rapidly, thereby having a limited effect on high-dose ENU mutagenesis.

Case study of a successful learner's epistemological framings of quantum mechanics

Science.gov (United States)

Dini, Vesal; Hammer, David

2017-06-01

Research on student epistemologies in introductory courses has highlighted the importance of understanding physics as "a refinement of everyday thinking" [A. Einstein, J. Franklin Inst. 221, 349 (1936), 10.1016/S0016-0032(36)91047-5]. That view is difficult to sustain in quantum mechanics, for students as for physicists. How might students manage the transition? In this article, we present a case study of a graduate student's approaches and reflections on learning over two semesters of quantum mechanics, based on a series of nine interviews. We recount his explicit grappling with the shift in epistemology from classical to quantum, and we argue that his success in learning largely involved his framing mathematics as expressing physical meaning. At the same time, we show he was not entirely stable in these framings, shifting away from them in particular during his study of scattering. The case speaks to literature on students' epistemologies, with respect to the roles of everyday thinking and mathematics. We discuss what this case suggests for further research, with possible implications for instruction.

Some aspects of transformation of the nonlinear plasma equations to the space-independent frame

International Nuclear Information System (INIS)

Paul, S.N.; Chakraborty, B.

1982-01-01

Relativistically correct transformation of nonlinear plasma equations are derived in a space-independent frame. This transformation is useful in many ways because in place of partial differential equations one obtains a set of ordinary differential equations in a single independent variable. Equations of Akhiezer and Polovin (1956) for nonlinear plasma oscillations have been generalized and the results of Arons and Max (1974), and others for wave number shift and precessional rotation of electromagnetic wave are recovered in a space-independent frame. (author)

Codon cassette mutagenesis: a general method to insert or replace individual codons by using universal mutagenic cassettes.

OpenAIRE

Kegler-Ebo, D M; Docktor, C M; DiMaio, D

1994-01-01

We describe codon cassette mutagenesis, a simple method of mutagenesis that uses universal mutagenic cassettes to deposit single codons at specific sites in double-stranded DNA. A target molecule is first constructed that contains a blunt, double-strand break at the site targeted for mutagenesis. A double-stranded mutagenic codon cassette is then inserted at the target site. Each mutagenic codon cassette contains a three base pair direct terminal repeat and two head-to-head recognition sequen...

Targeted mutagenesis using CRISPR/Cas in inbred potatoes

Science.gov (United States)

Targeted mutagenesis using sequence-specific nucleases (SSNs) has been well established in several important crop species, but is in need of improvement in potato (Solanum tuberosum L.). For over a century, potatoes have been bred as autotetraploids (2n = 4x = 48), relying on F1 selections and clona...

FULL ELECTROMAGNETIC SIMULATION OF FREE-ELECTRON LASER AMPLIFIER PHYSICS VIA THE LORENTZ-BOOSTED FRAME APPROACH

International Nuclear Information System (INIS)

Fawley, William M.; Vay, Jean-Luc

2009-01-01

Numerical simulation of some systems containing charged particles with highly relativistic directed motion can by speeded up by orders of magnitude by choice of the proper Lorentz-boosted frame. A particularly good example is that of short wavelength free-electron lasers (FELs) in which a high energy electron beam interacts with a static magnetic undulator. In the optimal boost frame with Lorentz factor gamma F , the red-shifted FEL radiation and blue shifted undulator have identical wavelengths and the number of required time-steps (presuming the Courant condition applies) decreases by a factor of 2(gamma F )**2 for fully electromagnetic simulation. We have adapted the WARP code to apply this method to several FEL problems involving coherent spontaneous emission (CSE) from pre-bunched ebeams, including that in a biharmonic undulator.

NChina16: A stable geodetic reference frame for geological hazard studies in North China

Science.gov (United States)

Wang, Guoquan; Bao, Yan; Gan, Weijun; Geng, Jianghui; Xiao, Gengru; Shen, Jack S.

2018-04-01

We have developed a stable North China Reference Frame 2016 (NChina16) using five years of continuous GPS observations (2011.8-2016.8) from 12 continuously operating reference stations (CORS) fixed to the North China Craton. Applications of NChina16 in landslide and subsidence studies are illustrated in this article. A method for realizing a regional geodetic reference frame is introduced. The primary result of this study is the seven parameters for transforming Cartesian ECEF (Earth-Centered, Earth-Fixed) coordinates X, Y, and Z from the International GNSS Service Reference Frame 2008 (IGS08) to NChina16. The seven parameters include the epoch that is used to align the regional reference frame to IGS08 and the time derivatives of three translations and three rotations. The GIPSY-OASIS (V6.4) software package was used to obtain the precise point positioning (PPP) daily solutions with respect to IGS08. The frame stability of NChina16 is approximately 0.5 mm/year in both horizontal and vertical directions. This study also developed a regional model for correcting seasonal motions superimposed into the vertical component of the GPS-derived displacement time series. Long-term GPS observations (1999-2016) from five CORS in North China were used to develop the seasonal model. According to this study, the PPP daily solutions with respect to NChina16 could achieve 2-3 mm horizontal accuracy and 4-5 mm vertical accuracy after being modified by the regional model. NChina16 will be critical to study geodynamic problems in North China, such as earthquakes, faulting, subsidence, and landslides. The regional reference frame will be periodically updated every few years to mitigate degradation of the frame with time and be synchronized with the update of IGS reference frame.

Fragile DNA Motifs Trigger Mutagenesis at Distant Chromosomal Loci in Saccharomyces cerevisiae

Science.gov (United States)

Saini, Natalie; Zhang, Yu; Nishida, Yuri; Sheng, Ziwei; Choudhury, Shilpa; Mieczkowski, Piotr; Lobachev, Kirill S.

2013-01-01

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. PMID:23785298

Laboratory of Mutagenesis and DNA Repair

International Nuclear Information System (INIS)

2000-01-01

Full text: Two main lines of research were continued: the first one concerned the mechanisms controlling the fidelity of DNA replication in Escherichia coli; the second concerned cellular responses of Saccharomyces cerevisiae to DNA damaging agents. We have been investigating the question whether during chromosomal DNA replication in Escherichia coli the two DNA strands may be replicated with differential accuracy. To address this question we set up a new system that allows the examination of mutagenesis either of the leading strand or the lagging strand. Our results suggest that the lagging strand replication of the E. coli chromosome may be more accurate than leading strand replication. More recently, we studied mutagenesis of the two strands in recA730 strains which exhibit constitutive expression of the SOS system. Our results clearly indicate that in recA730 strains there is a significant difference in the fidelity of replication between the two replicating strands. Based on our data we propose a model describing a possible mechanism of SOS mutagenesis. To get more insight into cellular responses to DNA damage we have isolated several novel genes of S. cerevisiae, the transcription of which is induced by DNA lesions. Main effort was concentrated on the characterization of the DIN7 gene. We found that Din7p specifically affects the metabolism of mitochondrial DNA (mtDNA). The elevated level of Din7p results in an increased frequency of mitochondrial petite mutants, as well as in a higher frequency of mitochondrial point mutations. Din7p affects also the stability of microsatellite sequences present in the mitochondrial genome. As expected, Din7p was found to be located in mitochondria. In another project, we found that the DIN8 gene isolated in our laboratory is identical with the UMP1 gene encoding a chaperone-like protein involved in 20S proteasome maturation. Interestingly, induction of UMP1 expression in response to DNA damage is subject to regulation

Media Framing

DEFF Research Database (Denmark)

Pedersen, Rasmus T.

2017-01-01

The concept of media framing refers to the way in which the news media organize and provide meaning to a news story by emphasizing some parts of reality and disregarding other parts. These patterns of emphasis and exclusion in news coverage create frames that can have considerable effects on news...... consumers’ perceptions and attitudes regarding the given issue or event. This entry briefly elaborates on the concept of media framing, presents key types of media frames, and introduces the research on media framing effects....

Minimizing off-Target Mutagenesis Risks Caused by Programmable Nucleases.

Science.gov (United States)

Ishida, Kentaro; Gee, Peter; Hotta, Akitsu

2015-10-16

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

Framing effects over time: comparing affective and cognitive news frames

NARCIS (Netherlands)

Lecheler, S.; Matthes, J.

2012-01-01

A growing number of scholars examine the duration of framing effects. However, duration is likely to differ from frame to frame, depending on how strong a frame is. This strength is likely to be enhanced by adding emotional components to a frame. By means of an experimental survey design (n = 111),

DNA polymerase III of Escherichia coli is required for UV and ethyl methanesulfonate mutagenesis

Energy Technology Data Exchange (ETDEWEB)

Hagensee, M.E.; Timme, T.L.; Bryan, S.K.; Moses, R.E.

1987-06-01

Strains of Escherichia coli possessing the pcbA1 mutation, a functional DNA polymerase I, and a temperature-sensitive mutation in DNA polymerase III can survive at the restrictive temperature (43 degrees C) for DNA polymerase III. The mutation rate of the bacterial genome of such strains after exposure to either UV light or ethyl methanesulfonate was measured by its rifampicin resistance or amino acid requirements. In addition, Weigle mutagenesis of preirradiated lambda phage was also measured. In all cases, no increase in mutagenesis was noted at the restrictive temperature for DNA polymerase III. Introduction of a cloned DNA polymerase III gene returned the mutation rate of the bacterial genome as well as the Weigle mutagenesis to normal at 43 degrees C. Using a recA-lacZ fusion, the SOS response after UV irradiation was measured and found to be normal at the restrictive and permissive temperature for DNA polymerase III, as was induction of lambda prophage. Recombination was also normal at either temperature. Our studies demonstrate that a functional DNA polymerase III is strictly required for mutagenesis at a step other than SOS induction.

News Media Framing of New York City’s Sugar-Sweetened Beverage Portion-Size Cap

Science.gov (United States)

Cohen, Joanna E.; Truant, Patricia L.; Rutkow, Lainie; Kanarek, Norma F.; Barry, Colleen L.

2015-01-01

Objectives. We assessed news media framing of New York City’s proposed regulation to prohibit the sale of sugar-sweetened beverages greater than 16 ounces. Methods. We conducted a quantitative content analysis of print and television news from within and outside New York City media markets. We examined support for and opposition to the portion-size cap in the news coverage from its May 31, 2012, proposal through the appellate court ruling on July 31, 2013. Results. News coverage corresponded to key events in the policy’s evolution. Although most stories mentioned obesity as a problem, a larger proportion used opposing frames (84%) than pro-policy frames (36%). Mention of pro-policy frames shifted toward the policy’s effect on special populations. The debate’s most prominent frame was the opposing frame that the policy was beyond the government’s role (69%). Conclusions. News coverage within and outside the New York City media market was more likely to mention arguments in opposition to than in support of the portion-size cap. Understanding how the news media framed this issue provides important insights for advocates interested in advancing similar measures in other jurisdictions. PMID:26378853

The role of misrepair in experimental mutagenesis

International Nuclear Information System (INIS)

Yamaguchi, Hikoyuki

1983-01-01

Mutagenesis is classified as being either mispairing occuring at the time of chromosome replication or as being misrepair occuring when damaged nucleotides are converted to the paired ones. In the cell population of the root meristem of barley which is considered to be steadystate, the possibility of the selective segregation of the newly synthesized and the older template strands of DNA at mitosis was studied by the incorporation of 3 H-thymidine. Stochastic removal of de novo synthesized DNA strand to a zone of non-dividing cell population was unlikely. Thus, it has been concluded that there is special mechanisms for protecting the integrity of the DNA by removing the mispairing lesions. Barly seeds first exposed to a low level γ-radiation before treating with ethylmethane sulfonate. Survival rate of M 1 plants as well as mutation frequency of M 2 were higher for the combined treatment than for single treatment of chemical mutagen. A mutational response of barley cell to DNA damaging agent was much affected by a previous treatment with mutagens. It is suggested that in the experimental mutagenesis misrepair plays rather an important role than mispairing. (author)

Determination of baryon-baryon elastic scattering phase shift from finite volume spectra in elongated boxes

Science.gov (United States)

Li, Ning; Wu, Ya-Jie; Liu, Zhan-Wei

2018-01-01

The relations between the baryon-baryon elastic scattering phase shifts and the two-particle energy spectrum in the elongated box are established. We studied the cases with both the periodic boundary condition and twisted boundary condition in the center of mass frame. The framework is also extended to the system of nonzero total momentum with periodic boundary condition in the moving frame. Moreover, we discussed the sensitivity functions σ (q ) that represent the sensitivity of higher scattering phases. Our analytical results will be helpful to extract the baryon-baryon elastic scattering phase shifts in the continuum from lattice QCD data by using elongated boxes.

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

International Nuclear Information System (INIS)

Bertram, Heidi

1988-01-01

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.)

DC-Analyzer-facilitated combinatorial strategy for rapid directed evolution of functional enzymes with multiple mutagenesis sites.

Science.gov (United States)

Wang, Xiong; Zheng, Kai; Zheng, Huayu; Nie, Hongli; Yang, Zujun; Tang, Lixia

2014-12-20

Iterative saturation mutagenesis (ISM) has been shown to be a powerful method for directed evolution. In this study, the approach was modified (termed M-ISM) by combining the single-site saturation mutagenesis method with a DC-Analyzer-facilitated combinatorial strategy, aiming to evolve novel biocatalysts efficiently in the case where multiple sites are targeted simultaneously. Initially, all target sites were explored individually by constructing single-site saturation mutagenesis libraries. Next, the top two to four variants in each library were selected and combined using the DC-Analyzer-facilitated combinatorial strategy. In addition to site-saturation mutagenesis, iterative saturation mutagenesis also needed to be performed. The advantages of M-ISM over ISM were that the screening effort is greatly reduced, and the entire M-ISM procedure was less time-consuming. The M-ISM strategy was successfully applied to the randomization of halohydrin dehalogenase from Agrobacterium radiobacter AD1 (HheC) when five interesting sites were targeted simultaneously. After screening 900 clones in total, six positive mutants were obtained. These mutants exhibited 4.0- to 9.3-fold higher k(cat) values than did the wild-type HheC toward 1,3-dichloro-2-propanol. However, with the ISM strategy, the best hit showed a 5.9-fold higher k(cat) value toward 1,3-DCP than the wild-type HheC, which was obtained after screening 4000 clones from four rounds of mutagenesis. Therefore, M-ISM could serve as a simple and efficient version of ISM for the randomization of target genes with multiple positions of interest.

Specificity determinants for autoproteolysis of LexA, a key regulator of bacterial SOS mutagenesis.

Science.gov (United States)

Mo, Charlie Y; Birdwell, L Dillon; Kohli, Rahul M

2014-05-20

Bacteria utilize the tightly regulated stress response (SOS) pathway to respond to a variety of genotoxic agents, including antimicrobials. Activation of the SOS response is regulated by a key repressor-protease, LexA, which undergoes autoproteolysis in the setting of stress, resulting in derepression of SOS genes. Remarkably, genetic inactivation of LexA's self-cleavage activity significantly decreases acquired antibiotic resistance in infection models and renders bacteria hypersensitive to traditional antibiotics, suggesting that a mechanistic study of LexA could help inform its viability as a novel target for combating acquired drug resistance. Despite structural insights into LexA, a detailed knowledge of the enzyme's protease specificity is lacking. Here, we employ saturation and positional scanning mutagenesis on LexA's internal cleavage region to analyze >140 mutants and generate a comprehensive specificity profile of LexA from the human pathogen Pseudomonas aeruginosa (LexAPa). We find that the LexAPa active site possesses a unique mode of substrate recognition. Positions P1-P3 prefer small hydrophobic residues that suggest specific contacts with the active site, while positions P5 and P1' show a preference for flexible glycine residues that may facilitate the conformational change that permits autoproteolysis. We further show that stabilizing the β-turn within the cleavage region enhances LexA autoproteolytic activity. Finally, we identify permissive positions flanking the scissile bond (P4 and P2') that are tolerant to extensive mutagenesis. Our studies shed light on the active site architecture of the LexA autoprotease and provide insights that may inform the design of probes of the SOS pathway.

A FRAMING OF FUTURE EUROPEAN PARLIAMENT ELECTIONS 2014 IN A SOCIAL MEDIA CONTEXT

Directory of Open Access Journals (Sweden)

Dorian Pocovnicu

2013-12-01

Full Text Available Communication in marketing has always been a continuous conceptual hybrid of input from various domains: marketing, P.R., communication, sociology. With the constant transformation of web 2.0. phenomenon, the demarcation lines between these domains and their influence has become more blured and difficult to pinpoint. As a result, specific research methods and theories have become adaptable instruments, laying the path for grounded theory approaches or new research methods. Framing theory, having as basis that the media focuses attention on certain events and then places them within a field of meaning, has shifted towards organisations, and further on, to institutions. Framing is a quality of communication that leads others to accept one meaning over another. Framing theory suggests that how something is presented (the “frame” influences the choices people make. In online communicative contexts, their own personal framings allows the communicative actors to make use of language and forethought so that specific embodiments of future evolutions may be depicted. In our case, we shall focus on the topic: European Parliament elections, which are to take place in 2014, and on the manner in which it has been framed in two online chat session with three MEPs. It is our intention to identify the framing techniques used, the framing links and the framing alignments.

Riesz frames and approximation of the frame coefficients

DEFF Research Database (Denmark)

Casazza, P.; Christensen, Ole

1998-01-01

A frame is a fmaily {f i } i=1 ∞ of elements in a Hilbert space with the property that every element in can be written as a (infinite) linear combination of the frame elements. Frame theory describes how one can choose the corresponding coefficients, which are called frame coefficients. From...... the mathematical point of view this is gratifying, but for applications it is a problem that the calculation requires inversion of an operator on . The projection method is introduced in order to avoid this problem. The basic idea is to consider finite subfamilies {f i } i=1 n of the frame and the orthogonal...... projection Pn onto its span. For has a representation as a linear combination of fi, i=1,2,..., n and the corresponding coefficients can be calculated using finite dimensional methods. We find conditions implying that those coefficients converge to the correct frame coefficients as n→∞, in which case we have...

A global vertical reference frame based on four regional vertical datums

Czech Academy of Sciences Publication Activity Database

Burša, Milan; Kenyon, S.; Kouba, J.; Šíma, Zdislav; Vatrt, V.; Vojtíšková, M.

2004-01-01

Roč. 48, č. 3 (2004), s. 493-502 ISSN 0039-3169 Institutional research plan: CEZ:AV0Z1003909 Keywords : geopotentinal * local vertical datums * global vertical reference frame Subject RIV: BN - Astronomy, Celestial Mechanics, Astrophysics Impact factor: 0.447, year: 2004

Radiation mutagenesis of subtropic plants

International Nuclear Information System (INIS)

Kerkadze, I.G.

1987-01-01

Possibilities of expansion of subtropic plant changeability and development of new gene bank for future selection-genetic studies are detected. New trends of radiation mutagenesis of subtropic plants are formulated as results of studies during many years. A lot of mutants is subjected to sufficient tests, and concrete results are obtained with the help of these tests for definite species. Summing genetic and selection estimations of the results, it is possible to make the conclusion that mutant selection represents one of the powerful methods of preparation of productive and qualitative species of subtropic plants, which are successfully introduced into practice

Can you see me? Experiences of nurses working night shift in Australian regional hospitals: a qualitative case study.

Science.gov (United States)

Powell, Idona

2013-10-01

To report a study that explored the experiences of night-shift nurses, focusing on employee interrelationships and work satisfaction. Night-shift nurses are a critical component in hospital care making it essential to understand the experiences that give meaning to their work and understand how these nurses and the organization can benefit from their contribution to hospital care. A literature review revealed minimal research in this area. Qualitative case study. A qualitative case study using semi-structured interviews and self-completed diaries was conducted in 2010 in regional public hospitals in Australia. Participants were 14 nurses working nights half or more of their shifts in medical or surgical wards. Thematic analysis identified four major areas of concern: work relationships, work environment, work practices and lifestyle impact. Notably, work relationships were most meaningful for nurses on the same shift; night-shift nurses experienced working conditions inferior to their daytime counterparts including a perception of minimal leadership. Despite limited education opportunities, night shift provided opportunity for professional growth for some nurses with a slippage in skills for others; night shift provided flexibility for family and social activities, yet impeded these same activities, primarily due to pervasive fatigue. Night-shift nurses considered their role critical, yet believed that they were poorly regarded. The strong interpersonal relationships developed between night-shift workers need to be capitalized on whilst developing a more effective leadership model, improved work environment, more equitable professional development, and genuine recognition of the critical role of night nurses. © 2013 Blackwell Publishing Ltd.

Frames of exponentials:lower frame bounds for finite subfamilies, and approximation of the inverse frame operator

DEFF Research Database (Denmark)

Christensen, Ole; Lindner, Alexander M

2001-01-01

We give lower frame bounds for finite subfamilies of a frame of exponentials {e(i lambdak(.))}k is an element ofZ in L-2(-pi,pi). We also present a method for approximation of the inverse frame operator corresponding to {e(i lambdak(.))}k is an element ofZ, where knowledge of the frame bounds for...

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

International Nuclear Information System (INIS)

Maenhaut-Michel, G.; Caillet-Fauquet, P.

1984-01-01

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)

Environmental Stress Induces Trinucleotide Repeat Mutagenesis in Human Cells by Alt-Nonhomologous End Joining Repair.

Science.gov (United States)

Chatterjee, Nimrat; Lin, Yunfu; Yotnda, Patricia; Wilson, John H

2016-07-31

Multiple pathways modulate the dynamic mutability of trinucleotide repeats (TNRs), which are implicated in neurodegenerative disease and evolution. Recently, we reported that environmental stresses induce TNR mutagenesis via stress responses and rereplication, with more than 50% of mutants carrying deletions or insertions-molecular signatures of DNA double-strand break repair. We now show that knockdown of alt-nonhomologous end joining (alt-NHEJ) components-XRCC1, LIG3, and PARP1-suppresses stress-induced TNR mutagenesis, in contrast to the components of homologous recombination and NHEJ, which have no effect. Thus, alt-NHEJ, which contributes to genetic mutability in cancer cells, also plays a novel role in environmental stress-induced TNR mutagenesis. Published by Elsevier Ltd.

The Immature Fiber Mutant Phenotype of Cotton (Gossypium hirsutum Is Linked to a 22-bp Frame-Shift Deletion in a Mitochondria Targeted Pentatricopeptide Repeat Gene

Directory of Open Access Journals (Sweden)

Gregory N. Thyssen

2016-06-01

Full Text Available Cotton seed trichomes are the most important source of natural fibers globally. The major fiber thickness properties influence the price of the raw material, and the quality of the finished product. The recessive immature fiber (im gene reduces the degree of fiber cell wall thickening by a process that was previously shown to involve mitochondrial function in allotetraploid Gossypium hirsutum. Here, we present the fine genetic mapping of the im locus, gene expression analysis of annotated proteins near the locus, and association analysis of the linked markers. Mapping-by-sequencing identified a 22-bp deletion in a pentatricopeptide repeat (PPR gene that is completely linked to the immature fiber phenotype in 2837 F2 plants, and is absent from all 163 cultivated varieties tested, although other closely linked marker polymorphisms are prevalent in the diversity panel. This frame-shift mutation results in a transcript with two long open reading frames: one containing the N-terminal transit peptide that targets mitochondria, the other containing only the RNA-binding PPR domains, suggesting that a functional PPR protein cannot be targeted to mitochondria in the im mutant. Taken together, these results suggest that PPR gene Gh_A03G0489 is involved in the cotton fiber wall thickening process, and is a promising candidate gene at the im locus. Our findings expand our understanding of the molecular mechanisms that modulate cotton fiber fineness and maturity, and may facilitate the development of cotton varieties with superior fiber attributes.

A framed, 16-image Kirkpatrick-Baez x-ray microscope

Science.gov (United States)

Marshall, F. J.; Bahr, R. E.; Goncharov, V. N.; Glebov, V. Yu.; Peng, B.; Regan, S. P.; Sangster, T. C.; Stoeckl, C.

2017-09-01

A 16-image Kirkpatrick-Baez (KB)-type x-ray microscope consisting of compact KB mirrors [F. J. Marshall, Rev. Sci. Instrum. 83, 10E518 (2012)] has been assembled for the first time with mirrors aligned to allow it to be coupled to a high-speed framing camera. The high-speed framing camera has four independently gated strips whose emission sampling interval is ˜30 ps. Images are arranged four to a strip with ˜60-ps temporal spacing between frames on a strip. By spacing the timing of the strips, a frame spacing of ˜15 ps is achieved. A framed resolution of ˜6-μm is achieved with this combination in a 400-μm region of laser-plasma x-ray emission in the 2- to 8-keV energy range. A principal use of the microscope is to measure the evolution of the implosion stagnation region of cryogenic DT target implosions on the University of Rochester's OMEGA Laser System [T. R. Boehly et al., Opt. Commun. 133, 495 (1997)]. The unprecedented time and spatial resolutions achieved with this framed, multi-image KB microscope have made it possible to accurately determine the cryogenic implosion core emission size and shape at the peak of stagnation. These core size measurements, taken in combination with those of ion temperature, neutron-production temporal width, and neutron yield allow for inference of core pressures, currently exceeding 50 Gbar in OMEGA cryogenic target implosions [Regan et al., Phys. Rev. Lett. 117, 025001 (2016)].

Prime tight frames

DEFF Research Database (Denmark)

Lemvig, Jakob; Miller, Christopher; Okoudjou, Kasso A.

2014-01-01

to suggest effective analysis and synthesis computation strategies for such frames. Finally, we describe all prime frames constructed from the spectral tetris method, and, as a byproduct, we obtain a characterization of when the spectral tetris construction works for redundancies below two.......We introduce a class of finite tight frames called prime tight frames and prove some of their elementary properties. In particular, we show that any finite tight frame can be written as a union of prime tight frames. We then characterize all prime harmonic tight frames and use thischaracterization...

Quantum frames

Science.gov (United States)

Brown, Matthew J.

2014-02-01

The framework of quantum frames can help unravel some of the interpretive difficulties i the foundation of quantum mechanics. In this paper, I begin by tracing the origins of this concept in Bohr's discussion of quantum theory and his theory of complementarity. Engaging with various interpreters and followers of Bohr, I argue that the correct account of quantum frames must be extended beyond literal space-time reference frames to frames defined by relations between a quantum system and the exosystem or external physical frame, of which measurement contexts are a particularly important example. This approach provides superior solutions to key EPR-type measurement and locality paradoxes.

Frame scaling function sets and frame wavelet sets in Rd

International Nuclear Information System (INIS)

Liu Zhanwei; Hu Guoen; Wu Guochang

2009-01-01

In this paper, we classify frame wavelet sets and frame scaling function sets in higher dimensions. Firstly, we obtain a necessary condition for a set to be the frame wavelet sets. Then, we present a necessary and sufficient condition for a set to be a frame scaling function set. We give a property of frame scaling function sets, too. Some corresponding examples are given to prove our theory in each section.

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

International Nuclear Information System (INIS)

Lytle, C.D.; Goddard, J.G.; Lin, C.H.

1980-01-01

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.)

Model building of a thermolysin-like protease by mutagenesis

NARCIS (Netherlands)

Frigerio, F; Margarit, [No Value; Nogarotto, R; Grandi, G; Vriend, G; Hardy, F; Veltman, OR; Venema, G; Eijsink, VGH

The present study concerns the use of site-directed mutagenesis experiments to optimize a three-dimensional model of the neutral protease of Bacillus subtilis (NP-sub), An initial model of NP-sub was constructed using the crystal structures of the homologous neutral proteases of Bacillus

Riesz Frames and Approximation of the Frame Coefficients

DEFF Research Database (Denmark)

Christensen, Ole

1996-01-01

A frame is a familyof elements in a Hilbert space with the propertythat every element in the Hilbert space can be written as a (infinite)linear combination of the frame elements. Frame theory describes howone can choose the corresponding coefficients, which are calledframe coefficients. From...... the mathematical point of view this isgratifying, but for applications it is a problem that the calculationrequires inversion of an operator on the Hilbert space.The projection method is introduced in order to avoid this problem.The basic idea is to consider finite subfamiliesof the frame and the orthogonal...... projection onto its span. Forfin QTR H,P_nf has a representation as a linear combinationof f_i,i=1,2,..,n, and the corresponding coefficients can be calculatedusing finite dimensional methods. We find conditions implying that thosecoefficients converge to the correct frame coefficients as n goes...

Fluorometric method of quantitative cell mutagenesis

Science.gov (United States)

Dolbeare, F.A.

1980-12-12

A method for assaying a cell culture for mutagenesis is described. A cell culture is stained first with a histochemical stain, and then a fluorescent stain. Normal cells in the culture are stained by both the histochemical and fluorescent stains, while abnormal cells are stained only by the fluorescent stain. The two stains are chosen so that the histochemical stain absorbs the wavelengths that the fluorescent stain emits. After the counterstained culture is subjected to exciting light, the fluorescence from the abnormal cells is detected.

Genetic separation of Escherichia coli recA functions for SOS mutagenesis and repressor cleavage

International Nuclear Information System (INIS)

Ennis, D.G.; Ossanna, N.; Mount, D.W.

1989-01-01

Evidence is presented that recA functions which promote the SOS functions of mutagenesis, LexA protein proteolysis, and lambda cI repressor proteolysis are each genetically separable from the others. This separation was observed in recombination-proficient recA mutants and rec+ (F' recA56) heterodiploids. recA430, recA433, and recA435 mutants and recA+ (F' recA56) heterodiploids were inducible for only one or two of the three functions and defective for mutagenesis. recA80 and recA432 mutants were constitutively activated for two of the three functions in that these mutants did not have to be induced to express the functions. We propose that binding of RecA protein to damaged DNA and subsequent interaction with small inducer molecules gives rise to conformational changes in RecA protein. These changes promote surface-surface interactions with other target proteins, such as cI and LexA proteins. By this model, the recA mutants are likely to have incorrect amino acids substituted as sites in the RecA protein structure which affect surface regions required for protein-protein interactions. The constitutively activated mutants could likewise insert altered amino acids at sites in RecA which are involved in the activation of RecA protein by binding small molecules or polynucleotides which metabolically regulate RecA protein

Localization Accuracy and Immobilization Effectiveness of a Stereotactic Body Frame for a Variety of Treatment Sites

Energy Technology Data Exchange (ETDEWEB)

Foster, Ryan, E-mail: Ryan.Foster@utsouthwestern.edu [Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas (United States); Meyer, Jeffrey; Iyengar, Puneeth; Pistenmaa, David; Timmerman, Robert; Choy, Hak [Department of Radiation Oncology, UT Southwestern Medical Center, Dallas, Texas (United States); Solberg, Timothy [Department of Radiation Oncology, University of Pennsylvania, Philadelphia, Pennsylvania (United States)

2013-12-01

Purpose: The purpose of this study was to analyze the pretreatment setup errors and intrafraction motion using cone beam computed tomography (CBCT) for stereotactic body radiation therapy patients immobilized and localized with a stereotactic body frame for a variety of treatment sites. Methods and Materials: Localization errors were recorded for patients receiving SBRT for 141 lung, 29 liver, 48 prostate, and 45 spine tumors representing 1005 total localization sessions. All patients were treated in a stereotactic body frame with a large custom-molded vacuum pillow. Patients were first localized to the frame using tattoos placed during simulation. Subsequently, the frame was aligned to the room lasers according to the stereotactic coordinates determined from the treatment plan. Every patient received a pretreatment and an intrafraction CBCT. Abdominal compression was used for all liver patients and for approximately 40% of the lung patients to reduce tumor motion due to respiration. Results: The mean ± standard deviation pretreatment setup errors from all localizations were −2.44 ± 3.85, 1.31 ± 5.84, and 0.11 ± 3.76 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean pretreatment localization results among all treatment sites were not significantly different (F test, P<.05). For all treatment sites, the mean ± standard deviation intrafraction shifts were 0.33 ± 1.34, 0.15 ± 1.45, and −0.02 ± 1.17 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean unidimensional intrafraction shifts were statistically different for several of the comparisons (P<.05) as assessed by the Tukey-Kramer test. Conclusions: Despite the varied tumor locations, the pretreatment mean localization errors for all sites were found to be consistent among the treatment sites and not significantly different, indicating that the body frame is a suitable immobilization and localization device for a variety of

Localization Accuracy and Immobilization Effectiveness of a Stereotactic Body Frame for a Variety of Treatment Sites

International Nuclear Information System (INIS)

Foster, Ryan; Meyer, Jeffrey; Iyengar, Puneeth; Pistenmaa, David; Timmerman, Robert; Choy, Hak; Solberg, Timothy

2013-01-01

Purpose: The purpose of this study was to analyze the pretreatment setup errors and intrafraction motion using cone beam computed tomography (CBCT) for stereotactic body radiation therapy patients immobilized and localized with a stereotactic body frame for a variety of treatment sites. Methods and Materials: Localization errors were recorded for patients receiving SBRT for 141 lung, 29 liver, 48 prostate, and 45 spine tumors representing 1005 total localization sessions. All patients were treated in a stereotactic body frame with a large custom-molded vacuum pillow. Patients were first localized to the frame using tattoos placed during simulation. Subsequently, the frame was aligned to the room lasers according to the stereotactic coordinates determined from the treatment plan. Every patient received a pretreatment and an intrafraction CBCT. Abdominal compression was used for all liver patients and for approximately 40% of the lung patients to reduce tumor motion due to respiration. Results: The mean ± standard deviation pretreatment setup errors from all localizations were −2.44 ± 3.85, 1.31 ± 5.84, and 0.11 ± 3.76 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean pretreatment localization results among all treatment sites were not significantly different (F test, P<.05). For all treatment sites, the mean ± standard deviation intrafraction shifts were 0.33 ± 1.34, 0.15 ± 1.45, and −0.02 ± 1.17 mm in the anteroposterior, superoinferior, and lateral directions, respectively. The mean unidimensional intrafraction shifts were statistically different for several of the comparisons (P<.05) as assessed by the Tukey-Kramer test. Conclusions: Despite the varied tumor locations, the pretreatment mean localization errors for all sites were found to be consistent among the treatment sites and not significantly different, indicating that the body frame is a suitable immobilization and localization device for a variety of

Scattering phase shift for elastic two pion scattering and the rho resonance in lattice QCD

Energy Technology Data Exchange (ETDEWEB)

Gutzwiller, Simone

2012-10-08

In this thesis we use lattice QCD to compute scattering phase shifts for elastic two-pion scattering in the isospin I=1 channel. Using Luescher's formalism, we derive the scattering phase shifts for different total momenta of the two-pion system in a non-rest frame. Furthermore we analyse the symmetries of the non-rest frame lattices and construct 2-pion and rho operators transforming in accordance with these symmetries. The data was collected for a 32{sup 3} x 64 and a 40{sup 3} x 64 lattice with N{sub f}=2 clover improved Wilson fermions at a pion mass around 290 MeV and a lattice spacing of about 0.072 fm.

Scattering phase shift for elastic two pion scattering and the rho resonance in lattice QCD

International Nuclear Information System (INIS)

Gutzwiller, Simone

2012-01-01

In this thesis we use lattice QCD to compute scattering phase shifts for elastic two-pion scattering in the isospin I=1 channel. Using Luescher's formalism, we derive the scattering phase shifts for different total momenta of the two-pion system in a non-rest frame. Furthermore we analyse the symmetries of the non-rest frame lattices and construct 2-pion and rho operators transforming in accordance with these symmetries. The data was collected for a 32 3 x 64 and a 40 3 x 64 lattice with N f =2 clover improved Wilson fermions at a pion mass around 290 MeV and a lattice spacing of about 0.072 fm.

Ionizing radiation-induced bystander mutagenesis and adaptation: Quantitative and temporal aspects

International Nuclear Information System (INIS)

Zhang Ying; Zhou Junqing; Baldwin, Joseph; Held, Kathryn D.; Prise, Kevin M.; Redmond, Robert W.; Liber, Howard L.

2009-01-01

This work explores several quantitative aspects of radiation-induced bystander mutagenesis in WTK1 human lymphoblast cells. Gamma-irradiation of cells was used to generate conditioned medium containing bystander signals, and that medium was transferred onto naive recipient cells. Kinetic studies revealed that it required up to 1 h to generate sufficient signal to induce the maximal level of mutations at the thymidine kinase locus in the bystander cells receiving the conditioned medium. Furthermore, it required at least 1 h of exposure to the signal in the bystander cells to induce mutations. Bystander signal was fairly stable in the medium, requiring 12-24 h to diminish. Medium that contained bystander signal was rendered ineffective by a 4-fold dilution; in contrast a greater than 20-fold decrease in the cell number irradiated to generate a bystander signal was needed to eliminate bystander-induced mutagenesis. This suggested some sort of feedback inhibition by bystander signal that prevented the signaling cells from releasing more signal. Finally, an ionizing radiation-induced adaptive response was shown to be effective in reducing bystander mutagenesis; in addition, low levels of exposure to bystander signal in the transferred medium induced adaptation that was effective in reducing mutations induced by subsequent γ-ray exposures.

Frames and counter-frames giving meaning to dementia: a framing analysis of media content.

Science.gov (United States)

Van Gorp, Baldwin; Vercruysse, Tom

2012-04-01

Media tend to reinforce the stigmatization of dementia as one of the most dreaded diseases in western society, which may have repercussions on the quality of life of those with the illness. The persons with dementia, but also those around them become imbued with the idea that life comes to an end as soon as the diagnosis is pronounced. The aim of this paper is to understand the dominant images related to dementia by means of an inductive framing analysis. The sample is composed of newspaper articles from six Belgian newspapers (2008-2010) and a convenience sample of popular images of the condition in movies, documentaries, literature and health care communications. The results demonstrate that the most dominant frame postulates that a human being is composed of two distinct parts: a material body and an immaterial mind. If this frame is used, the person with dementia ends up with no identity, which is in opposition to the Western ideals of personal self-fulfilment and individualism. For each dominant frame an alternative counter-frame is defined. It is concluded that the relative absence of counter-frames confirms the negative image of dementia. The inventory might be a help for caregivers and other professionals who want to evaluate their communication strategy. It is discussed that a more resolute use of counter-frames in communication about dementia might mitigate the stigma that surrounds dementia. Copyright © 2012 Elsevier Ltd. All rights reserved.

New mutations affecting induced mutagenesis in yeast.

Science.gov (United States)

Lawrence, C W; Krauss, B R; Christensen, R B

1985-01-01

Previously isolated mutations in baker's yeast, Saccharomyces cerevisiae, that impair induced mutagenesis were all identified with the aid of tests that either exclusively or predominantly detect base-pair substitutions. To avoid this bias, we have screened 11 366 potentially mutant clones for UV-induced reversion of the frameshift allele, his4-38, and have identified 10 mutants that give much reduced yields of revertants. Complementation and recombination tests show that 6 of these carry mutations at the previously known REV1, REV1 and REV3 loci, while the remaining 4 define 3 new genes, REV4 (2 mutations), REV5 and REV6. The rev4 mutations are readily suppressed in many genetic backgrounds and, like the rev5 mutation, impart only a limited deficiency for induced mutagenesis: it is likely, therefore that the REV4+ and REV5+ gene functions are only remotely concerned with this process. The rev6 mutants have a more general deficiency, however, as well as marked sensitivity to UV and an increased spontaneous mutation rate, properties that suggest the REV6 gene is directly involved in mutation induction. The REV5 gene is located about 1 cM proximal to CYC1 on chromosome X.

Anandan quantum phase for a neutral particle with Fermi-Walker reference frame in the cosmic string background

International Nuclear Information System (INIS)

Bakke, Knut; Furtado, C.

2010-01-01

We study geometric quantum phases in the relativistic and non-relativistic quantum dynamics of a neutral particle with a permanent magnetic dipole moment interacting with two distinct field configurations in a cosmic string spacetime. We consider the local reference frames of the observers are transported via Fermi-Walker transport and study the influence of the non-inertial effects on the phase shift of the wave function of the neutral particle due to the choice of this local frame. We show that the wave function of the neutral particle acquires non-dispersive relativistic and non-relativistic quantum geometric phases due to the topology of the spacetime, the interaction between the magnetic dipole moment with external fields and the spin-rotation coupling. However, due to the Fermi-Walker reference frame, no phase shift associated to the Sagnac effect appears in the quantum dynamics of a neutral particle. We show that in the absence of topological defect, the contribution to the quantum phase due to the spin-rotation coupling is equivalent to the Mashhoon effect in non-relativistic dynamics. (orig.)

Framing narrative journalism as a new genre: A case study of the Netherlands.

Science.gov (United States)

van Krieken, Kobie; Sanders, José

2017-11-01

Although narrative journalism has a long history in the Netherlands, it is in recent years being promoted as a 'new' genre. This study examines the motives underlying this promotional tactic. To that end, we analyze how narrative journalism is framed in (1) public expressions of the initiatives aimed at professionalization of the genre and (2) interviews with journalists and lecturers in journalism programs. Results indicate that in public discourse on narrative journalism, the genre is framed as moving , essential , and as high quality journalism . These frames indicate that the current promotion of narrative journalism as 'new' can be seen as a strategy that journalists apply to withstand the pressures they are facing in the competition with new media. These frames are deepened in the interviews with lecturers and practitioners, who frame narrative journalism as a dangerous game , a paradigm shift , and as the Holy Grail . These frames indicate that narrative journalism is regarded as the highest achievable goal for journalists, but that its practice comes with dangers and risks: it tempts journalists to abandon the traditional principles of objectivity and factuality, which can ultimately cause journalism to lose its credibility and authority. We discuss these findings in terms of boundary work and reflect on implications for narrative journalism's societal function.

Body frames and frame singularities for three-atom systems

International Nuclear Information System (INIS)

Littlejohn, R.G.; Mitchell, K.A.; Aquilanti, V.; Cavalli, S.

1998-01-01

The subject of body frames and their singularities for three-particle systems is important not only for large-amplitude rovibrational coupling in molecular spectroscopy, but also for reactive scattering calculations. This paper presents a geometrical analysis of the meaning of body frame conventions and their singularities in three-particle systems. Special attention is devoted to the principal axis frame, a certain version of the Eckart frame, and the topological inevitability of frame singularities. The emphasis is on a geometrical picture, which is intended as a preliminary study for the more difficult case of four-particle systems, where one must work in higher-dimensional spaces. The analysis makes extensive use of kinematic rotations. copyright 1998 The American Physical Society

Use of Random and Site-Directed Mutagenesis to Probe Protein Structure-Function Relationships: Applied Techniques in the Study of Helicobacter pylori.

Science.gov (United States)

Whitmire, Jeannette M; Merrell, D Scott

2017-01-01

Mutagenesis is a valuable tool to examine the structure-function relationships of bacterial proteins. As such, a wide variety of mutagenesis techniques and strategies have been developed. This chapter details a selection of random mutagenesis methods and site-directed mutagenesis procedures that can be applied to an array of bacterial species. Additionally, the direct application of the techniques to study the Helicobacter pylori Ferric Uptake Regulator (Fur) protein is described. The varied approaches illustrated herein allow the robust investigation of the structural-functional relationships within a protein of interest.

Radiation induced COX-2 expression and mutagenesis at non-targeted lung tissues of gpt delta transgenic mice

Science.gov (United States)

Chai, Y; Calaf, G M; Zhou, H; Ghandhi, S A; Elliston, C D; Wen, G; Nohmi, T; Amundson, S A; Hei, T K

2013-01-01

Background: Although radiation-induced bystander effects have been confirmed using a variety of endpoints, the mechanism(s) underlying these effects are not well understood, especially for in vivo study. Methods: A 1-cm2 area (1 cm × 1 cm) in the lower abdominal region of gpt delta transgenic mice was irradiated with 5 Gy of 300 keV X-rays, and changes in out-of-field lung and liver were observed. Results: Compared with sham-treated controls, the Spi− mutation frequency increased 2.4-fold in non-targeted lung tissues at 24 h after partial body irradiation (PBIR). Consistent with dramatic Cyclooxygenase 2 (COX-2) induction in the non-targeted bronchial epithelial cells, increasing levels of prostaglandin, together with 8-hydroxydeoxyguanosine, in the out-of-field lung tissues were observed after PBIR. In addition, DNA double-strand breaks and apoptosis were induced in bystander lung tissues after PBIR. Conclusion: The PBIR induces DNA damage and mutagenesis in non-targeted lung tissues, especially in bronchial epithelial cells, and COX-2 has an essential role in bystander mutagenesis. PMID:23321513

Mutational spectrum analysis of umuC-independent and umuC-dependent γ-radiation mutagenesis in Escherichia coli

International Nuclear Information System (INIS)

Sargentini, N.J.; Smith, K.C.

1989-01-01

γ-radiation mutagenesis Escherichia coli K-12. Mutagenesis (argE3(OC) A rg + ) was blocked in a δ(recA-srlR)306 strain at the same doses that induced mutations in umuC122::Tn5 and wild-type strains, indicating that both umuC-independent and umuC-dependent mechanisms function within recA-dependent misrepair. Analyses of various suppressor and back mutations that result in argE3 and hisG4 ochre reversion and an analysis of trpE9777 reversion were performed on umuC and wild-type cells irradiated in the presence and absence of oxygen. While the umuC strain showed the γ-radiation induction of base substitution and frameshifts when irradiated in the absence of oxygen, the umuC mutation blocked all oxygen-dependent base-substitution mutagenesis, but non all oxygen-dependent frameshift mutagenesis. For anoxically irradiated cells, the yields of GC T and AT GC transitions were essentially umuC independent, while the yields of (AT or GC) TA transversions were heavily umuC dependent. These data suggest new concepts about the nature of the DNA lesions and the mutagenic mechanisms that lead to γ-radiation mutagenesis. (author). 48 refs.; 1 tab.; 6 refs

A Mutant Mouse with a Highly Specific Contextual Fear-Conditioning Deficit Found in an N-Ethyl-N-Nitrosourea (ENU) Mutagenesis Screen

Science.gov (United States)

Pletcher, Mathew T.; Wiltshire, Tim; Tarantino, Lisa M.; Mayford, Mark; Reijmers, Leon G.; Coats, Jennifer K.

2006-01-01

Targeted mutagenesis in mice has shown that genes from a wide variety of gene families are involved in memory formation. The efficient identification of genes involved in learning and memory could be achieved by random mutagenesis combined with high-throughput phenotyping. Here, we provide the first report of a mutagenesis screen that has…

Frame on frames: an annotated bibliography

International Nuclear Information System (INIS)

Wright, T.; Tsao, H.J.

1983-01-01

The success or failure of any sample survey of a finite population is largely dependent upon the condition and adequacy of the list or frame from which the probability sample is selected. Much of the published survey sampling related work has focused on the measurement of sampling errors and, more recently, on nonsampling errors to a lesser extent. Recent studies on data quality for various types of data collection systems have revealed that the extent of the nonsampling errors far exceeds that of the sampling errors in many cases. While much of this nonsampling error, which is difficult to measure, can be attributed to poor frames, relatively little effort or theoretical work has focused on this contribution to total error. The objective of this paper is to present an annotated bibliography on frames with the hope that it will bring together, for experimenters, a number of suggestions for action when sampling from imperfect frames and that more attention will be given to this area of survey methods research

Moderate repetitions (mobile elements) and hot points of chromosomal mutagenesis in Drozophila melanogaster

International Nuclear Information System (INIS)

Aleksandrova, M.V.; Sevan'kaev, A.V.; Aleksandrov, I.D.

1989-01-01

The results of experimental examination of hypothesis on mobile elements (ME) as target for radiation-induced chromosomal mutagenesis do not confirm it in this direct variant though indicate on the presence of nonincidental connection between sites of ME localization of certain type and points of chromosomal mutagenesis are presented. The presented regularity is explained by assumption that settling of the ME by genome is going along postulated static chromomer-binding-DNA complexes, playing an important role in space organization of interphase chromatin. 11 refs.; 2 figs.; 2 tabs

Forsythia improvement by mutagenesis

International Nuclear Information System (INIS)

Cadic, A.; Martin, Denise; Renoux, A.

1980-01-01

Mutagenesis is a method used by selectors to modify the genetic heritage of a species. Since about twenty years ago the list of varieties obtained has lengthened steadily. For various reasons, plants which propagate vegetatively, and amongst these a large number of decorative plants, have been especially improved by this method. Of the mutagenic agents known at present a favourite choice has often been the gamma radiations emitted by radioactive cobalt ( 60 Co). Several clones of forsythia, very irregular in decorative value, were exposed to gamma radiation for the purpose of judging the breadth of the easily identifiable mutation range and creating new varieties. From the results it is hoped very soon to release compact varieties with short internodes and varieties better suited to forcing because of their earlier flowering season [fr

Amino acid substitutions in random mutagenesis libraries: lessons from analyzing 3000 mutations.

Science.gov (United States)

Zhao, Jing; Frauenkron-Machedjou, Victorine Josiane; Kardashliev, Tsvetan; Ruff, Anna Joëlle; Zhu, Leilei; Bocola, Marco; Schwaneberg, Ulrich

2017-04-01

The quality of amino acid substitution patterns in random mutagenesis libraries is decisive for the success in directed evolution campaigns. In this manuscript, we provide a detailed analysis of the amino acid substitutions by analyzing 3000 mutations of three random mutagenesis libraries (1000 mutations each; epPCR with a low-mutation and a high-mutation frequency and SeSaM-Tv P/P) employing lipase A from Bacillus subtilis (bsla). A comparison of the obtained numbers of beneficial variants in the mentioned three random mutagenesis libraries with a site saturation mutagenesis (SSM) (covering the natural diversity at each amino acid position of BSLA) concludes the diversity analysis. Seventy-six percent of the SeSaM-Tv P/P-generated substitutions yield chemically different amino acid substitutions compared to 64% (epPCR-low) and 69% (epPCR-high). Unique substitutions from one amino acid to others are termed distinct amino acid substitutions. In the SeSaM-Tv P/P library, 35% of all theoretical distinct amino acid substitutions were found in the 1000 mutation library compared to 25% (epPCR-low) and 26% (epPCR-high). Thirty-six percent of distinct amino acid substitutions found in SeSaM-Tv P/P were unobtainable by epPCR-low. Comparison with the SSM library showed that epPCR-low covers 15%, epPCR-high 18%, and SeSaM-Tv P/P 21% of obtainable beneficial amino acid positions. In essence, this study provides first insights on the quality of epPCR and SeSaM-Tv P/P libraries in terms of amino acid substitutions, their chemical differences, and the number of obtainable beneficial amino acid positions.

What Can a Micronucleus Teach? Learning about Environmental Mutagenesis

Science.gov (United States)

Linde, Ana R.; Garcia-Vazquez, Eva

2009-01-01

The micronucleus test is widely employed in environmental health research. It can also be an excellent tool for learning important concepts in environmental health. In this article we present an inquiry-based laboratory exercise where students explore several theoretical and practical aspects of environmental mutagenesis employing the micronucleus…

A phenomenological view of language shift.

Science.gov (United States)

Tsitsipis, Lukas D

2004-01-01

Sociolinguistic studies of language shift have in their majority framed their research object in a horizon of theoretically received variables such as class, ethnicity, locality, attitudes etc. In spite of a limited usefulness of such conceptual variables, and of a recently emerging focus on agency, negotiation, and praxis the best results we obtain have not questioned in a coherent and theoretically sound manner the continuing hegemony of mechanistic-metaphorical models (language death, language suicide). In this paper I propose to examine language shift as a multifaceted phenomenon, joining in this respect work by other linguistic anthropologists researching similar areas. I specifically argue that by replacing vertical concepts such as age and generation, and dichotomous logics such as center and periphery with phenomenologically inspired concepts such as typifications, consociateship, contemporariness, and stream of consciousness we are in a better position to generalize about language shift dynamics. Data for this work is derived primarily from the Albanian speech communities of modern Greece, but also from other communities for comparative purposes.

Genome-wide comparison of ultraviolet and ethyl methanesulphonate mutagenesis methods for the brown alga Ectocarpus.

Science.gov (United States)

Godfroy, Olivier; Peters, Akira F; Coelho, Susana M; Cock, J Mark

2015-12-01

Ectocarpus has emerged as a model organism for the brown algae and a broad range of genetic and genomic resources are being generated for this species. The aim of the work presented here was to evaluate two mutagenesis protocols based on ultraviolet irradiation and ethyl methanesulphonate treatment using genome resequencing to measure the number, type and distribution of mutations generated by the two methods. Ultraviolet irradiation generated a greater number of genetic lesions than ethyl methanesulphonate treatment, with more than 400 mutations being detected in the genome of the mutagenised individual. This study therefore confirms that the ultraviolet mutagenesis protocol is suitable for approaches that require a high density of mutations, such as saturation mutagenesis or Targeting Induced Local Lesions in Genomes (TILLING). Copyright © 2015 Elsevier B.V. All rights reserved.

RecA-mediated cleavage activates UmuD for mutagenesis: Mechanistic relationship between transcriptional derepression and posttranslational activation

International Nuclear Information System (INIS)

Nohmi, Takehiko; Battista, J.R.; Dodson, L.A.; Walker, G.C.

1988-01-01

The products of the SOS-regulated umuDC operon are required for most UV and chemical mutagenesis in Escherichia coli. It has been shown that the UmuD protein shares homology with LexA, the repressor of the SOS genes. In this paper the authors describe a series of genetic experiments that indicate that the purpose of RecA-mediated cleavage of UmuD at its bond between Cys-24 and Gly-25 is to activate UmuD for its role in mutagenesis and that the COOH-terminal fragment of UmuD is necessary and sufficient for the role of UmuD in UV mutagenesis. Other genetic experiments are presented that (i) support the hypothesis that the primary role of Ser-60 in UmuD function is to act as a nucleophile in the RecA-mediated cleavage reaction and (ii) raise the possibility that RecA has a third role in UV mutagenesis besides mediating the cleavage of LexA and UmuD

Shifts in climate suitability for wine production as a result of climate change in a temperate climate wine region of Romania

Science.gov (United States)

Irimia, Liviu Mihai; Patriche, Cristian Valeriu; Quenol, Hervé; Sfîcă, Lucian; Foss, Chris

2018-02-01

Climate change is causing important shifts in the suitability of regions for wine production. Fine scale mapping of these shifts helps us to understand the evolution of vineyard climates, and to find solutions through viticultural adaptation. The aim of this study is to identify and map the structural and spatial shifts that occurred in the climatic suitability for wine production of the Cotnari wine growing region (Romania) between 1961 and 2013. Discontinuities in trends of temperature were identified, and the averages and trends of 13 climatic parameters for the 1961 to 1980 and 1981 to 2013 time periods were analysed. Using the averages of these climatic parameters, climate suitability for wine production was calculated at a resolution of 30 m and mapped for each time period, and the changes analysed. The results indicate shifts in the area's historic climatic profile, due to an increase of heliothermal resources and precipitation constancy. The area's climate suitability for wine production was modified by the loss of climate suitability for white table wines, sparkling wines and wine for distillates; shifts in suitability to higher altitudes by about 67 m, and a 48.6% decrease in the area suitable for quality white wines; and the occurrence of suitable climates for red wines at lower altitudes. The study showed that climate suitability for wine production has a multi-level spatial structure, with classes requiring a cooler climate being located at a higher altitude than those requiring a warmer climate. Climate change has therefore resulted in the shift of climate suitability classes for wine production to higher altitudes.

ALICE's main austenitic stainless steel support structure (the Space Frame)

CERN Multimedia

Maximilien Brice

2006-01-01

This structure is constructed to hold the large volume detectors, such as the Time Projection Chamber, Transition Radiation Detector and Time of Flight inside the ALICE solenoid magnet. After the final assembly at CERN, two large mobile cranes were needed for the job of lifting and turning the 14 tonne frame onto its side. Once shifted, it was placed in Building SX2, one of the surface assembly areas designated for ALICE.

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

International Nuclear Information System (INIS)

Basha, S.G.; Krasavin, E.A.; Kozubek, S.; Amirtaev, K.G.

1990-01-01

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)=kD x . DMF values of the induced mutagenesis amounted to 2 for strains TA100 and TA102, and 1.5 for strain TA98

Study on the binding sites of radiosensitivity associated transcription factor in the promoter region of Ier5 gene

International Nuclear Information System (INIS)

Cui Wei; Yin Lingling; Dong Lingyue

2012-01-01

Objective: To clarify the mechanism of immediate early response gene 5 (Ier5) transcription induced by radiation. Methods: Deletant construction, site-specific mutagenesis,electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) were used to forecast the promoter region, binding sites and transcription factors of Ier5 gene in HeLa cells. Results: The promoter region of Ier5 gene might be in the region of Ier5 -8 deletant (-408 - -238 bp). The Ier5 gene had two transcription factors of GCF and NFI, and GCF had two binding sites located in the region of -388 - -382 bp and -274 - -270 bp of Ier5 promoter. The binding site of NFI was located in -362 - -357 bp of Ier5 promoter. GCF could inhibit the expression of Ier5 gene and this inhibition was diminished when the radiation dose increased. In contrast, NFI increased the expression of Ier5. Conclusions: The most possible region of Ier5 promoter is from -408 to -238 bp which has two binding sites for the radiosensitivity transcription factors of GCF and NFI that could negatively and positively regulate the expression of Ier5 respectively. (authors)

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

International Nuclear Information System (INIS)

Abdul Rahim Harun; Shuhami Shamsuddin; Ghazali Hussin

2000-01-01

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

Actions on climate change, Intended Reducing carbon emissions in China via optimal industry shifts: Toward hi-tech industries, cleaner resources and higher carbon shares in less-develop regions

International Nuclear Information System (INIS)

Fu, Xue; Lahr, Michael; Yaxiong, Zhang; Meng, Bo

2017-01-01

This paper uses an optimal interregional input-output model to focus on how interregional industrial shifts alone might enable China to reduce carbon intensity instead of national shifts. The optimal industry shifts assure integration of all regions by regional products and goods in which carbon emissions are embodied via energy consumption. Generally speaking, high-tech industries concentrate in affluent regions to replace construction. Selected services increase output shares across most of regions. Meanwhile, energy-intensive manufacturing, rather than agriculture, decrease their shares to achieve the national annual growth constrained by nation’s carbon targets. Due to the need to decelerate energy use, carbon intensity goal puts particularly extreme pressure on less-developed regions to shutter heavy industries. Explicit shifts toward cleaner resources and renewable energy appear to be quite important for coal mines in Central China. - Highlights: • The model optimizes GDP constrained by industry-based emissions targets. • Scenario on carbon intensity, growth rate, energy mix, and technology advance. • Interregional I-O table informs technology, industry mix, and interregional trade. • China could raise the output of high-tech in South Coast and of selected services. • Shifts toward cleaner resources and renewable energy are important in the Central.

CYTOTOXICITY AND MUTAGENESIS METHODS FOR EVALUATING TOXICITY REMOVAL FROM WASTEWATERS

Science.gov (United States)

This project was a feasibility study of the effectiveness of a mammalian cell cytotoxicity assay and a mammalian cell mutagenesis assay for monitoring the toxicity and mutagenicity of influent and effluent wastewater at treatment plants. In the cytotoxicity assay, ambient samples...

Integrating structural and mutagenesis data to elucidate GPCR ligand binding

DEFF Research Database (Denmark)

Munk, Christian; Harpsøe, Kasper; Hauser, Alexander S

2016-01-01

is reported that exhibit activity through multiple receptors, binding in allosteric sites, and bias towards different intracellular signalling pathways. Furthermore, a wealth of single point mutants has accumulated in literature and public databases. Integrating these structural and mutagenesis data will help...

Issue Framing and Sector Character as Critical Parameters for Government Contracting-Out in the UK

DEFF Research Database (Denmark)

Bækkeskov, Erik

2011-01-01

This article shows that variations in how two UK governments justified contracting-out (issue framing), combined with shifting sector-derived incentives for union activism (sector character), can help explain the extent of contracting-out. Janitorial service, an activity of the UK government......, and its reform faced unions that stood to lose a great deal from movement of janitorial jobs to private firms. In contrast, the New Labour government framed contracting-out broadly, as a means to efficient social justice, and faced unions with low stakes in government janitors. As a consequence, UK...

Application of In Vitro Transposon Mutagenesis to Erythromycin Strain Improvement in Saccharopolyspora erythraea.

Science.gov (United States)

Weber, J Mark; Reeves, Andrew; Cernota, William H; Wesley, Roy K

2017-01-01

Transposon mutagenesis is an invaluable technique in molecular biology for the creation of random mutations that can be easily identified and mapped. However, in the field of microbial strain improvement, transposon mutagenesis has scarcely been used; instead, chemical and physical mutagenic methods have been traditionally favored. Transposons have the advantage of creating single mutations in the genome, making phenotype to genotype assignments less challenging than with traditional mutagens which commonly create multiple mutations in the genome. The site of a transposon mutation can also be readily mapped using DNA sequencing primer sites engineered into the transposon termini. In this chapter an in vitro method for transposon mutagenesis of Saccharopolyspora erythraea is presented. Since in vivo transposon tools are not available for most actinomycetes including S. erythraea, an in vitro method was developed. The in vitro method involves a significant investment in time and effort to create the mutants, but once the mutants are made and screened, a large number of highly relevant mutations of direct interest to erythromycin production can be found.

Behaviour of Strengthened RC Frames with Eccentric Steel Braced Frames

Science.gov (United States)

Kamanli, Mehmet; Unal, Alptug

2017-10-01

After devastating earthquakes in recent years, strengthening of reinforced concrete buildings became an important research topic. Reinforced concrete buildings can be strengthened by steel braced frames. These steel braced frames may be made of concentrically or eccentrically indicated in Turkish Earthquake Code 2007. In this study pushover analysis of the 1/3 scaled 1 reinforced concrete frame and 1/3 scaled 4 strengthened reinforced concrete frames with internal eccentric steel braced frames were conducted by SAP2000 program. According to the results of the analyses conducted, load-displacement curves of the specimens were compared and evaluated. Adding eccentric steel braces to the bare frame decreased the story drift, and significantly increased strength, stiffness and energy dissipation capacity. In this strengthening method lateral load carrying capacity, stiffness and dissipated energy of the structure can be increased.

A semi-automatic 2D-to-3D video conversion with adaptive key-frame selection

Science.gov (United States)

Ju, Kuanyu; Xiong, Hongkai

2014-11-01

To compensate the deficit of 3D content, 2D to 3D video conversion (2D-to-3D) has recently attracted more attention from both industrial and academic communities. The semi-automatic 2D-to-3D conversion which estimates corresponding depth of non-key-frames through key-frames is more desirable owing to its advantage of balancing labor cost and 3D effects. The location of key-frames plays a role on quality of depth propagation. This paper proposes a semi-automatic 2D-to-3D scheme with adaptive key-frame selection to keep temporal continuity more reliable and reduce the depth propagation errors caused by occlusion. The potential key-frames would be localized in terms of clustered color variation and motion intensity. The distance of key-frame interval is also taken into account to keep the accumulated propagation errors under control and guarantee minimal user interaction. Once their depth maps are aligned with user interaction, the non-key-frames depth maps would be automatically propagated by shifted bilateral filtering. Considering that depth of objects may change due to the objects motion or camera zoom in/out effect, a bi-directional depth propagation scheme is adopted where a non-key frame is interpolated from two adjacent key frames. The experimental results show that the proposed scheme has better performance than existing 2D-to-3D scheme with fixed key-frame interval.

Visualization of tandem repeat mutagenesis in Bacillus subtilis.

Science.gov (United States)

Dormeyer, Miriam; Lentes, Sabine; Ballin, Patrick; Wilkens, Markus; Klumpp, Stefan; Kohlheyer, Dietrich; Stannek, Lorena; Grünberger, Alexander; Commichau, Fabian M

2018-03-01

Mutations are crucial for the emergence and evolution of proteins with novel functions, and thus for the diversity of life. Tandem repeats (TRs) are mutational hot spots that are present in the genomes of all organisms. Understanding the molecular mechanism underlying TR mutagenesis at the level of single cells requires the development of mutation reporter systems. Here, we present a mutation reporter system that is suitable to visualize mutagenesis of TRs occurring in single cells of the Gram-positive model bacterium Bacillus subtilis using microfluidic single-cell cultivation. The system allows measuring the elimination of TR units due to growth rate recovery. The cultivation of bacteria carrying the mutation reporter system in microfluidic chambers allowed us for the first time to visualize the emergence of a specific mutation at the level of single cells. The application of the mutation reporter system in combination with microfluidics might be helpful to elucidate the molecular mechanism underlying TR (in)stability in bacteria. Moreover, the mutation reporter system might be useful to assess whether mutations occur in response to nutrient starvation. Copyright © 2018 Elsevier B.V. All rights reserved.

Approximately dual frames in Hilbert spaces and applications to Gabor frames

OpenAIRE

Christensen, Ole; Laugesen, Richard S.

2011-01-01

Approximately dual frames are studied in the Hilbert space setting. Approximate duals are easier to construct than classical dual frames, and can be tailored to yield almost perfect reconstruction. Bounds on the deviation from perfect reconstruction are obtained for approximately dual frames constructed via perturbation theory. An alternative bound is derived for the rich class of Gabor frames, by using the Walnut representation of the frame operator to estimate the deviation from equality in...

Framing the frame: How task goals determine the likelihood and direction of framing effects

OpenAIRE

Todd McElroy; John J. Seta

2007-01-01

We examined how the goal of a decision task influences the perceived positive, negative valence of the alternatives and thereby the likelihood and direction of framing effects. In Study 1 we manipulated the goal to increase, decrease or maintain the commodity in question and found that when the goal of the task was to increase the commodity, a framing effect consistent with those typically observed in the literature was found. When the goal was to decrease, a framing effect opposite to the ty...

Framing the ultimatum game: the contribution of simulation.

Science.gov (United States)

Tomasino, Barbara; Lotto, Lorella; Sarlo, Michela; Civai, Claudia; Rumiati, Rino; Rumiati, Raffaella I

2013-01-01

It has now become widely accepted that economic decisions are influenced by cognitive and emotional processes. In the present study, we aimed at disentangling the neural mechanisms associated with the way in which the information is formulated, i.e., framing effect, in terms of gain or loss, which influences people's decisions. Participants played a fMRI version of the Ultimatum Game (UG) where we manipulated bids through two different frames: the expression "I give you" (gain) focusing on money the respondent would receive if she/he agreed with the proponent, and the expression "I take" (loss) focusing on the money that would be removed from the respondent in the event that she/he accepted the offer. Neuroimaging data revealed a frame by response interaction, showing an increase of neural activity in the right rolandic operculum/insular cortex, the anterior cingulate, among other regions, for accepting the frame "I take" vs. rejecting, as compared to accepting the frame "I give you" vs. rejecting. In addition, the left occipito-temporal junction was activated for "I take" vs. "I give you" for offer 5, corresponding to the equal offer made unpleasant by the presence of the frame "I take," where is the proposer that takes the money. Our data extend the current understanding of the neural substrates of social decision making, by disentangling the structures sensitive to the way in which the information is formulated (i.e., framing effect), in terms of gain or loss.

Framing the Ultimatum Game: The contribution of simulation

Directory of Open Access Journals (Sweden)

Barbara eTomasino

2013-07-01

Full Text Available It has now become widely accepted that economic decisions are influenced by cognitive and emotional processes. In the present study, we aimed at disentangling the neural mechanisms associated with the way in which the information is formulated, i.e., framing effect, in terms of gain or loss, which influences people’s decisions. Participants played a fMRI version of the Ultimatum Game where we manipulated bids through two different frames: the expression "I give you" (gain focusing on money the respondent would receive if she/he agreed with the proponent, and the expression "I take" (loss focusing on the money that would be removed from the respondent in the event that she/he accepted the offer. Neuroimaging data revealed a frame by response interaction, showing an increase of neural activity in the right rolandic operculum/insular cortex, the anterior cingulate, among other regions, for accepting the frame I take vs. rejecting, as compared to accepting the frame I give you vs. rejecting. In addition, the left occipito-temporal junction was activated for ‘I take vs. I give you for offer 5, corresponding to the equal offer made unpleasant by the presence of the frame I take, where is the proposer that takes the money. Our data extend the current understanding of the neural substrates of social decision making, by disentangling the structures sensitive to the way in which the information is formulated (i.e., framing effect, in terms of gain or loss.

Genetic analysis of gamma-ray mutagenesis in yeast. I. Reversion in radiation-sensitive strains

International Nuclear Information System (INIS)

McKee, R.H.; Lawrence, C.W.

1979-01-01

The frequency of revertants induced by 60 Co γ rays of the ochre allele, cyc1-9, has been measured in radiation-sensitive strains carrying one of 19 nonallelic mutations and in wild-type strains. The results indicate that ionizing radiation mutagenesis depends on the activity of the RAD6 group of genes and that the gene functions employed are very similar, but probably not identical, to those that mediate uv mutagenesis. Repair activities dependent on the functions of the RAD50 through RAD57 loci, the major pathway for the repair of damage caused by ionizing radiation, do not appear to play any part in mutagenesis. A comparison between the γ-ray data and those obtained previously with uv and chemical mutagens suggests that the RAD6 mutagenic pathway is in fact composed of a set of processes, some of which are concerned with error-prone, and some with error-free, recovery activities

Mars Science Laboratory Frame Manager for Centralized Frame Tree Database and Target Pointing

Science.gov (United States)

Kim, Won S.; Leger, Chris; Peters, Stephen; Carsten, Joseph; Diaz-Calderon, Antonio

2013-01-01

The FM (Frame Manager) flight software module is responsible for maintaining the frame tree database containing coordinate transforms between frames. The frame tree is a proper tree structure of directed links, consisting of surface and rover subtrees. Actual frame transforms are updated by their owner. FM updates site and saved frames for the surface tree. As the rover drives to a new area, a new site frame with an incremented site index can be created. Several clients including ARM and RSM (Remote Sensing Mast) update their related rover frames that they own. Through the onboard centralized FM frame tree database, client modules can query transforms between any two frames. Important applications include target image pointing for RSM-mounted cameras and frame-referenced arm moves. The use of frame tree eliminates cumbersome, error-prone calculations of coordinate entries for commands and thus simplifies flight operations significantly.

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

International Nuclear Information System (INIS)

Aleshkin, G.I.; Brukhanskij, G.V.; Skavronskaya, A.G.

1985-01-01

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

A plasmid-transposon hybrid mutagenesis system effective in a broad range of Enterobacteria

Directory of Open Access Journals (Sweden)

Rita eMonson

2015-12-01

Full Text Available Random transposon mutagenesis is a powerful technique used to generate libraries of genetic insertions in many different bacterial strains. Here we develop a system facilitating random transposon mutagenesis in a range of different Gram-negative bacterial strains, including Pectobacterium atrosepticum, Citrobacter rodentium, Serratia sp. ATCC39006, Serratia plymuthica, Dickeya dadantii and many more. Transposon mutagenesis was optimized in each of these strains and three studies are presented to show the efficacy of this system. Firstly, the important agricultural pathogen D. dadantii was mutagenized. Two mutants that showed reduced protease production and one mutant producing the previously cryptic pigment, indigoidine, were identified and characterized. Secondly, the enterobacterium, Serratia sp. ATCC39006 was mutagenized and mutants incapable of producing gas vesicles, proteinaceous intracellular organelles, were identified. One of these contained a β-galactosidase transcriptional fusion within the gene gvpA1, essential for gas vesicle production. Finally, the system was used to mutate the biosynthetic gene clusters of the antifungal, anti-oomycete and anticancer polyketide, oocydin A, in the plant-associated enterobacterium, Dickeya solani MK10. The mutagenesis system was developed to allow easy identification of transposon insertion sites by sequencing, after facile generation of a replicon encompassing the transposon and adjacent DNA, post-excision. Furthermore, the system can also create transcriptional fusions with either β-galactosidase or β-glucuronidase as reporters, and exploits a variety of drug resistance markers so that multiple selectable fusions can be generated in a single strain. This system of various transposons has wide utility and can be combined in many different ways.

Lack of mutational hot spots during decitabine-mediated HIV-1 mutagenesis.

Science.gov (United States)

Rawson, Jonathan M O; Landman, Sean R; Reilly, Cavan S; Bonnac, Laurent; Patterson, Steven E; Mansky, Louis M

2015-11-01

Decitabine has previously been shown to induce lethal mutagenesis of human immunodeficiency virus type 1 (HIV-1). However, the factors that determine the susceptibilities of individual sequence positions in HIV-1 to decitabine have not yet been defined. To investigate this, we performed Illumina high-throughput sequencing of multiple amplicons prepared from proviral DNA that was recovered from decitabine-treated cells infected with HIV-1. We found that decitabine induced an ≈4.1-fold increase in the total mutation frequency of HIV-1, primarily due to a striking ≈155-fold increase in the G-to-C transversion frequency. Intriguingly, decitabine also led to an ≈29-fold increase in the C-to-G transversion frequency. G-to-C frequencies varied substantially (up to ≈80-fold) depending upon sequence position, but surprisingly, mutational hot spots (defined as upper outliers within the mutation frequency distribution) were not observed. We further found that every single guanine position examined was significantly susceptible to the mutagenic effects of decitabine. Taken together, these observations demonstrate for the first time that decitabine-mediated HIV-1 mutagenesis is promiscuous and occurs in the absence of a clear bias for mutational hot spots. These data imply that decitabine-mediated G-to-C mutagenesis is a highly effective antiviral mechanism for extinguishing HIV-1 infectivity. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Chromosomal damages and mutagenesis in mammalian and human cells induced by ionizing radiations with different LET

International Nuclear Information System (INIS)

Govorun, R.D.

1997-01-01

On the basis of literature and proper data the inference was made about essential role of structural chromosomal (and gene) damages in spontaneous and radiation-induced mutagenesis of mammalian and human cells on HPRT-loci. The evidences of increasing role of these damages in the mutagenesis after the influence of ionizing radiations with high LET are adduced. The consequences of HPRT-gene damages have been examined hypothetically. The geterogeneity of mutant subclones on their cytogenetical properties were revealed experimentally. The data reflect a phenomenon of the reproductive chromosomal instability in many generations of mutant cell. The mutagenesis of mammalian cells is also accompanied by the impairment of chromosome integrity with high probability as a stage of appropriate genome reorganization because of changed vital conditions

p53 Mutagenesis by Benzo[a]pyrene derived Radical Cations

Science.gov (United States)

Sen, Sushmita; Bhojnagarwala, Pratik; Francey, Lauren; Lu, Ding; Jeffrey Field, Trevor M. Penning

2013-01-01

Benzo[a]pyrene (B[a]P), a major human carcinogen in combustion products such as cigarette smoke and diesel exhaust, is metabolically activated into DNA-reactive metabolites via three different enzymatic pathways. The pathways are the anti-(+)-benzo[a]pyrene 7,8-diol 9, 10-epoxide pathway (P450/ epoxide hydrolase catalyzed) (B[a]PDE), the benzo[a]pyrene o-quinone pathway (aldo ketose reductase (AKR) catalyzed) and the B[a]P radical cation pathway (P450 peroxidase catalyzed). We used a yeast p53 mutagenesis system to assess mutagenesis by B[a]P radical cations. Because radical cations are short-lived, they were generated in situ by reacting B[a]P with cumene hydroperoxide (CuOOH) and horse radish peroxidase (HRP) and then monitoring the generation of the more stable downstream products, B[a]P-1,6-dione and B[a]P-3,6-dione. Based on the B[a]P-1,6 and 3,6-dione formation, approximately 4µM of radical cation was generated. In the mutagenesis assays, the radical cations produced in situ showed a dose-dependent increase in mutagenicity from 0.25 µM to 10 µM B[a]P with no significant increase seen with further escalation to 50 µM B[a]P. However, mutagenesis was 200-fold less than with the AKR pathway derived B[a]P, 7–8 dione. Mutant p53 plasmids, which yield red colonies, were recovered from the yeast to study the pattern and spectrum of mutations. The mutation pattern observed was G to T (31%) > G to C (29%) > G to A (14%). The frequency of codons mutated by the B[a]P radical cations was essentially random and not enriched at known cancer hotspots. The quinone products of radical cations, B[a]P-1,6-dione and B[a]P-3,6-dione were more mutagenic than the radical cation reactions, but still less mutagenic than AKR derived B[a]P-7,8-dione. We conclude that B[a]P radical cations and their quinone products are weakly mutagenic in this yeast-based system compared to redox cycling PAH o-quinones. PMID:22768918

Behaviour of Strengthened RC Frames with Eccentric Steel Braced Frames

Directory of Open Access Journals (Sweden)

Kamanli Mehmet

2017-01-01

Full Text Available After devastating earthquakes in recent years, strengthening of reinforced concrete buildings became an important research topic. Reinforced concrete buildings can be strengthened by steel braced frames. These steel braced frames may be made of concentrically or eccentrically indicated in Turkish Earthquake Code 2007. In this study pushover analysis of the 1/3 scaled 1 reinforced concrete frame and 1/3 scaled 4 strengthened reinforced concrete frames with internal eccentric steel braced frames were conducted by SAP2000 program. According to the results of the analyses conducted, load-displacement curves of the specimens were compared and evaluated. Adding eccentric steel braces to the bare frame decreased the story drift, and significantly increased strength, stiffness and energy dissipation capacity. In this strengthening method lateral load carrying capacity, stiffness and dissipated energy of the structure can be increased.

Genetic analysis of gamma-ray mutagenesis in yeast. II. Allele-specific control of mutagenesis

International Nuclear Information System (INIS)

McKee, R.H.; Lawrence, C.W.

1979-01-01

We find that partially different sets of gene functions are required for the production of different kinds of mutations induced by 60 Co γ rays in Saccharomyces cerevisiae. This observation is very similar to others made previously with respect to uv mutagenesis and confirms the conclusion that such distinctive patterns of genetic control reflect properties of the test alleles and their genetic locations, rather than the kinds of lesions required to revert them. The data also support the model of mutagenic repair outlined in the first paper of this series in which partially different sets of gene functions are required for the production of different kinds of mutations, the formation of mutations at different genetic sites and the induction of mutations by different mutagens

Multivariate wavelet frames

CERN Document Server

Skopina, Maria; Protasov, Vladimir

2016-01-01

This book presents a systematic study of multivariate wavelet frames with matrix dilation, in particular, orthogonal and bi-orthogonal bases, which are a special case of frames. Further, it provides algorithmic methods for the construction of dual and tight wavelet frames with a desirable approximation order, namely compactly supported wavelet frames, which are commonly required by engineers. It particularly focuses on methods of constructing them. Wavelet bases and frames are actively used in numerous applications such as audio and graphic signal processing, compression and transmission of information. They are especially useful in image recovery from incomplete observed data due to the redundancy of frame systems. The construction of multivariate wavelet frames, especially bases, with desirable properties remains a challenging problem as although a general scheme of construction is well known, its practical implementation in the multidimensional setting is difficult. Another important feature of wavelet is ...

USP7 Is a Suppressor of PCNA Ubiquitination and Oxidative-Stress-Induced Mutagenesis in Human Cells.

Science.gov (United States)

Kashiwaba, Shu-ichiro; Kanao, Rie; Masuda, Yuji; Kusumoto-Matsuo, Rika; Hanaoka, Fumio; Masutani, Chikahide

2015-12-15

Mono-ubiquitinated PCNA activates error-prone DNA polymerases; therefore, strict regulation of PCNA mono-ubiquitination is crucial in avoiding undesired mutagenesis. In this study, we used an in vitro assay system to identify USP7 as a deubiquitinating enzyme of mono-ubiquitinated PCNA. Suppression of USP1, a previously identified PCNA deubiquitinase, or USP7 increased UV- and H2O2-induced PCNA mono-ubiquitination in a distinct and additive manner, suggesting that USP1 and USP7 make different contributions to PCNA deubiquitination in human cells. Cell-cycle-synchronization analyses revealed that USP7 suppression increased H2O2-induced PCNA ubiquitination throughout interphase, whereas USP1 suppression specifically increased ubiquitination in S-phase cells. UV-induced mutagenesis was elevated in USP1-suppressed cells, whereas H2O2-induced mutagenesis was elevated in USP7-suppressed cells. These results suggest that USP1 suppresses UV-induced mutations produced in a manner involving DNA replication, whereas USP7 suppresses H2O2-induced mutagenesis involving cell-cycle-independent processes such as DNA repair. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

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

International Nuclear Information System (INIS)

Qi Hongyan; Yin Xinyun

1988-03-01

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 F 358 were treated with fast neutron and 60 Co-γ ray irradiation Two mutants have been selected from 20025 treated single colonies. The output of cytokinins from them is higher than from strain F 358 . 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

Decisions during Negatively-Framed Messages Yield Smaller Risk-Aversion-Related Brain Activation in Substance-Dependent Individuals

Science.gov (United States)

Fukunaga, Rena; Bogg, Tim; Finn, Peter R.; Brown, Joshua W.

2012-01-01

A sizable segment of addiction research investigates the effects of persuasive message appeals on risky and deleterious behaviors. However, to date, little research has examined how various forms of message framing and corresponding behavioral choices might by mediated by risk-related brain regions. Using event-related functional magnetic resonance imaging, we investigated brain regions hypothesized to mediate the influence of message appeals on decision making in substance-dependent (SD) compared to non-substance-dependent (non-SD) individuals. The Iowa Gambling Task (IGT) was modified to include positively-framed, negatively-framed, and control messages about long-term deck payoffs. In the positively-framed condition, the SD and non-SD groups showed improved decision-making performance that corresponded to higher risk-aversion-related brain activity in the anterior cingulate cortex (ACC) and anterior insula (AI). In contrast, in the negatively-framed condition, the SD group showed poorer performance that corresponded to lower risk-aversion-related brain activity in the AI region. In addition, only the non-SD group showed a positive association between decision quality and greater risk-related activity in the ACC, regardless of message type. The findings suggest substance-dependent individuals may have reduced neurocognitive sensitivity in the ACC and AI regions involved in risk perception and aversion during decision-making, especially in response to framed messages that emphasize reduced prospects for long-term gains. PMID:23148798

Different efficiency of UmuDC and MucAB proteins in UV light induced mutagenesis in Escherichia coli

International Nuclear Information System (INIS)

Blanco, M.; Herrera, G.; Aleixandre, V.

1986-01-01

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 + uvr + bacteria, plasmid pIC80, mucAB + mediated UV mutagenesis more efficiently than did plasmid pSE 117, umuDC + . 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 + 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 + 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. (orig.)

Frames and outer frames for Hilbert C^*-modules

OpenAIRE

Arambašić, Ljiljana; Bakić, Damir

2015-01-01

The goal of the present paper is to extend the theory of frames for countably generated Hilbert $C^*$-modules over arbitrary $C^*$-algebras. In investigating the non-unital case we introduce the concept of outer frame as a sequence in the multiplier module $M(X)$ that has the standard frame property when applied to elements of the ambient module $X$. Given a Hilbert $\\A$-module $X$, we prove that there is a bijective correspondence of the set of all adjointable surjections from the generalize...

Roles for the yeast RAD18 and RAD52 DNA repair genes in UV mutagenesis.

Science.gov (United States)

Armstrong, J D; Chadee, D N; Kunz, B A

1994-11-01

Experimental evidence indicates that although the Saccharomyces cerevisiae RAD18 and RAD52 genes are not required for nucleotide excision repair, they function in the processing of UV-induced DNA damage in yeast. Conflicting statements regarding the UV mutability of strains deleted for RAD18 prompted us to re-examine the influence of RAD18, and RAD52, on UV mutagenesis. To do so, we characterized mutations induced by UV in SUP4-o, a yeast suppressor tRNA gene. SUP4-o was maintained on a plasmid in isogenic strains that either carried one of two different rad18 deletions (rad18 delta) or had RAD52 disrupted. Both rad18 deletions decreased the frequency of UV-induced SUP4-o mutations to levels close to those for spontaneous mutagenesis in the rad18 delta backgrounds, and prevented a net increase in mutant yield. A detailed analysis of mutations isolated after UV irradiation of one of the rad18 delta strains uncovered little evidence of the specificity features typical for UV mutagenesis in the isogenic repair-proficient (RAD) parent (e.g., predominance of G.C-->A.T transitions). Evidently, UV induction of SUP4-o mutations is highly dependent on the RAD18 gene. Compared to the RAD strain, disruption of RAD52 reduced the frequency and yield of UV mutagenesis by about two-thirds. Closer inspection revealed that 80% of this reduction was due to a decrease in the frequency of G.C-->A.T transitions. In addition, there were differences in the distributions and site specificities of single base-pair substitutions. Thus, RAD52 also participates in UV mutagenesis of a plasmid-borne gene in yeast, but to a lesser extent than RAD18.

On frame multiresolution analysis

DEFF Research Database (Denmark)

Christensen, Ole

2003-01-01

We use the freedom in frame multiresolution analysis to construct tight wavelet frames (even in the case where the refinable function does not generate a tight frame). In cases where a frame multiresolution does not lead to a construction of a wavelet frame we show how one can nevertheless...

Shifting Cultivation : Promoting Innovative Policy and Development ...

International Development Research Centre (IDRC) Digital Library (Canada)

Shifting Cultivation : Promoting Innovative Policy and Development Options in the Eastern Himalayas. Shifting ... pressure and market forces. The idea is to share good policies and practices related to shifting cultivation and alternative options through regional exchange. ... Les chaînes de valeur comme leviers stratégiques.

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

Energy Technology Data Exchange (ETDEWEB)

Datta, S.K. [CSIR, Madhyamgram Experimental Farm, Bose Institute, Kolkata (India)], E-mail: subodhskdatta@rediffmail.com

2008-07-01

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

Framing the ultimatum game: the contribution of simulation

Science.gov (United States)

Tomasino, Barbara; Lotto, Lorella; Sarlo, Michela; Civai, Claudia; Rumiati, Rino; Rumiati, Raffaella I.

2013-01-01

It has now become widely accepted that economic decisions are influenced by cognitive and emotional processes. In the present study, we aimed at disentangling the neural mechanisms associated with the way in which the information is formulated, i.e., framing effect, in terms of gain or loss, which influences people's decisions. Participants played a fMRI version of the Ultimatum Game (UG) where we manipulated bids through two different frames: the expression “I give you” (gain) focusing on money the respondent would receive if she/he agreed with the proponent, and the expression “I take” (loss) focusing on the money that would be removed from the respondent in the event that she/he accepted the offer. Neuroimaging data revealed a frame by response interaction, showing an increase of neural activity in the right rolandic operculum/insular cortex, the anterior cingulate, among other regions, for accepting the frame “I take” vs. rejecting, as compared to accepting the frame “I give you” vs. rejecting. In addition, the left occipito-temporal junction was activated for “I take” vs. “I give you” for offer 5, corresponding to the equal offer made unpleasant by the presence of the frame “I take,” where is the proposer that takes the money. Our data extend the current understanding of the neural substrates of social decision making, by disentangling the structures sensitive to the way in which the information is formulated (i.e., framing effect), in terms of gain or loss. PMID:23847507

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.

The Mechanism of Nucleotide Excision Repair-Mediated UV-Induced Mutagenesis in Nonproliferating Cells

Science.gov (United States)

Kozmin, Stanislav G.; Jinks-Robertson, Sue

2013-01-01

Following the irradiation of nondividing yeast cells with ultraviolet (UV) light, most induced mutations are inherited by both daughter cells, indicating that complementary changes are introduced into both strands of duplex DNA prior to replication. Early analyses demonstrated that such two-strand mutations depend on functional nucleotide excision repair (NER), but the molecular mechanism of this unique type of mutagenesis has not been further explored. In the experiments reported here, an ade2 adeX colony-color system was used to examine the genetic control of UV-induced mutagenesis in nondividing cultures of Saccharomyces cerevisiae. We confirmed a strong suppression of two-strand mutagenesis in NER-deficient backgrounds and demonstrated that neither mismatch repair nor interstrand crosslink repair affects the production of these mutations. By contrast, proteins involved in the error-prone bypass of DNA damage (Rev3, Rev1, PCNA, Rad18, Pol32, and Rad5) and in the early steps of the DNA-damage checkpoint response (Rad17, Mec3, Ddc1, Mec1, and Rad9) were required for the production of two-strand mutations. There was no involvement, however, for the Pol η translesion synthesis DNA polymerase, the Mms2-Ubc13 postreplication repair complex, downstream DNA-damage checkpoint factors (Rad53, Chk1, and Dun1), or the Exo1 exonuclease. Our data support models in which UV-induced mutagenesis in nondividing cells occurs during the Pol ζ-dependent filling of lesion-containing, NER-generated gaps. The requirement for specific DNA-damage checkpoint proteins suggests roles in recruiting and/or activating factors required to fill such gaps. PMID:23307894

The contribution of Nth and Nei DNA glycosylases to mutagenesis in Mycobacterium smegmatis.

Science.gov (United States)

Moolla, Nabiela; Goosens, Vivianne J; Kana, Bavesh D; Gordhan, Bhavna G

2014-01-01

The increased prevalence of drug resistant strains of Mycobacterium tuberculosis (Mtb) indicates that significant mutagenesis occurs during tuberculosis disease in humans. DNA damage by host-derived reactive oxygen/nitrogen species is hypothesized to be critical for the mutagenic process in Mtb thus, highlighting an important role for DNA repair enzymes in maintenance of genome fidelity. Formamidopyrimidine (Fpg/MutM/Fapy) and EndonucleaseVIII (Nei) constitute the Fpg/Nei family of DNA glycosylases and together with EndonucleaseIII (Nth) are central to the base excision repair pathway in bacteria. In this study we assess the contribution of Nei and Nth DNA repair enzymes in Mycobacterium smegmatis (Msm), which retains a single nth homologue and duplications of the Fpg (fpg1 and fpg2) and Nei (nei1 and nei2) homologues. Using an Escherichia coli nth deletion mutant, we confirm the functionality of the mycobacterial nth gene in the base excision repair pathway. Msm mutants lacking nei1, nei2 and nth individually or in combination did not display aberrant growth in broth culture. Deletion of nth individually results in increased UV-induced mutagenesis and combinatorial deletion with the nei homologues results in reduced survival under oxidative stress conditions and an increase in spontaneous mutagenesis to rifampicin. Deletion of nth together with the fpg homolgues did not result in any growth/survival defects or changes in mutation rate. Furthermore, no differential emergence of the common rifampicin resistance conferring genotypes were noted. Collectively, these data confirm a role for Nth in base excision repair in mycobacteria and further highlight a novel interplay between the Nth and Nei homologues in spontaneous mutagenesis. Copyright © 2013 Elsevier B.V. All rights reserved.

Plasma rest frame distributions of suprathermal ions in the earth's foreshock region

International Nuclear Information System (INIS)

Sentman, D.D.; Kennel, C.F.; Frank, L.A.

1981-01-01

We present rest frame ion distributions computed from three-dimensional observations of upstream superthermal ions gained by the Universtiy of Iowa Quadrispherical Lepedea on ISEE-1. The observations are for a single inbound, midmorning pass starting upstream from the ion foreshock and continuing across the quasiparallel bow shock into the magnetosheath. The crossing of the ion foreshock boundary is marked by a several minute burst of ions of temperature 100--200 eV moving along the IMF away from the bow shock at 500 km/s relative to the solar wind. The observation of these 'reflected' ions is followed by an extended interval of 'diffuse' ions of temperatures 2--3 keV flowing at approx.250 km/s relative to the solar wind and persisting until the bow shock is crossed. The diffuse ion β has a value of approximately 6 in the region of the superthermal ions, exceeding the normal thermal β of the solar wind by roughly an order of magnitude. Both types of superthermal ions constitute roughly 2% of the total ion density and carry a parallel heat flux of approx.2 x 10 -2 ergs cm -2 s -2 . When integrated over an assumed 10 x 10 R/sub E/ bow shock emission area, this implies an upstream dissipation that may approach 10 17 to 10 18 ergs/s, comparable to a modest substorm

Comparing Different Strategies in Directed Evolution of Enzyme Stereoselectivity: Single- versus Double-Code Saturation Mutagenesis.

Science.gov (United States)

Sun, Zhoutong; Lonsdale, Richard; Li, Guangyue; Reetz, Manfred T

2016-10-04

Saturation mutagenesis at sites lining the binding pockets of enzymes constitutes a viable protein engineering technique for enhancing or inverting stereoselectivity. Statistical analysis shows that oversampling in the screening step (the bottleneck) increases astronomically as the number of residues in the randomization site increases, which is the reason why reduced amino acid alphabets have been employed, in addition to splitting large sites into smaller ones. Limonene epoxide hydrolase (LEH) has previously served as the experimental platform in these methodological efforts, enabling comparisons between single-code saturation mutagenesis (SCSM) and triple-code saturation mutagenesis (TCSM); these employ either only one or three amino acids, respectively, as building blocks. In this study the comparative platform is extended by exploring the efficacy of double-code saturation mutagenesis (DCSM), in which the reduced amino acid alphabet consists of two members, chosen according to the principles of rational design on the basis of structural information. The hydrolytic desymmetrization of cyclohexene oxide is used as the model reaction, with formation of either (R,R)- or (S,S)-cyclohexane-1,2-diol. DCSM proves to be clearly superior to the likewise tested SCSM, affording both R,R- and S,S-selective mutants. These variants are also good catalysts in reactions of further substrates. Docking computations reveal the basis of enantioselectivity. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Framed School--Frame Factors, Frames and the Dynamics of Social Interaction in School

Science.gov (United States)

Persson, Anders

2015-01-01

This paper aims to show how the Goffman frame perspective can be used in an analysis of school and education and how it can be combined, in such analysis, with the frame factor perspective. The latter emphasizes factors that are determined outside the teaching process, while the former stresses how actors organize their experiences and define…

Use of the Lorentz-Boosted Frame Transformation to Simulate Free-Electron Laser Amplifier Physics

International Nuclear Information System (INIS)

Fawley, W.M.; Vay, J.-L.

2008-01-01

Recently it has been pointed out that numerical simulation of some systems containing charged particles with highly relativistic directed motion can by speeded up by orders of magnitude by choice of the proper Lorentz boosted frame. A particularly good example is that of short wavelength free-electron lasers (FELs) in which a high energy (E0 (ge) 250 MeV) electron beam interacts with a static magnetic undulator. In the optimal boost frame with Lorentz factor gamma F, the red-shifted FEL radiation and blue shifted undulator have identical wavelengths and the number of required time-steps (presuming the Courant condition applies) decreases by a factor of g2 F for fully electromagnetic simulation. We have adapted the WARP code to apply this method to several FEL problems including coherent spontaneous emission (CSE) from pre-bunched e-beams, and strong exponential gain in a single pass amplifier configuration. We discuss our results and compare with those from the 'standard' FEL simulation approach which adopts the eikonal approximation for propagation of the radiation field

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.

Geospatial techniques for developing a sampling frame of watersheds across a region

Science.gov (United States)

Gresswell, Robert E.; Bateman, Douglas S.; Lienkaemper, George; Guy, T.J.

2004-01-01

Current land-management decisions that affect the persistence of native salmonids are often influenced by studies of individual sites that are selected based on judgment and convenience. Although this approach is useful for some purposes, extrapolating results to areas that were not sampled is statistically inappropriate because the sampling design is usually biased. Therefore, in recent investigations of coastal cutthroat trout (Oncorhynchus clarki clarki) located above natural barriers to anadromous salmonids, we used a methodology for extending the statistical scope of inference. The purpose of this paper is to apply geospatial tools to identify a population of watersheds and develop a probability-based sampling design for coastal cutthroat trout in western Oregon, USA. The population of mid-size watersheds (500-5800 ha) west of the Cascade Range divide was derived from watershed delineations based on digital elevation models. Because a database with locations of isolated populations of coastal cutthroat trout did not exist, a sampling frame of isolated watersheds containing cutthroat trout had to be developed. After the sampling frame of watersheds was established, isolated watersheds with coastal cutthroat trout were stratified by ecoregion and erosion potential based on dominant bedrock lithology (i.e., sedimentary and igneous). A stratified random sample of 60 watersheds was selected with proportional allocation in each stratum. By comparing watershed drainage areas of streams in the general population to those in the sampling frame and the resulting sample (n = 60), we were able to evaluate the how representative the subset of watersheds was in relation to the population of watersheds. Geospatial tools provided a relatively inexpensive means to generate the information necessary to develop a statistically robust, probability-based sampling design.

Optical Ramsey spectroscopy in a rotating frame: Sagnac effect in a matter-wave interferometer

International Nuclear Information System (INIS)

Riehle, F.; Kisters, T.; Witte, A.; Helmcke, J.; Borde, C.J.

1991-01-01

A calcium atomic beam excited in an optical Ramsey geometry was rotated about an axis perpendicular to the plane defined by the laser beams and the atomic beam. A frequency shift of the Ramsey fringes of several kHz has been measured which is proportional to the rotation frequency of the apparatus and to the distance between the laser beams. The results can be interpreted in three equivalent ways as the Sagnac effect in a calcium-atomic-beam interferometer: in the rotating frame of the laser beams either along straight paths or along the curved trajectories of the atoms, or in the inertial atomic frame

Tissue culture and mutagenesis of rain lily (zephyranthes)

International Nuclear Information System (INIS)

Mohd Nazir Basiran; Zaiton Ahmad; Shakinah Salleh; Shuhaimi Shamsudin; Aiza Shaliha Jamaludin

2004-01-01

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 60 Co source. Three variants with different flower colour and morphology have been achieved so far and are now being propagated in the nursery. (Author)

Mechanisms of Base Substitution Mutagenesis in Cancer Genomes

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Albino Bacolla

2014-03-01

Full Text Available Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs. Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS and other endogenous or exogenous electron-abstracting molecules.

Mechanisms of base substitution mutagenesis in cancer genomes.

Science.gov (United States)

Bacolla, Albino; Cooper, David N; Vasquez, Karen M

2014-03-05

Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.

Goos–Hänchen and Imbert–Fedorov beam shifts: an overview

International Nuclear Information System (INIS)

Bliokh, K Y; Aiello, A

2013-01-01

We consider reflection and transmission of polarized paraxial light beams at a plane dielectric interface. The field transformations taking into account a finite beam width are described based on the plane-wave representation and geometric rotations. Using geometrical-optics coordinate frames accompanying the beams, we construct an effective Jones matrix characterizing spatial-dispersion properties of the interface. This results in a unified self-consistent description of the Goos–Hänchen and Imbert–Fedorov shifts (the latter being also known as the spin Hall effect of light). Our description reveals the intimate relation of the transverse Imbert–Fedorov shift to the geometric phases between constituent waves in the beam spectrum and to the angular momentum conservation for the whole beam. Both spatial and angular shifts are considered as well as their analogues for higher-order vortex beams carrying intrinsic orbital angular momentum. We also give a brief overview of various extensions and generalizations of the basic beam-shift phenomena and related effects. (review article)

Regulation of mutagenesis by exogenous biological factors in the eukaryotic cell systems

Directory of Open Access Journals (Sweden)

Lukash L. L.

2013-07-01

Full Text Available The representations of the mutations and the nature of spontaneous mutation process and mutagenesis induced by exogenous oncoviruses, DNAs and proteins-mitogens are analysed. Exogenous biological factors induce DNA damages in regulatory-informational way, acting on the cellular systems for maintenance of genetical stability. Molecular mechanisms are the same as at spontaneous mutagenesis but they are realized with the participation of alien genetical material. Among biological mutagens, the oncoviruses and mobile genetic elements (MGEs are distinguished as the strongest destabilizing factors which direct tumor transformation of somatic mammalian cells. Genetical reprogramming or changing the programs of gene expression at the differentiation of stem and progenitor cells under growth factors and citokines is probably followed by mutations and recombinations as well.

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

International Nuclear Information System (INIS)

Klein, C.B.; Rossman, T.G.

1990-01-01

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

Sheep head frame validation for CT and MRI studies

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marco trovatelli

2017-05-01

Full Text Available Abstract   Introductions Aim of EDEN 2020 project’s Milestone 5 is the development of a steerable catheter for CED system in glioblastoma therapy. The VET group is involved in realization and validation of the proper animal model. Materials and methods In this part of the study two fresh sheep’s head from the local slaughter were used. The heads were located into an ad hoc Frame system based on anatomical measures and CT images, producted by Renishaw plc partner in this project. The frame was adapted and every components were checked for the ex vivo validation tests. CT imaging was taken in Lodi at Università degli studi di Milano, Facoltà di Medicina Veterinaria, with CT scanner and MRI imaging was taken in La Cittadina, Cremona Results System validation was approved by the ex vivo trial. The frame system doesn’t compromise the imaging acquisition in MRI and CT systems. Every system components are functional to their aims. Discussion The Frame system is adapted to the sheep head. It is composed by elements able to lock the head during the imaging acquisition. Frame system is characterized by a support base helpings the animals to keep the head straight forward during imaging time, under general anesthesia. The design of these device support the airways anatomy, avoiding damaging or obstruction of airflows during anesthesia period. The role of elements like mouth bar and ovine head pins is to lock the head in a stable position during imaging acquisition; fixing is guaranteed by V shape head pins, that are arranged against the zygomatic arches. Lateral compression forces to the cranium, and the V shape pins avoid the vertical shifting of the head and any kind of rotations. (fig. 1

Network-based H.264/AVC whole frame loss visibility model and frame dropping methods.

Science.gov (United States)

Chang, Yueh-Lun; Lin, Ting-Lan; Cosman, Pamela C

2012-08-01

We examine the visual effect of whole frame loss by different decoders. Whole frame losses are introduced in H.264/AVC compressed videos which are then decoded by two different decoders with different common concealment effects: frame copy and frame interpolation. The videos are seen by human observers who respond to each glitch they spot. We found that about 39% of whole frame losses of B frames are not observed by any of the subjects, and over 58% of the B frame losses are observed by 20% or fewer of the subjects. Using simple predictive features which can be calculated inside a network node with no access to the original video and no pixel level reconstruction of the frame, we developed models which can predict the visibility of whole B frame losses. The models are then used in a router to predict the visual impact of a frame loss and perform intelligent frame dropping to relieve network congestion. Dropping frames based on their visual scores proves superior to random dropping of B frames.

Decisions during negatively-framed messages yield smaller risk-aversion-related brain activation in substance-dependent individuals.

Science.gov (United States)

Fukunaga, Rena; Bogg, Tim; Finn, Peter R; Brown, Joshua W

2013-12-01

A sizable segment of addiction research investigates the effects of persuasive message appeals on risky and deleterious behaviors. However, to date, little research has examined how various forms of message framing and corresponding behavioral choices might by mediated by risk-related brain regions. Using event-related functional MRI, we investigated brain regions hypothesized to mediate the influence of message appeals on decision making in substance-dependent (SD) compared with nonsubstance-dependent (non-SD) individuals. The Iowa Gambling Task (IGT) was modified to include positively-framed, negatively-framed, and control messages about long-term deck payoffs. In the positively-framed condition, the SD and non-SD groups showed improved decision-making performance that corresponded to higher risk-aversion-related brain activity in the anterior cingulate cortex (ACC) and anterior insula (AI). In contrast, in the negatively-framed condition, the SD group showed poorer performance that corresponded to lower risk-aversion-related brain activity in the AI region. In addition, only the non-SD group showed a positive association between decision quality and greater risk-related activity in the ACC, regardless of message type. The findings suggest substance-dependent individuals may have reduced neurocognitive sensitivity in the ACC and AI regions involved in risk perception and aversion during decision-making, especially in response to framed messages that emphasize reduced prospects for long-term gains. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Framing Failures in Wood-Frame Hip Roofs under Extreme Wind Loads

Directory of Open Access Journals (Sweden)

Sarah A. Stevenson

2018-02-01

Full Text Available Wood-frame residential roof failures are among the most common and expensive types of wind damage. Hip roofs are commonly understood to be more resilient during extreme wind in relation to gable roofs. However, inspection of damage survey data from recent tornadoes has revealed a previously unstudied failure mode in which hip roofs suffer partial failure of the framing structure. In the current study, evidence of partial framing failures and statistics of their occurrence are explored and discussed, while the common roof design and construction practice are reviewed. Two-dimensional finite element models are developed to estimate the element-level load effects on hip roof trusses and stick-frame components. The likelihood of failure in each member is defined based on relative demand-to-capacity ratios. Trussed and stick-frame structures are compared to assess the relative performance of the two types of construction. The present analyses verify the common understanding that toenailed roof-to-wall connections are likely to be the most vulnerable elements in the structure of a wood-frame hip roof. However, the results also indicate that certain framing members and connections display significant vulnerability under the same wind uplift, and the possibility of framing failure is not to be discounted. Furthermore, in the case where the roof-to-wall connection uses hurricane straps, certain framing members and joints become the likely points of failure initiation. The analysis results and damage survey observations are used to expand the understanding of wood-frame residential roof failures, as they relate to the Enhanced Fujita Scale and provide assessment of potential gaps in residential design codes.

Random mutagenesis of the hyperthermophilic archaeon Pyrococcus furiosus using in vitro mariner transposition and natural transformation.

Science.gov (United States)

Guschinskaya, Natalia; Brunel, Romain; Tourte, Maxime; Lipscomb, Gina L; Adams, Michael W W; Oger, Philippe; Charpentier, Xavier

2016-11-08

Transposition mutagenesis is a powerful tool to identify the function of genes, reveal essential genes and generally to unravel the genetic basis of living organisms. However, transposon-mediated mutagenesis has only been successfully applied to a limited number of archaeal species and has never been reported in Thermococcales. Here, we report random insertion mutagenesis in the hyperthermophilic archaeon Pyrococcus furiosus. The strategy takes advantage of the natural transformability of derivatives of the P. furiosus COM1 strain and of in vitro Mariner-based transposition. A transposon bearing a genetic marker is randomly transposed in vitro in genomic DNA that is then used for natural transformation of P. furiosus. A small-scale transposition reaction routinely generates several hundred and up to two thousands transformants. Southern analysis and sequencing showed that the obtained mutants contain a single and random genomic insertion. Polyploidy has been reported in Thermococcales and P. furiosus is suspected of being polyploid. Yet, about half of the mutants obtained on the first selection are homozygous for the transposon insertion. Two rounds of isolation on selective medium were sufficient to obtain gene conversion in initially heterozygous mutants. This transposition mutagenesis strategy will greatly facilitate functional exploration of the Thermococcales genomes.

Explicitly given pairs of dual frames with compactly supported generators and applications to irregular B-splines

DEFF Research Database (Denmark)

Christensen, Ole; Sun, Wenchang

2008-01-01

We consider systems of functions appearing by letting a class of modulations act on a countable collection of functions. These systems correspond to shift-invariant systems, considered on the Fourier side. We provide sufficient conditions for the system to be a frame, as well as an explicit...

Scoring function to predict solubility mutagenesis

Directory of Open Access Journals (Sweden)

Deutsch Christopher

2010-10-01

Full Text Available Abstract Background Mutagenesis is commonly used to engineer proteins with desirable properties not present in the wild type (WT protein, such as increased or decreased stability, reactivity, or solubility. Experimentalists often have to choose a small subset of mutations from a large number of candidates to obtain the desired change, and computational techniques are invaluable to make the choices. While several such methods have been proposed to predict stability and reactivity mutagenesis, solubility has not received much attention. Results We use concepts from computational geometry to define a three body scoring function that predicts the change in protein solubility due to mutations. The scoring function captures both sequence and structure information. By exploring the literature, we have assembled a substantial database of 137 single- and multiple-point solubility mutations. Our database is the largest such collection with structural information known so far. We optimize the scoring function using linear programming (LP methods to derive its weights based on training. Starting with default values of 1, we find weights in the range [0,2] so that predictions of increase or decrease in solubility are optimized. We compare the LP method to the standard machine learning techniques of support vector machines (SVM and the Lasso. Using statistics for leave-one-out (LOO, 10-fold, and 3-fold cross validations (CV for training and prediction, we demonstrate that the LP method performs the best overall. For the LOOCV, the LP method has an overall accuracy of 81%. Availability Executables of programs, tables of weights, and datasets of mutants are available from the following web page: http://www.wsu.edu/~kbala/OptSolMut.html.

When message-frame fits salient cultural-frame, messages feel more persuasive

OpenAIRE

Uskul, Ayse K.; Oyserman, Daphna

2010-01-01

The present study examines the persuasive effects of tailored health messages comparing those tailored to match (versus not match) both chronic cultural frame and momentarily salient cultural frame. Evidence from two studies (Study 1: n = 72 European Americans; Study 2: n = 48 Asian Americans) supports the hypothesis that message persuasiveness increases when chronic cultural frame, health message tailoring and momentarily salient cultural frame all match. The hypothesis was tested using a me...

Transcriptional mutagenesis: causes and involvement in tumor development

Science.gov (United States)

Brégeon, Damien; Doetsch, Paul W.

2013-01-01

The majority of normal cells in a human do not multiply continuously but are quiescent and devote most of their energy to gene transcription. When DNA damages in the transcribed strand of an active gene are bypassed by an RNA polymerase, they can miscode at the damaged site and produce mutant transcripts. This process known as transcriptional mutagenesis can lead to the production of mutant proteins that could be important in tumor development. PMID:21346784

Photodynamic action of methylene blue: mutagenesis and synergism

International Nuclear Information System (INIS)

Capella, M.A.M.

1988-01-01

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.) [pt

History of the science of mutagenesis from a personal perspective.

Science.gov (United States)

Malling, Heinrich V

2004-01-01

A career in the study of mutagenesis spanning 50 years is a gift few scientists have been bestowed. My tenure in the field started in 1953, the year the structure of DNA became known (Watson and Crick [1953]: Nature 171:737). Before that time, it was suspected that DNA was the genetic material based on the research of Oswald T. Avery (Avery et al. [1944]: J Exp Med 79:137), but many scientists still believed that proteins or polysaccharides could be the genetic material. The present article describes a lifetime of personal experience in the field of chemical mutagenesis. The methods used to treat viruses with chemical mutagens were well developed in the 1950s. Here I review the early use of nitrous acid and hydroxylamine as mutagens in eukaryotes, the development of methods for the metabolic activation of mutagens by microsomal preparations, and the selection of a mutant tester set for the qualitative characterization of the mutagenic activity of chemicals. These studies provided critical background information that was used by Bruce Ames in the development of his Salmonella/microsome assay, widely known as the Ames test (Ames et al. [1973]: Proc Nat Acad Sci USA 70:2281-2285). This article also describes how a set of diagnostic chemical mutagens was selected and used to identify the molecular nature of gene mutations. Today, DNA sequencing has replaced the use of diagnostic mutagens, but studies of this kind formed the foundation of modern mutation research. They also helped set the stage for the organization of the Environmental Mutagen Society and the Environmental Mutagen Information Center, which are described. The article ends with the development of mammalian single-cell mutation assays, the first system for studying in vivo mutagenesis using recoverable vectors in transgenic animals, other mutation assays in intact mammals, and my thoughts on the critically important area of germ cell mutagenesis. This narrative is not a complete autobiographical account

p21-ras effector domain mutants constructed by "cassette" mutagenesis

DEFF Research Database (Denmark)

Stone, J C; Vass, W C; Willumsen, B M

1988-01-01

A series of mutations encoding single-amino-acid substitutions within the v-rasH effector domain were constructed, and the ability of the mutants to induce focal transformation of NIH 3T3 cells was studied. The mutations, which spanned codons 32 to 40, were made by a "cassette" mutagenesis...

Value Framing: A Prelude to Software Problem Framing

NARCIS (Netherlands)

Wieringa, Roelf J.; Gordijn, Jaap; van Eck, Pascal; Cox, K.; Hall, J.G.; Rapanotti, L.

2004-01-01

Software problem framing is a way to find specifications for software. Software problem frames can be used to structure the environment of a software system (the machine) and specify desired software properties in such a way that we can show that software with these properties will help achieve the

Molecular frame and recoil frame angular distributions in dissociative photoionization of small molecules

International Nuclear Information System (INIS)

Lucchese, R R; Carey, R; Elkharrat, C; Houver, J C; Dowek, D

2008-01-01

Photoelectron angular distributions in the dipole approximation can be written with respect to several different reference frames. A brief review of the molecular frame and recoil frame are given. Experimentally, one approach for obtaining such angular distributions is through angle-resolved coincidence measurements of dissociative ionization. If the system dissociates into two heavy fragments, then the recoil frame angular distribution can be measured. Computed molecular frame and recoil frame photoelectron angular distributions are compared to experimental data for the Cl 2p ionization of CH 3 Cl.

Filtering SVM frame-by-frame binary classification in a detection framework

NARCIS (Netherlands)

Betancourt Arango, A.; Morerio, P.; Marcenaro, L.; Rauterberg, G.W.M.; Regazzoni, C.S.

2015-01-01

Classifying frames, or parts of them, is a common way of carrying out detection tasks in computer vision. However, frame by frame classification suffers from sudden significant variations in image texture, colour and luminosity, resulting in noise in the extracted features and consequently in the

Novel Blind Recognition Algorithm of Frame Synchronization Words Based on Soft-Decision in Digital Communication Systems.

Science.gov (United States)

Qin, Jiangyi; Huang, Zhiping; Liu, Chunwu; Su, Shaojing; Zhou, Jing

2015-01-01

A novel blind recognition algorithm of frame synchronization words is proposed to recognize the frame synchronization words parameters in digital communication systems. In this paper, a blind recognition method of frame synchronization words based on the hard-decision is deduced in detail. And the standards of parameter recognition are given. Comparing with the blind recognition based on the hard-decision, utilizing the soft-decision can improve the accuracy of blind recognition. Therefore, combining with the characteristics of Quadrature Phase Shift Keying (QPSK) signal, an improved blind recognition algorithm based on the soft-decision is proposed. Meanwhile, the improved algorithm can be extended to other signal modulation forms. Then, the complete blind recognition steps of the hard-decision algorithm and the soft-decision algorithm are given in detail. Finally, the simulation results show that both the hard-decision algorithm and the soft-decision algorithm can recognize the parameters of frame synchronization words blindly. What's more, the improved algorithm can enhance the accuracy of blind recognition obviously.

New characterizations of fusion frames (frames of subspaces)

Indian Academy of Sciences (India)

Theory (College Park, MD, 2003) Contemp. Math. 345, Amer. Math. Soc. (RI: Provi- dence) (2004) 87–113. [4] Casazza P G and Kutyniok G, Robustness of Fusion Frames under Erasures of sub- spaces and of Local Frame Vectors, Radon transforms, geometry, and wavelets (LA: New Orleans) (2006) Contemp. Math., Amer.

R-prime site-directed transposon Tn7 mutagenesis of the photosynthetic apparatus in Rhodopseudomonas capsulata

Energy Technology Data Exchange (ETDEWEB)

Youvan, D C [Univ. of California, Berkeley; Elder, J T; Sandlin, D E; Zsebo, K; Alder, D P; Panopoulos, N J; Marrs, B L; Hearst, J E

1982-01-01

Site-directed mutagenesis of the photosynthetic apparatus (PSA) genes in Rhodopseudomonas capsulata is presented utilizing a transposon Tn7 mutagenized R-prime. The R-prime, pRPS404, bears most of the genes necessary for the differentiation of the photosynthetic apparatus. Mutagenesis of the R-prime with Tn7 in Escherichia coli, conjugation into R. capsulata, and homologous recombination with the wild-type alleles efficiently generates photosynthetic apparatus lesions. Wild-type alleles are lost spontaneously and the Tn7-induced lesions are revealed by subsequent intramolecular recombination between IS21 insertion elements that bracket the prime sequences in direct repeat. The molecular nature of the intermediates involved in the transposition, recombination and deletion have been investigated by Southern hybridization analysis. The spontaneous loss of wild-type alleles after homologous recombination with the chromosome may be of general use to other prokaryotic site-directed transposon mutagenesis schemes. The IS21-mediated deletion of the prime DNA is dependent on the RecA protein in E. coli, generating the parental R-factor bearing one IS21 element. A genetic-physical map exists for a portion of the prime photosynthetic apparatus DNA. When Tn7 is inserted into a bacteriochlorophyll gene in the R-prime and then crossed into R. capsulata, mutants are produced that accumulate a bacteriochlorophyll precursor, which is in excellent agreement with the existing genetic-physical map. This corroborates the mutagenesis scheme.

Changing climate, changing frames

International Nuclear Information System (INIS)

Vink, Martinus J.; Boezeman, Daan; Dewulf, Art; Termeer, Catrien J.A.M.

2013-01-01

Highlights: ► We show development of flood policy frames in context of climate change attention. ► Rising attention on climate change influences traditional flood policy framing. ► The new framing employs global-scale scientific climate change knowledge. ► With declining attention, framing disregards climate change, using local knowledge. ► We conclude that frames function as sensemaking devices selectively using knowledge. -- Abstract: Water management and particularly flood defence have a long history of collective action in low-lying countries like the Netherlands. The uncertain but potentially severe impacts of the recent climate change issue (e.g. sea level rise, extreme river discharges, salinisation) amplify the wicked and controversial character of flood safety policy issues. Policy proposals in this area generally involve drastic infrastructural works and long-term investments. They face the difficult challenge of framing problems and solutions in a publicly acceptable manner in ever changing circumstances. In this paper, we analyse and compare (1) how three key policy proposals publicly frame the flood safety issue, (2) the knowledge referred to in the framing and (3) how these frames are rhetorically connected or disconnected as statements in a long-term conversation. We find that (1) framings of policy proposals differ in the way they depict the importance of climate change, the relevant timeframe and the appropriate governance mode; (2) knowledge is selectively mobilised to underpin the different frames and (3) the frames about these proposals position themselves against the background of the previous proposals through rhetorical connections and disconnections. Finally, we discuss how this analysis hints at the importance of processes of powering and puzzling that lead to particular framings towards the public at different historical junctures

Framing Gangnam Style

Directory of Open Access Journals (Sweden)

Hyunsun Catherine Yoon

2017-08-01

Full Text Available This paper examines the way in which news about Gangnam Style was framed in the Korean press. First released on 15th July 2012, it became the first video to pass two billion views on YouTube. 400 news articles between July 2012 and March 2013 from two South Korean newspapers - Chosun Ilbo and Hankyoreh were analyzed using the frame analysis method in five categories: industry/economy, globalization, cultural interest, criticism, and competition. The right-left opinion cleavage is important because news frames interact with official discourses, audience frames and prior knowledge which consequently mediate effects on public opinion, policy debates, social movement and individual interpretations. Whilst the existing literature on Gangnam Style took rather holistic approach, this study aimed to fill the lacuna, considering this phenomenon as a dynamic process, by segmenting different stages - recognition, spread, peak and continuation. Both newspapers acknowledged Gangnam Style was an epochal event but their perspectives and news frames were different; globalization frame was most frequently used in Chosun Ilbo whereas cultural interest frame was most often used in Hankyoreh. Although more critical approaches were found in Hankyoreh, reflecting the right-left opinion cleavage, both papers lacked in critical appraisal and analysis of Gangnam Style’s reception in a broader context of the new Korean Wave.

Market shifting

Energy Technology Data Exchange (ETDEWEB)

Forst, Michael

2013-11-01

After years of oversupply and artificially low module pricing, market analysts believe that the solar industry will begin to stabilize by 2017. While the market activities are shifting from Europe to the Asia Pacific region and the United States, the solar shakeout continues to be in full swing including solar cell and module manufacturing. (orig.)

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

International Nuclear Information System (INIS)

Huberman, E.; Langenbach, R.

1977-01-01

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

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly

DEFF Research Database (Denmark)

Genee, Hans Jasper; Bonde, Mads Tvillinggaard; Bagger, Frederik Otzen

2015-01-01

USER cloning is a fast and versatile method for engineering of plasmid DNA. We have developed a user friendly Web server tool that automates the design of optimal PCR primers for several distinct USER cloning-based applications. Our Web server, named AMUSER (Automated DNA Modifications with USER...... cloning), facilitates DNA assembly and introduction of virtually any type of site-directed mutagenesis by designing optimal PCR primers for the desired genetic changes. To demonstrate the utility, we designed primers for a simultaneous two-position site-directed mutagenesis of green fluorescent protein...... (GFP) to yellow fluorescent protein (YFP), which in a single step reaction resulted in a 94% cloning efficiency. AMUSER also supports degenerate nucleotide primers, single insert combinatorial assembly, and flexible parameters for PCR amplification. AMUSER is freely available online at ....

Application of monosymmetrical I-beams in light metal frames with variable stiffness

Directory of Open Access Journals (Sweden)

I.O. Sklyarov

2016-05-01

Full Text Available The article is devoted to effectiveness of using of monosymmetrical I-beams with flexible wall frame structures of variable section, features of their calculation and design. Aim: The aim of research is to confirm the feasibility of I-beams with flexible wall bearing as light metal skeletons for buildings of the universal assignment. Materials and Methods: In order to reduce the metal consumption a frame is conventionally divided into several sections according to bending moment diagrams so that in the more compressed zone section the belt of great area was located, and in the stretched or less intense zone the lesser belt was installed. The resulting sections have smaller area in compare to symmetric profiles. Additional reduce bending moments provided as a result of displacement of elements axes with variable cross section. Results: The calculations and selection of sections of the frame have shown that it can be achieved the reducing of bearing elements weight by 10% compared to the symmetrical profiles of variable stiffness due to using monosymmetrical sections. The effectiveness of the proposed constructive solution is confirmed by compare of the projected weight frame construction with existing analogue. The symmetrical frame profile is 15.3% lighter; the monosymmetrical frame profile is 27% lighter. Conclusions: Analysis of stress-strain state structures shown: first, through asymmetrical profile there is a shifting of the center of gravity section, which leads to a redistribution of internal forces in the frame; secondly, because of the small cross-sectional area of the stretched zones more difficult to ensure the stability of the plane form of bending beams, which leads to the necessity to disconnect areas curtain beams by constraints of smaller steps.

Improvement of lipid production by the oleaginous yeast Rhodosporidium toruloides through UV mutagenesis.

Science.gov (United States)

Yamada, Ryosuke; Kashihara, Tomomi; Ogino, Hiroyasu

2017-05-01

Oleaginous yeasts are considered a promising alternative lipid source for biodiesel fuel production. In this study, we attempted to improve the lipid productivity of the oleaginous yeast Rhodosporidium toruloides through UV irradiation mutagenesis and selection based on ethanol and H 2 O 2 tolerance or cerulenin, a fatty acid synthetase inhibitor. Glucose consumption, cell growth, and lipid production of mutants were evaluated. The transcription level of genes involved in lipid production was also evaluated in mutants. The ethanol and H 2 O 2 tolerant strain 8766 2-31M and the cerulenin resistant strain 8766 3-11C were generated by UV mutagenesis. The 8766 2-31M mutant showed a higher lipid production rate, and the 8766 3-11C mutant produced a larger amount of lipid and had a higher lipid production rate than the wild type strain. Transcriptional analysis revealed that, similar to the wild type strain, the ACL1 and GND1 genes were expressed at significantly low levels, whereas IDP1 and ME1 were highly expressed. In conclusion, lipid productivity in the oleaginous yeast R. toruloides was successfully improved via UV mutagenesis and selection. The study also identified target genes for improving lipid productivity through gene recombination.

Frames for undergraduates

CERN Document Server

Han, Deguang; Larson, David; Weber, Eric

2007-01-01

Frames for Undergraduates is an undergraduate-level introduction to the theory of frames in a Hilbert space. This book can serve as a text for a special-topics course in frame theory, but it could also be used to teach a second semester of linear algebra, using frames as an application of the theoretical concepts. It can also provide a complete and helpful resource for students doing undergraduate research projects using frames. The early chapters contain the topics from linear algebra that students need to know in order to read the rest of the book. The later chapters are devoted to advanced topics, which allow students with more experience to study more intricate types of frames. Toward that end, a Student Presentation section gives detailed proofs of fairly technical results with the intention that a student could work out these proofs independently and prepare a presentation to a class or research group. The authors have also presented some stories in the Anecdotes section about how this material has moti...

Changing quantum reference frames

OpenAIRE

Palmer, Matthew C.; Girelli, Florian; Bartlett, Stephen D.

2013-01-01

We consider the process of changing reference frames in the case where the reference frames are quantum systems. We find that, as part of this process, decoherence is necessarily induced on any quantum system described relative to these frames. We explore this process with examples involving reference frames for phase and orientation. Quantifying the effect of changing quantum reference frames serves as a first step in developing a relativity principle for theories in which all objects includ...

The Experimental Research on Seismic Capacity of the Envelope Systems with Steel Frame

Science.gov (United States)

Li, Jiuyang; Wang, Bingbing; Li, Hengxu

2017-09-01

In this paper, according to the present application situation of the external envelope systems steel frame in the severe cold region, the stuffed composite wall panels are improved, the flexible connection with the steel frame is designed, the reduced scale specimens are made, the seismic capacity test is made and some indexes of the envelope systems such as bearing capacity, energy consumption and ductility, etc. are compared, which provide reference for the development and application of the steel frame envelope systems.

Purification and site-directed mutagenesis of linoleate 9S-dioxygenase-allene oxide synthase of Fusarium oxysporum confirms the oxygenation mechanism.

Science.gov (United States)

Chen, Yang; Jernerén, Fredrik; Oliw, Ernst H

2017-07-01

Plants and fungi form jasmonic acid from α-linolenic acid. The first two steps of biosynthesis in plants occur by sequential transformation by 13S-lipoxygenase and allene oxide synthase (AOS). The biosynthesis in fungi may follow this classical scheme, but the only fungal AOS discovered so far are cytochromes P450 (CYP) fused to 8- and 9-dioxygenases (DOX). In the present report, we purified recombinant 9S-DOX-AOS of Fusarium oxysporum from cell lysate by cobalt affinity chromatography to near homogeneity and studied key residues by site-directed mutagenesis. Sequence homology with 8R-DOX-linoleate diol synthases (8R-DOX-LDS) suggested that Tyr414 catalyzes hydrogen abstraction and that Cys1051 forms the heme thiolate ligand. Site-directed mutagenesis (Tyr414Phe; Cys1051Ser) led to loss of 9S-DOX and 9S-AOS activities, respectively, but other important residues in the CYP parts of 5,8- and 7,8-LDS or 9R-AOS were not conserved. The UV-visible spectrum of 9S-DOX-AOS showed a Soret band at 409 nm, which shifted to 413 nm in the Cys1051Ser mutant. The 9S-AOS of the Tyr414Phe mutant transformed 9S-hydroperoxides of α-linolenic and linoleic acids to allene oxides/α-ketols, but it did not transform 13-hydroperoxides. We conclude that 9S- and 8R-DOX catalyze hydrogen abstraction at C-11 and C-8, respectively, by homologous Tyr residues. Copyright © 2017 Elsevier Inc. All rights reserved.

Local news media framing of obesity in the context of a sugar-sweetened beverage reduction media campaign.

Science.gov (United States)

Jeong, Michelle; Gilmore, Joelle Sano; Bleakley, Amy; Jordan, Amy

2014-01-01

This study examined local news media's framing of obesity preceding and surrounding the Philadelphia sugar-sweetened beverage reduction media campaign. Using key search terms pertaining to obesity and sugary beverages, the authors searched the LexisNexis database and gathered local news stories (n = 167) that were aired or published between October, 2010 and March, 2011. They conducted a content analysis, coding for framing-related outcome measures (underlying factors, action steps, and contextual agents). Overall, the news media employed individual-level framing in the majority of stories when discussing obesity, both before and after the campaign launch. After the campaign launched, however, stories were significantly more likely to mention systemic-level contextual agents such as food companies (P = .008), beverage companies (P = .03), and champions or advocates (P = .001). The researchers observed a shift in the local news media discourse toward more thematic framing of obesity, and suggest that public health officials consider the potential impact of news media frames on garnering public support for future policy implementations. Copyright © 2014 Society for Nutrition Education and Behavior. Published by Elsevier Inc. All rights reserved.

Guns, Culture or Mental Health? Framing Mass Shootings as a Public Health Crisis.

Science.gov (United States)

DeFoster, Ruth; Swalve, Natashia

2017-08-25

In recent years, public health scholars and policymakers have been calling for increased research on the public health implications of gun violence. However, scientific research on this issue has been stifled by a 1996 budget rider that eliminated Centers for Disease Control and Prevention's (CDC) funding for gun research. In this study, we examined newspaper coverage of three mass shootings that took place over a 20-year period before and after the passage of this budget rider. We found that sources and frames provided by news media to contextualize gun violence shifted markedly over time, progressing from episodic and individual-level frames to broader thematic societal-level concerns, with increased discussion of mental health but limited discourse explicitly related to public health.

On Framing

DEFF Research Database (Denmark)

Peder Pedersen, Claus

2018-01-01

On framing as artistic and conceptual tool in the works of Claudia Carbone. Contribution to exhibition at the Aarhus School of Architecture.......On framing as artistic and conceptual tool in the works of Claudia Carbone. Contribution to exhibition at the Aarhus School of Architecture....

Establishment of frame image in dynamic function renal studies

International Nuclear Information System (INIS)

Guedes, Germano P.; Brunetto, Sergio Q.

1996-01-01

Statistical procedures applied to a set of images of renal function study are described to define a region of interest (ROI) on the kidneys's contours. The kidneys geometry is considered to adapt to the emitting area in every frames

Is radiation an appropriate model for chemical mutagenesis and carcinogenesis

International Nuclear Information System (INIS)

Bond, V.P.

1982-01-01

This chapter attempts to show why the quadratic, or ''linear quadratic,'' relationship holds for organ dose-single cell radiation effects, and to explore the extension of this relationship to chemical exposures in general. Demonstrates that although the ''αD + βD 2 relationship'' may be unexpected for normal pharmacologicalmedical dose-response relationships, a linear, no-threshold curve of this kind is expected for all stochastic-type (accidental or risk) situations with health consequences (e.g. all common accidents) including exposure to ''low-level radiation'' (LLR). Discusses the stochastic or risk approach, relevant radiobiology, and the stochastic for chemicals. Assumes that even though actual mutational rates cannot be expected to apply to the relevance of Tradescantia or any other single cell system as a predictor for mutagenesis and carcinogenesis in animals and man, the cardinal principles of genetics largely transcend species and the particular environment in which the cell is located. Concludes that with regard to LLR, the curve shapes and other relationships developed for Tradescantia would be expected to apply in principle to animal and human mutagenesis and carcinogenesis

Genetic analysis of γ-ray mutagenesis in yeast. Vol. 3

International Nuclear Information System (INIS)

McKee, R.H.; Lawrence, C.W.

1980-01-01

Comparisons between the 60 Co γ-ray survival curves of diploid strains of the yeast Saccharomyces cerevisiae that are homozygous for two non-allelic radiation-sensitive mutations and the corresponding single-mutant diploids suggest that there are two main types of repair of ionizing radiation damage in this organism. The first, which is defined by the rad52 epistasis group, depends on the activities of the RAD50 through RAD57 genes and is responsible for repairing the larger amount of lethal damage. Previous work [22] shows that this type of repair is essentially error-free. The second, defined by the rad6 epistasis group, depends on the activities of the RAD6, RAD9, RAD18, REV1 and REV3 genes and repairs a smaller, though still substantial, amount of lethal damage. It is also responsible for induced mutagenesis [22,23]. Data for survival and mutation induction after irradiation in air and partial anoxia show that oxygen-dependent damage can be repaired by either of these two pathways. They also show similar oxygen-enhancement ratios for survival and mutagenesis. (orig.)

Electric-field assisted spin torque nano-oscillator and binary frequency shift keying modulation

Science.gov (United States)

Zhang, Xiangli; Chen, Hao-Hsuan; Zhang, Zongzhi; Liu, Yaowen

2018-04-01

Electric-controlled magnetization precession introduces technologically relevant possibility for developing spin torque nano-oscillators (STNO) with potential applications in microwave emission. Using the perpendicularly magnetized magnetic tunnel junction (MTJ), we show that the magnetization oscillation frequency can be tuned by the co-action of electric field and spin polarized current. The dynamical phase diagram of MTJ-based STNO is analytically predicted through coordinate transformation from the laboratory frame to the rotation frame, by which the nonstationary out-of-plane magnetization precession process is therefore transformed into the stationary process in the rotation frame. Furthermore, using this STNO as a microwave source, we numerically demonstrate that the bit signal can be transmitted by a binary frequency shift keying (BFSK) modulation technique. The BFSK scheme shows good modulation features with no transient state.

Crowding depression of UV-mutagenesis in E. coli

International Nuclear Information System (INIS)

Bockrath, R.; Harper, D.; Kristoff, S.; Stanford Univ., CA

1980-01-01

Strains of E. coli Br were exposed to UV radiation and assayed for reversion mutation, using a standard selection medium. If more irradiated bacteria were assayed per petri dish, a proportional increase in the number of indicated reversion mutants was oud only up to a limiting plating density. Beyond a density of about 10 8 viable bacteria per petri dish, the number of indicated revertants per viable bacteriy assayed (the mutation frequency) decreased as the plating density was increased. The crowding depression of mutagenesis was more severe for de novo and converted suppressor mutations, the mutation frequency being reduced 100-fold at a plating density of about 6 x 10 9 viable bacteria per plate. The effect on backmutation was 10 times less. Crowding depression of mutagenesis occured in excision-proficient and -deficient strains, with identical effects in the 2 strains on de novo and converted suppressor mutation, but different effects on backmutations. There were no accompanying effects on viability. Irreversible loss of potential mutants during crowded growth was indicated in wash-off experiments. The kinetics suggested a half-life of approximately 1 h. Kinetics for accumulation by the bacteria of the limiting metabolite (tyrosine) on the assay plate indicated a short period of time for protein synthesis, but direct examination of the proteins synthesized during early growth on a crowded plate demonstrated successful induction of recA protein. (orig.)

Location of frame overlap choppers on pulsed source instruments

International Nuclear Information System (INIS)

Narehood, D.G.; Pearce, J.V.; Sokol, P.E.

2002-01-01

A detailed study has been performed to investigate the effect of frame overlap in a cold neutron chopper spectrometer. The basic spectrometer is defined by two high-speed choppers, one near the moderator to shape the pulse from the moderator, and one near the sample to define energy resolution. Using ray-tracing timing diagrams, we have observed that there are regions along the guide where the trajectories of neutrons with different velocities converge temporally at characteristic points along the spectrometer. At these points of convergence, a frame overlap chopper would be totally ineffective, allowing neutrons of all velocities to pass through. Conversely, at points where trajectories of different velocity neutrons are divergent, a frame overlap chopper is most effective. An analytical model to describe this behaviour has been developed, and leads us to the counterintuitive conclusion that the optimum position for a frame overlap chopper is as close to the initial chopper as possible. We further demonstrate that detailed Monte Carlo simulations produce results which are consistent with this model

Social closeness and feedback modulate susceptibility to the framing effect

Science.gov (United States)

Sip, Kamila E.; Smith, David V.; Porcelli, Anthony J.; Kar, Kohitij; Delgado, Mauricio R.

2014-01-01

Although, we often seek social feedback from others to help us make decisions, little is known about how social feedback affects decisions under risk, particularly from a close peer. We conducted two experiments using an established framing task to probe how decision making is modulated by social feedback valence (positive, negative) and the level of closeness with feedback provider (friend, confederate). Participants faced mathematically equivalent decisions framed as either an opportunity to keep (gain frame) or lose (loss frame) part of an initial endowment. Periodically, participants were provided with positive (e.g., “Nice!”) or negative (e.g., “Lame!”) feedback about their choices. Such feedback was provided by either a confederate (Experiment 1), or a gender-matched close friend (Experiment 2). As expected, the framing effect was observed in both experiments. Critically, an individual’s susceptibility to the framing effect was modulated by the valence of the social feedback, but only when the feedback provider was a close friend. This effect was reflected in the activation patterns of ventromedial prefrontal cortex and posterior cingulate cortex, regions involved in complex decision making. Taken together, these results highlight social closeness as an important factor in understanding the impact of social feedback on neural mechanisms of decision making. PMID:25074501

Social closeness and feedback modulate susceptibility to the framing effect.

Science.gov (United States)

Sip, Kamila E; Smith, David V; Porcelli, Anthony J; Kar, Kohitij; Delgado, Mauricio R

2015-01-01

Although we often seek social feedback (SFB) from others to help us make decisions, little is known about how SFB affects decisions under risk, particularly from a close peer. We conducted two experiments using an established framing task to probe how decision-making is modulated by SFB valence (positive, negative) and the level of closeness with feedback provider (friend, confederate). Participants faced mathematically equivalent decisions framed as either an opportunity to keep (gain frame) or lose (loss frame) part of an initial endowment. Periodically, participants were provided with positive (e.g., "Nice!") or negative (e.g., "Lame!") feedback about their choices. Such feedback was provided by either a confederate (Experiment 1) or a gender-matched close friend (Experiment 2). As expected, the framing effect was observed in both experiments. Critically, an individual's susceptibility to the framing effect was modulated by the valence of the SFB, but only when the feedback provider was a close friend. This effect was reflected in the activation patterns of ventromedial prefrontal cortex and posterior cingulate cortex, regions involved in complex decision-making. Taken together, these results highlight social closeness as an important factor in understanding the impact of SFB on neural mechanisms of decision-making.

Ascorbate enhances u.v.-mutagenesis in E. coli but inhibits it in Chinese hamster cells

International Nuclear Information System (INIS)

Rossman, T.G.; Klein, C.B.; Naslund, M.

1986-01-01

Ascorbic acid (vitamin C) causes an increase in the mutation frequency of u.v.-irradiated Escherichia coli WP2. The enhancement occurs at all u.v. fluences, and is dependent upon the ascorbate concentration in the medium. A maximum effect (approx. 8- to 13-fold) is seen at 100-150 μg/ml, although some enhancement can be seen even at 10 μg/ml. The comutagenic effect of ascorbate with u.v. in E. coli is dependent upon peptone, a constituent of nutrient broth. The enhancement of u.v.-mutagenesis by ascorbate is absent in strains WP2sub(s) (uvrA) amd WP6 (polA), suggesting that ascorbate affects the repair of pyrimidine dimers. The opposite results are observed for u.v.-mutagenesis in Chinese hamster V79 cells. The presence of ascorbate (50 μg/ml) during u.v. irradiation does not enhance the u.v. effect, but rather decreases it approx. 30%. These results are discussed with regard to differences in the mechanism of u.v.-mutagenesis and DNA repair in bacterial and mammalian cells. (author)

Functional studies of human intestinal alkaline sphingomyelinase by deglycosylation and mutagenesis

DEFF Research Database (Denmark)

Wu, Jun; Hansen, Gert H; Nilsson, Ake

2005-01-01

in NPP are conserved, and those of the active core are modified. We examined the functional changes of the enzyme induced by deglycosylation and mutagenesis. Treating alk-SMase cDNA-transfected COS-7 cells with tunicamycin rendered the expressed enzyme completely inactive. Mutations of the five potential...

Frame by Frame II: A Filmography of the African American Image, 1978-1994.

Science.gov (United States)

Klotman, Phyllis R.; Gibson, Gloria J.

A reference guide on African American film professionals, this book is a companion volume to the earlier "Frame by Frame I." It focuses on giving credit to African Americans who have contributed their talents to a film industry that has scarcely recognized their contributions, building on the aforementioned "Frame by Frame I,"…

Evaluating the traditional day and night shift in an acute care surgery fellowship: Is the swing shift a better choice?

Science.gov (United States)

Chestovich, Paul J; McNicoll, Christopher F; Ingalls, Nichole K; Kuhls, Deborah A; Fraser, Douglas R; Morrissey, Shawna L; Fildes, John J

2018-01-01

Fellowship trainees in acute care surgery require experience in the management of complex and operative trauma cases. Trauma center staffing usually follows standard 12-hour or 24-hour shifts, with resident and fellow trainees following a similar schedule. Although trauma admissions can be generally unpredictable, we analyzed temporal trends of trauma patient arrival times to determine the best time frame to maximize trainee experience during each day. We reviewed 10 years (2007-2016) of trauma registry data for blunt and penetrating trauma activations. Hourly volumetric trends were observed, and three specific events were chosen for detailed analysis: (1) trauma activation with Injury Severity Score (ISS) greater than 15, (2) laparotomy for trauma, and (3) thoracotomy for trauma. A retrospective shift log was created, which included day (7:00 AM to 7:00 PM), night (7:00 PM to 7:00 AM), and swing (noon to midnight) shifts. A swing shift was chosen because it captures the peak volume for all three events. Means and 95% confidence intervals were calculated, and comparisons were made between shifts using the Wilcoxon matched-pairs signed rank test with Bonferroni correction, and p less than 0.05 considered significant. During the 10-year study period, 28,287 patients were treated at our trauma center. This included the evaluation and management of 7,874 patients with ISS greater than 15, performance of 1,766 laparotomies, and 392 thoracotomies for trauma. Swing shift was superior to both day and night shifts for ISS greater than 15 (p night shifts were superior to day shift for laparotomies (p day shift (p night shift (p = 0.031). Shifts with the highest yield of ISS greater than 15, laparotomies, and thoracotomies include night and swing shifts on Fridays and Saturdays. Projected experience of acute care surgery fellows in managing complex trauma patients increases with the integration of swing shifts into the schedule. Daily trauma volume follows a temporal pattern

Framing theory

NARCIS (Netherlands)

de Vreese, C.H.; Lecheler, S.; Mazzoleni, G.; Barnhurst, K.G.; Ikeda, K.; Maia, R.C.M.; Wessler, H.

2016-01-01

Political issues can be viewed from different perspectives and they can be defined differently in the news media by emphasizing some aspects and leaving others aside. This is at the core of news framing theory. Framing originates within sociology and psychology and has become one of the most used

Framing politics

NARCIS (Netherlands)

Lecheler, S.K.

2010-01-01

This dissertation supplies a number of research findings that add to a theory of news framing effects, and also to the understanding of the role media effects play in political communication. We show that researchers must think more about what actually constitutes a framing effect, and that a

Serialising languages: Satellite-framed, verb-framed or neither ...

African Journals Online (AJOL)

The diversity in the coding of the core schema of motion, i.e., Path, has led to a traditional typology of languages into verb-framed and satellite-framed languages. In the former Path is encoded in verbs and in the latter it is encoded in non-verb elements that function as sisters to co-event expressing verbs such as manner ...

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)

Von Wright, A.; Bridges, B.A.

1980-01-01

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 43 0 C (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 43 0 C than at 32 0 C 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)

Displacement-Based Seismic Design Procedure for Framed Buildings with Dissipative Braces Part II: Numerical Results

International Nuclear Information System (INIS)

Mazza, Fabio; Vulcano, Alfonso

2008-01-01

For a widespread application of dissipative braces to protect framed buildings against seismic loads, practical and reliable design procedures are needed. In this paper a design procedure based on the Direct Displacement-Based Design approach is adopted, assuming the elastic lateral storey-stiffness of the damped braces proportional to that of the unbraced frame. To check the effectiveness of the design procedure, presented in an associate paper, a six-storey reinforced concrete plane frame, representative of a medium-rise symmetric framed building, is considered as primary test structure; this structure, designed in a medium-risk region, is supposed to be retrofitted as in a high-risk region, by insertion of diagonal braces equipped with hysteretic dampers. A numerical investigation is carried out to study the nonlinear static and dynamic responses of the primary and the damped braced test structures, using step-by-step procedures described in the associate paper mentioned above; the behaviour of frame members and hysteretic dampers is idealized by bilinear models. Real and artificial accelerograms, matching EC8 response spectrum for a medium soil class, are considered for dynamic analyses

Modification of a deoxynivalenol-antigen-mimicking nanobody to improve immunoassay sensitivity by site-saturation mutagenesis.

Science.gov (United States)

Qiu, Yu-Lou; He, Qing-Hua; Xu, Yang; Wang, Wei; Liu, Yuan-Yuan

2016-01-01

A nanobody (N-28) which can act as a deoxynivalenol (DON) antigen has been generated, and its residues Thr102-Ser106 were identified to bind with anti-DON monoclonal antibody by alanine-scanning mutagenesis. Site-saturation mutagenesis was used to analyze the plasticity of five residues and to improve the sensitivity of the N-28-based immunoassay. After mutagenesis, three mutants were selected by phage immunoassay and were sequenced. The half-maximal inhibitory concentrations of the immunoassay based on mutants N-28-T102Y, N-28-V103L, and N-28-Y105F were 24.49 ± 1.0, 51.83 ± 2.5, and 35.65 ± 1.6 ng/mL, respectively, showing the assay was, respectively, 3.2, 1.5, and 2.2 times more sensitive than the wild-type-based assay. The best mutant, N-28-T102Y, was used to develop a competitive phage ELISA to detect DON in cereals with high specificity and accuracy. In addition, the structural properties of N-28-T102Y and N-28 were investigated, revealing that the affinity of N-28-T102Y decreased because of increased steric hindrance with the large side chain. The lower-binding-affinity antigen mimetic may contribute to the improvement of the sensitivity of competitive immunoassays. These results demonstrate that nanobodies would be a favorable tool for engineering. Moreover, our results have laid a solid foundation for site-saturation mutagenesis of antigen-mimicking nanobodies to improve immunoassay sensitivity for small molecules.

Ocean currents modify the coupling between climate change and biogeographical shifts.

Science.gov (United States)

García Molinos, J; Burrows, M T; Poloczanska, E S

2017-05-02

Biogeographical shifts are a ubiquitous global response to climate change. However, observed shifts across taxa and geographical locations are highly variable and only partially attributable to climatic conditions. Such variable outcomes result from the interaction between local climatic changes and other abiotic and biotic factors operating across species ranges. Among them, external directional forces such as ocean and air currents influence the dispersal of nearly all marine and many terrestrial organisms. Here, using a global meta-dataset of observed range shifts of marine species, we show that incorporating directional agreement between flow and climate significantly increases the proportion of explained variance. We propose a simple metric that measures the degrees of directional agreement of ocean (or air) currents with thermal gradients and considers the effects of directional forces in predictions of climate-driven range shifts. Ocean flows are found to both facilitate and hinder shifts depending on their directional agreement with spatial gradients of temperature. Further, effects are shaped by the locations of shifts in the range (trailing, leading or centroid) and taxonomic identity of species. These results support the global effects of climatic changes on distribution shifts and stress the importance of framing climate expectations in reference to other non-climatic interacting factors.

Sparse Matrices in Frame Theory

DEFF Research Database (Denmark)

Lemvig, Jakob; Krahmer, Felix; Kutyniok, Gitta

2014-01-01

Frame theory is closely intertwined with signal processing through a canon of methodologies for the analysis of signals using (redundant) linear measurements. The canonical dual frame associated with a frame provides a means for reconstruction by a least squares approach, but other dual frames...... yield alternative reconstruction procedures. The novel paradigm of sparsity has recently entered the area of frame theory in various ways. Of those different sparsity perspectives, we will focus on the situations where frames and (not necessarily canonical) dual frames can be written as sparse matrices...

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.

Phase retrieval from the phase-shift moiré fringe patterns in simultaneous dual-wavelength interferometry

Science.gov (United States)

Cheng, Jinlong; Gao, Zhishan; Bie, Shuyou; Dou, Yimeng; Ni, Ruihu; Yuan, Qun

2018-02-01

Simultaneous dual-wavelength interferometry (SDWI) could extend the measured range of each single-wavelength interferometry. The moiré fringe generated in SDWI indirectly represents the information of the measured long synthetic-wavelength ({λ }{{S}}) phase, thus the phase demodulation is rather arduous. To address this issue, we present a method to convert the moiré fringe pattern into a synthetic-wavelength interferogram (moiré to synthetic-wavelength, MTS). After the square of the moiré fringe pattern in the MTS method, the additive moiré pattern is turned into a multiplicative one. And the synthetic-wavelength interferogram could be obtained by a low-pass filtering in spectrum of the multiplicative moiré fringe pattern. Therefore, when the dual-wavelength interferometer is implemented with the π/2 phase shift at {λ }{{S}}, a sequence of synthetic-wavelength phase-shift interferograms with π/2 phase shift could be obtained after the MTS method processing on the captured moiré fringe patterns. And then the synthetic-wavelength phase could be retrieved by the conventional phase-shift algorithm. Compared with other methods in SDWI, the proposed MTS approach could reduce the restriction of the phase shift and frame numbers for the adoption of the conventional phase-shift algorithm. Following, numerical simulations are executed to evaluate the performance of the MTS method in processing time, frames of interferograms and the phase shift error compensation. And the necessary linear carrier for MTS method is less than 0.11 times of the traditional dual-wavelength spatial-domain Fourier transform method. Finally, the deviations for MTS method in experiment are 0.97% for a step with the height of 7.8 μm and 1.11% for a Fresnel lens with the step height of 6.2328 μm.

When message-frame fits salient cultural-frame, messages feel more persuasive.

Science.gov (United States)

Uskul, Ayse K; Oyserman, Daphna

2010-03-01

The present study examines the persuasive effects of tailored health messages comparing those tailored to match (versus not match) both chronic cultural frame and momentarily salient cultural frame. Evidence from two studies (Study 1: n = 72 European Americans; Study 2: n = 48 Asian Americans) supports the hypothesis that message persuasiveness increases when chronic cultural frame, health message tailoring and momentarily salient cultural frame all match. The hypothesis was tested using a message about health risks of caffeine consumption among individuals prescreened to be regular caffeine consumers. After being primed for individualism, European Americans who read a health message that focused on the personal self were more likely to accept the message-they found it more persuasive, believed they were more at risk and engaged in more message-congruent behaviour. These effects were also found among Asian Americans who were primed for collectivism and who read a health message that focused on relational obligations. The findings point to the importance of investigating the role of situational cues in persuasive effects of health messages and suggest that matching content to primed frame consistent with the chronic frame may be a way to know what to match messages to.

Shifting policy priorities in EU-China energy relations: Implications for Chinese energy investments in Europe

International Nuclear Information System (INIS)

Gippner, Olivia; Torney, Diarmuid

2017-01-01

Shifting energy policy priorities both in China and the EU (European Union) have transformed their bilateral relationship. In order to assess the impact of domestic policy priorities on bilateral energy cooperation and climate policy, this comparative study traces the evolution of EU and Chinese approaches to energy policy – and their relative emphasis on factors and frames such as availability, efficiency, affordability and environmental stewardship. Drawing on government documents and a data set of interviews with Chinese policy-makers, experts and academics in 2015–2016, the article argues that while the EU started with a strong emphasis on environmental stewardship and moved towards a focus on affordability and availability, China started with a strong emphasis on availability and has moved towards a greater emphasis on environmental stewardship. This shift in frames on the Chinese side and subsequent changes in subsidy structures and targets can partially explain the increase in investments in renewable energy technologies. The article concludes that the Chinese and EU perspectives have become more aligned over the past ten years, coinciding with an increasing trend towards renewable energy in Chinese energy investments in the EU, for example in Italy and the UK. - Highlights: • Compares dominant frames of energy policy in China and the European Union in the period 2005–2015. • Shows that there has been a convergence of policy frames between China and the EU. • Convergence on environmental stewardship is necessary but not sufficient for FDI in clean energy.

Neural substrates of framing effects in social contexts: A meta-analytical approach.

Science.gov (United States)

Wang, X T; Rao, Li-Lin; Zheng, Hongming

2017-06-01

We hypothesize that framing effects (risk-averse in the positive frame and risk-seeking in the negative frame) are likely to occur when ambiguous social contexts result in ambiguous or ambivalent risk preferences, leading the decision-maker to search for more subtle cues, such as verbal framing. In a functional magnetic resonance imaging (fMRI) study, we examined framing effects in both unambiguous homogeneous group and more ambiguous heterogeneous group contexts. We began by conducting a meta-analysis and identified three regions of interest: the right inferior frontal gyrus, the left anterior cingulate (ACC)/ventromedial prefrontal cortex (vmPFC), and the left amygdala. Our own fMRI data were collected while the participants made choices between a sure option and a gamble framed in terms of the number of lives to either save or die. The framing effect was evident in a heterogeneous context with a mixture of kin and strangers, but disappeared in a homogeneous group of either all kin-members or all strangers. The fMRI results revealed a greater activation in the right middle/inferior frontal gyrus under the negative than the positive framing, and less ACC/vmPFC deactivation under positive framing in the heterogamous/ambiguous context. The activation of the amygdala was correlated with greater risk-seeking preference in homogeneous kinship contexts.

Einstein and Jordan frames reconciled: A frame-invariant approach to scalar-tensor cosmology

International Nuclear Information System (INIS)

Catena, Riccardo; Pietroni, Massimo; Scarabello, Luca

2007-01-01

Scalar-tensor theories of gravity can be formulated in different frames, most notably, the Einstein and the Jordan one. While some debate still persists in the literature on the physical status of the different frames, a frame transformation in scalar-tensor theories amounts to a local redefinition of the metric, and then should not affect physical results. We analyze the issue in a cosmological context. In particular, we define all the relevant observables (redshift, distances, cross sections, ...) in terms of frame-independent quantities. Then, we give a frame-independent formulation of the Boltzmann equation, and outline its use in relevant examples such as particle freeze-out and the evolution of the cosmic microwave background photon distribution function. Finally, we derive the gravitational equations for the frame-independent quantities at first order in perturbation theory. From a practical point of view, the present approach allows the simultaneous implementation of the good aspects of the two frames in a clear and straightforward way

column frame for design of reinforced concrete sway frames

African Journals Online (AJOL)

adminstrator

design of slender reinforced concrete columns in sway frames according .... concrete,. Ac = gross cross-sectional area of the columns. Step 3: Effective Buckling Length Factors. The effective buckling length factors of columns in a sway frame shall be computed by .... shall have adequate resistance to failure in a sway mode ...

Genetic toxicology of metal compounds. II. Enhancement of ultraviolet light-induced mutagenesis in Escherichia coli WP2

International Nuclear Information System (INIS)

Rossman, T.G.; Molina, M.

1986-01-01

Salts of metals which are carcinogenic, noncarcinogenic, or of unknown carcinogenicity were assayed for their abilities to modulate ultraviolet (UV)-induced mutagenesis in Escherichia coli WP2. In addition to the previously reported comutagenic effect of arsenite, salts of three other compounds were found to enhance UV mutagenesis. CuCl 2 , MnCl 2 (and a small effect by KMnO 4 ), and NaMoO 4 acted as comutagens in E coli WP2, which has wild-type DNA repair capability, but were much less comutagenic in the repair deficient strain WP2/sub s/ (uvrA). The survival of irradiated or unirradiated cells was not affected by these compounds. No effects on UV mutagenesis were seen for 16 other metal compounds. We suggest that the comutagenic effects might occur either via metal-induced decreases in the fidelity of repair replication or via metal-induced depurination

Improved constraints on isotropic shift and anisotropies of the speed of light using rotating cryogenic sapphire oscillators

International Nuclear Information System (INIS)

Hohensee, Michael A.; Stanwix, Paul L.; Tobar, Michael E.; Parker, Stephen R.; Phillips, David F.; Walsworth, Ronald L.

2010-01-01

We demonstrate that Michelson-Morley tests, which detect direction-dependent anisotropies in the speed of light, can also be used to place limits upon isotropic deviations of the vacuum speed of light from c, as described by the photon-sector standard model extension parameter κ-tilde tr . A shift in the speed of light that is isotropic in one inertial frame implies anisotropic shifts in others. Using observer Lorentz covariance, we derive the time-dependent variations in the relative resonance frequencies of a pair of electromagnetic resonators that would be generated by such a shift in the rest frame of the Sun. A new analysis of a recent experimental test of relativity using this result constrains κ-tilde tr with a precision of 7.4x10 -9 . This represents the first constraint on κ-tilde tr by a Michelson-Morley experiment and the first analysis of a single experiment to simultaneously set limits on all nine nonbirefringent terms in the photon sector of the minimal standard model extension.

Weaving Hilbert space fusion frames

OpenAIRE

Neyshaburi, Fahimeh Arabyani; Arefijamaal, Ali Akbar

2018-01-01

A new notion in frame theory, so called weaving frames has been recently introduced to deal with some problems in signal processing and wireless sensor networks. Also, fusion frames are an important extension of frames, used in many areas especially for wireless sensor networks. In this paper, we survey the notion of weaving Hilbert space fusion frames. This concept can be had potential applications in wireless sensor networks which require distributed processing using different fusion frames...

Wavelet frames and their duals

DEFF Research Database (Denmark)

Lemvig, Jakob

2008-01-01

frames with good time localization and other attractive properties. Furthermore, the dual wavelet frames are constructed in such a way that we are guaranteed that both frames will have the same desirable features. The construction procedure works for any real, expansive dilation. A quasi-affine system....... The signals are then represented by linear combinations of the building blocks with coefficients found by an associated frame, called a dual frame. A wavelet frame is a frame where the building blocks are stretched (dilated) and translated versions of a single function; such a frame is said to have wavelet...... structure. The dilation of the wavelet building blocks in higher dimension is done via a square matrix which is usually taken to be integer valued. In this thesis we step away from the "usual" integer, expansive dilation and consider more general, expansive dilations. In most applications of wavelet frames...

Novel Blind Recognition Algorithm of Frame Synchronization Words Based on Soft-Decision in Digital Communication Systems.

Directory of Open Access Journals (Sweden)

Jiangyi Qin

Full Text Available A novel blind recognition algorithm of frame synchronization words is proposed to recognize the frame synchronization words parameters in digital communication systems. In this paper, a blind recognition method of frame synchronization words based on the hard-decision is deduced in detail. And the standards of parameter recognition are given. Comparing with the blind recognition based on the hard-decision, utilizing the soft-decision can improve the accuracy of blind recognition. Therefore, combining with the characteristics of Quadrature Phase Shift Keying (QPSK signal, an improved blind recognition algorithm based on the soft-decision is proposed. Meanwhile, the improved algorithm can be extended to other signal modulation forms. Then, the complete blind recognition steps of the hard-decision algorithm and the soft-decision algorithm are given in detail. Finally, the simulation results show that both the hard-decision algorithm and the soft-decision algorithm can recognize the parameters of frame synchronization words blindly. What's more, the improved algorithm can enhance the accuracy of blind recognition obviously.

Role of RecA protein in untargeted UV mutagenesis of bacteriophage lambda: evidence for the requirement for the dinB gene

International Nuclear Information System (INIS)

Brotcorne-Lannoye, A.; Maenhaut-Michel, G.

1986-01-01

Untargeted UV mutagenesis of bacteriophage lambda--i.e., the increased recovery of lambda mutants when unirradiated lambda infects UV-irradiated Escherichia coli--is thought to be mediated by a transient decrease in DNA replication fidelity, generating mutations in the newly synthesized strands. Using the bacteriophage lambda cI857----lambda c mutation system, we provide evidence that the RecA protein, shown previously to be required for this mutagenic pathway, is no longer needed when the LexA protein is inactivated by mutation. We suggest that the error-prone DNA replication responsible for UV-induced untargeted mutagenesis is turned on by the presence of replication-blocking lesions in the host cell DNA and that the RecA protein is required only to derepress the relevant din gene(s). This is in contrast to mutagenesis of irradiated bacteria or irradiated phage lambda, in which activated RecA protein has a second role in mutagenesis in addition to the cleavage of the LexA protein. Among the tested din genes, the dinB gene product (in addition to the uvrA and uvrB gene products) was found to be required for untargeted mutagenesis of bacteriophage lambda. To our knowledge, a phenotype associated with the dinB gene has not been reported previously

Ultra-fast framing camera tube

Science.gov (United States)

Kalibjian, Ralph

1981-01-01

An electronic framing camera tube features focal plane image dissection and synchronized restoration of the dissected electron line images to form two-dimensional framed images. Ultra-fast framing is performed by first streaking a two-dimensional electron image across a narrow slit, thereby dissecting the two-dimensional electron image into sequential electron line images. The dissected electron line images are then restored into a framed image by a restorer deflector operated synchronously with the dissector deflector. The number of framed images on the tube's viewing screen is equal to the number of dissecting slits in the tube. The distinguishing features of this ultra-fast framing camera tube are the focal plane dissecting slits, and the synchronously-operated restorer deflector which restores the dissected electron line images into a two-dimensional framed image. The framing camera tube can produce image frames having high spatial resolution of optical events in the sub-100 picosecond range.

Time delay control of power converters: Mixed frame and stationary-frame variants

DEFF Research Database (Denmark)

Blaabjerg, Frede; Loh, P.C.; Tang, Y.

2008-01-01

In this paper, a mixed-frame and a stationary-frame time delay current controller are proposed for high precision reference tracking and disturbance rejection of power converters. In particular, the controllers use a proportional-resonant regulator in the stationary frame for regulating...... the positive and negative-sequence fundamental currents, which are known to directly influence the flow of active and reactive power in most energy conversion systems. Moreover, for the tracking or compensation of harmonics, the controllers include a time delay control path in either the synchronous...... or stationary frame, whose inherent feedback and feedforward structure can be proven to resemble a bank of resonant filters in either reference frames. Unlike other existing controllers, the proposed time delay controllers function by introducing multiple resonant peaks at only those harmonic frequencies...

Loss of BRCA1 or BRCA2 markedly increases the rate of base substitution mutagenesis and has distinct effects on genomic deletions

DEFF Research Database (Denmark)

Zamborszky, J.; Szikriszt, B.; Gervai, J. Z.

2017-01-01

-genome sequencing of multiple isogenic chicken DT40 cell clones to precisely determine the consequences of BRCA1/2 loss on all types of genomic mutagenesis. Spontaneous base substitution mutation rates increased sevenfold upon the disruption of either BRCA1 or BRCA2, and the arising mutation spectra showed strong...... of stalled replication forks as the cause of increased mutagenesis. The high rate of base substitution mutagenesis demonstrated by our experiments is likely to significantly contribute to the oncogenic effect of the inactivation of BRCA1 or BRCA2....

Mutagenesis and cytotoxicity in human epithelial cells by far- and near-ultraviolet radiations: action spectra

International Nuclear Information System (INIS)

Jones, C.A.; Huberman, E.; Cunningham, M.L.; Peak, M.J.

1987-01-01

Action spectra were determined for cell killing and mutation by monochromatic ultraviolet and visible radiations (254-434 nm) in cultured human epithelial P3 cells. Cell killing was more efficient following radiation at the shorter wavelengths (254-434 nm) than at longer wavelengths (365-434 nm). At 254 nm, for example, a fluence of 11 Jm-2 gave 37% cell survival, while at 365 nm, 17 X 10(5) Jm-2 gave equivalent survival. At 434 nm little killing was observed with fluences up to 3 X 10(6) Jm-2. Mutant induction, determined at the hypoxanthine-guanine phosphoribosyltransferase locus, was caused by radiation at 254, 313, and 365 nm. There was no mutant induction at 334 nm although this wavelength was highly cytotoxic. Mutagenesis was not induced by 434 nm radiation, either. There was a weak response at 405 nm; the mutant frequencies were only slightly increased above background levels. For the mutagenic wavelengths, log-log plots of the mutation frequency against fluence showed linear regressions with positive slopes of 2.5, consistent with data from a previous study using Escherichia coli. The data points of the action spectra for lethality and mutagenesis were similar to the spectrum for DNA damage at wavelengths shorter than 313 nm, whereas at longer wavelengths the lethality spectrum had a shoulder, and the mutagenesis spectrum had a secondary peak at 365 nm. No correlation was observed for the P3 cells between the spectra for cell killing and mutagenesis caused by wavelengths longer than 313 nm and the induction of DNA breakage or the formation of DNA-to-protein covalent bonds in these cells

Framing effects in medical situations: distinctions of attribute, goal and risky choice frames.

Science.gov (United States)

Peng, Jiaxi; Jiang, Yuan; Miao, Danmin; Li, Rui; Xiao, Wei

2013-06-01

To verify whether three different framing effects (risky choice, attribute and goal) exist in simulated medical situations and to analyse any differences. Medical decision-making problems were established, relating to medical skill evaluation, patient compliance and a selection of treatment options. All problems were described in positive and negative frame conditions. Significantly more positive evaluations were made if the doctor's medical records were described as 'of 100 patients, 70 patients became better' compared with those described as 'of 100 patients, 30 patients didn't become better'. Doctor's advice described in a negative frame resulted in significantly more decisions to comply, compared with advice described in a positive frame. Treatment options described in terms of survival rates resulted in significantly more adventurous choices compared with options described in terms of mortality rates. Decision-making reversal appeared in the risky choice and attribute frames, but not the goal frame. Framing effects were shown to exist in simulated medical situations, but there were significant differences among the three kinds of such effects.

Message framing and perinatal decisions.

Science.gov (United States)

Haward, Marlyse F; Murphy, Ryan O; Lorenz, John M

2008-07-01

The purpose of this study was to explore the effect of information framing on parental decisions about resuscitation of extremely premature infants. Secondary outcomes focused on elucidating the impact of other variables on treatment choices and determining whether those effects would take precedence over any framing effects. This confidential survey study was administered to adult volunteers via the Internet. The surveys depicted a hypothetical vignette of a threatened delivery at gestational age of 23 weeks, with prognostic outcome information framed as either survival with lack of disability (positive frame) or chance of dying and likelihood of disability among survivors (negative frame). Participants were randomly assigned to receive either the positively or negatively framed vignette. They were then asked to choose whether they would prefer resuscitation or comfort care. After completing the survey vignette, participants were directed to a questionnaire designed to test the secondary hypothesis and to explore possible factors associated with treatment decisions. A total of 146 subjects received prognostic information framed as survival data and 146 subjects received prognostic information framed as mortality data. Overall, 24% of the sample population chose comfort care and 76% chose resuscitation. A strong trend was detected toward a framing effect on treatment preference; respondents for whom prognosis was framed as survival data were more likely to elect resuscitation. This framing effect was significant in a multivariate analysis controlling for religiousness, parental status, and beliefs regarding the sanctity of life. Of these covariates, only religiousness modified susceptibility to framing; participants who were not highly religious were significantly more likely to be influenced to opt for resuscitation by the positive frame than were participants who were highly religious. Framing bias may compromise efforts to approach prenatal counseling in a

Simulation and estimation of gene number in a biological pathway using almost complete saturation mutagenesis screening of haploid mouse cells.

Science.gov (United States)

Tokunaga, Masahiro; Kokubu, Chikara; Maeda, Yusuke; Sese, Jun; Horie, Kyoji; Sugimoto, Nakaba; Kinoshita, Taroh; Yusa, Kosuke; Takeda, Junji

2014-11-24

Genome-wide saturation mutagenesis and subsequent phenotype-driven screening has been central to a comprehensive understanding of complex biological processes in classical model organisms such as flies, nematodes, and plants. The degree of "saturation" (i.e., the fraction of possible target genes identified) has been shown to be a critical parameter in determining all relevant genes involved in a biological function, without prior knowledge of their products. In mammalian model systems, however, the relatively large scale and labor intensity of experiments have hampered the achievement of actual saturation mutagenesis, especially for recessive traits that require biallelic mutations to manifest detectable phenotypes. By exploiting the recently established haploid mouse embryonic stem cells (ESCs), we present an implementation of almost complete saturation mutagenesis in a mammalian system. The haploid ESCs were mutagenized with the chemical mutagen N-ethyl-N-nitrosourea (ENU) and processed for the screening of mutants defective in various steps of the glycosylphosphatidylinositol-anchor biosynthetic pathway. The resulting 114 independent mutant clones were characterized by a functional complementation assay, and were shown to be defective in any of 20 genes among all 22 known genes essential for this well-characterized pathway. Ten mutants were further validated by whole-exome sequencing. The predominant generation of single-nucleotide substitutions by ENU resulted in a gene mutation rate proportional to the length of the coding sequence, which facilitated the experimental design of saturation mutagenesis screening with the aid of computational simulation. Our study enables mammalian saturation mutagenesis to become a realistic proposition. Computational simulation, combined with a pilot mutagenesis experiment, could serve as a tool for the estimation of the number of genes essential for biological processes such as drug target pathways when a positive selection of

Dominant negative umuD mutations decreasing RecA-mediated cleavage suggest roles for intact UmuD in modulation of SOS mutagenesis

International Nuclear Information System (INIS)

Battista, J.R.; Ohta, Toshihiro; Nohmi, Takehiko; Sun, W.; Walker, G.C.

1990-01-01

The products of the SOS-regulated umuDC operon are required for most UV and chemical mutagenesis in Escherichia coli. The UmuD protein shares homology with a family of proteins that includes LexA and several bacteriophage repressors. UmuD is posttranslationally activated for its role n mutagenesis by a RecA-mediated proteolytic cleavage that yields UmuD'. A set of missense mutants of umuD was isolated and shown to encode mutant UmuD proteins that are deficient in RecA-mediated cleavage in vivo. Most of these mutations are dominant to umuD + with respect to UV mutagenesis yet do not interfere with SOS induction. Although both UmuD and UmuD' form homodimers, the authors provide evidence that they preferentially form heterodimers. The relationship of UmuD to LexA, λ repressor, and other members of the family of proteins is discussed and possible roles intact UmuD in modulating SOS mutagenesis are discussed

100-ps framing-camera tube

International Nuclear Information System (INIS)

Kalibjian, R.

1978-01-01

The optoelectronic framing-camera tube described is capable of recording two-dimensional image frames with high spatial resolution in the <100-ps range. Framing is performed by streaking a two-dimensional electron image across narrow slits. The resulting dissected electron line images from the slits are restored into framed images by a restorer deflector operating synchronously with the dissector deflector. The number of framed images on the tube's viewing screen equals the number of dissecting slits in the tube. Performance has been demonstrated in a prototype tube by recording 135-ps-duration framed images of 2.5-mm patterns at the cathode. The limitation in the framing speed is in the external drivers for the deflectors and not in the tube design characteristics. Faster frame speeds in the <100-ps range can be obtained by use of faster deflection drivers

Study of UV-mutagenesis in Bacillus subtilis

International Nuclear Information System (INIS)

Lotareva, O.V.; Filippov, V.D.

1974-01-01

The sensitivity of Bac. subtilis to the inactivating and mutagenic effects of UV-mutants has been determined: uvr, which does not extract pyrimidine dimers from damaged DNA; recsub(x), which exhibits a reduced activity of ATP-dependent DNAase; poll, which is devoid of DNA polymerase, and wild strains (DT). The sensitivity of these strains to the inactivating effects of UV rays increases in the order: DT<= recsub(x) << uvr < poll, and UV mutability in the order: DT = rec(sub(x) < poll<< uvr. A comparison of UV mutagenesis in Bac. subtilis and E. coli suggests the hypothesis that the mechanisms of UV mutation formation are similar in these two organisms. (author)

The effect of essential oil of basil (Ocimum basilicum L.) on UV-induced mutagenesis in Escherichia coli and Saccharomyces cerevisiae

Energy Technology Data Exchange (ETDEWEB)

Stanojević, Jasna; Berić, Tanja; Opačić, Biljana; Vuković-Gačić, Branka; Simić, Draga; Knežević-Vukčević, Jelena [Institute of Botany, Faculty of Biology, University of Belgrade, 11000 Belgrade (Serbia)

2008-07-01

The antimutagenic potential of essential oil (EO) of basil (Ocimum basilicum L.) and its major constituent linalool were studied with the E. coli K12 and S. cerevisiae D7 assays. In the E. coli assay, EO and linalool inhibited UV-induced mutagenesis in a repair-proficient strain, but had no effect on spontaneous mutagenesis in repair-proficient, nucleotide excision repair-deficient, and mismatch-deficient strains. By testing participation of different mechanisms involved in antimutagenesis, it was concluded that the antimutagenic effect against UV-induced mutagenesis involved decrease of protein synthesis and cell proliferation which led to increased efficiency of nucleotide excision repair. An antimutagenic effect of basil derivatives in S. cerevisiae was not detected. (author)

The effect of essential oil of basil (Ocimum basilicum L.) on UV-induced mutagenesis in Escherichia coli and Saccharomyces cerevisiae

International Nuclear Information System (INIS)

Stanojević, Jasna; Berić, Tanja; Opačić, Biljana; Vuković-Gačić, Branka; Simić, Draga; Knežević-Vukčević, Jelena

2008-01-01

The antimutagenic potential of essential oil (EO) of basil (Ocimum basilicum L.) and its major constituent linalool were studied with the E. coli K12 and S. cerevisiae D7 assays. In the E. coli assay, EO and linalool inhibited UV-induced mutagenesis in a repair-proficient strain, but had no effect on spontaneous mutagenesis in repair-proficient, nucleotide excision repair-deficient, and mismatch-deficient strains. By testing participation of different mechanisms involved in antimutagenesis, it was concluded that the antimutagenic effect against UV-induced mutagenesis involved decrease of protein synthesis and cell proliferation which led to increased efficiency of nucleotide excision repair. An antimutagenic effect of basil derivatives in S. cerevisiae was not detected. (author)

Nature, nurture, or that fast food hamburger: media framing of diabetes in the New York Times from 2000 to 2010.

Science.gov (United States)

Stefanik-Sidener, Kelsey

2013-01-01

Diabetes is a growing yet misunderstood health concern in the United States. This study examined the ways in which diabetes has been framed by the New York Times over the past decade. The public's perception of the causes and solutions to complex problems such as diabetes has significant implications for the way public policy interventions are viewed; therefore, understanding how diabetes is being framed in the media can be an important first step in shifting public opinion about ways to combat the disease. A content analysis of 239 articles published in the New York Times between 2000 and 2010 revealed that nearly one-third of articles failed to differentiate between type 1, type 2, and gestational diabetes, which may cause confusion given substantial differences in the root cause and treatment of each. An examination of frames used within each type of diabetes showed that the overall dominant frame across types was either a medical frame or a behavioral frame, with deficient use of a societal frame. The limited use of societal-level framing may make it difficult for the public to see the wider consequences of diabetes and decreases the likelihood of public support for policy solutions to combat the disease.

Conformal frame dependence of inflation

International Nuclear Information System (INIS)

Domènech, Guillem; Sasaki, Misao

2015-01-01

Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case

Conformal frame dependence of inflation

Energy Technology Data Exchange (ETDEWEB)

Domènech, Guillem; Sasaki, Misao, E-mail: guillem.domenech@yukawa.kyoto-u.ac.jp, E-mail: misao@yukawa.kyoto-u.ac.jp [Yukawa Institute for Theoretical Physics, Kyoto University, Kyoto 606-8502 (Japan)

2015-04-01

Physical equivalence between different conformal frames in scalar-tensor theory of gravity is a known fact. However, assuming that matter minimally couples to the metric of a particular frame, which we call the matter Jordan frame, the matter point of view of the universe may vary from frame to frame. Thus, there is a clear distinction between gravitational sector (curvature and scalar field) and matter sector. In this paper, focusing on a simple power-law inflation model in the Einstein frame, two examples are considered; a super-inflationary and a bouncing universe Jordan frames. Then we consider a spectator curvaton minimally coupled to a Jordan frame, and compute its contribution to the curvature perturbation power spectrum. In these specific examples, we find a blue tilt at short scales for the super-inflationary case, and a blue tilt at large scales for the bouncing case.

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

Variable Frame Rate and Length Analysis for Data Compression in Distributed Speech Recognition

DEFF Research Database (Denmark)

Kraljevski, Ivan; Tan, Zheng-Hua

2014-01-01

This paper addresses the issue of data compression in distributed speech recognition on the basis of a variable frame rate and length analysis method. The method first conducts frame selection by using a posteriori signal-to-noise ratio weighted energy distance to find the right time resolution...... length for steady regions. The method is applied to scalable source coding in distributed speech recognition where the target bitrate is met by adjusting the frame rate. Speech recognition results show that the proposed approach outperforms other compression methods in terms of recognition accuracy...... for noisy speech while achieving higher compression rates....

Making students' frames explicit

DEFF Research Database (Denmark)

Nielsen, Louise Møller; Hansen, Poul Henrik Kyvsgaard

2016-01-01

Framing is a vital part of the design and innovation process. Frames are cognitive shortcuts (i.e. metaphors) that enable designers to connect insights about i.e. market opportunities and users needs with a set of solution principles and to test if this connection makes sense. Until now, framing...

Random transposon mutagenesis of the Saccharopolyspora erythraea genome reveals additional genes influencing erythromycin biosynthesis

Science.gov (United States)

Fedashchin, Andrij; Cernota, William H.; Gonzalez, Melissa C.; Leach, Benjamin I.; Kwan, Noelle; Wesley, Roy K.; Weber, J. Mark

2015-01-01

A single cycle of strain improvement was performed in Saccharopolyspora erythraea mutB and 15 genotypes influencing erythromycin production were found. Genotypes generated by transposon mutagenesis appeared in the screen at a frequency of ∼3%. Mutations affecting central metabolism and regulatory genes were found, as well as hydrolases, peptidases, glycosyl transferases and unknown genes. Only one mutant retained high erythromycin production when scaled-up from micro-agar plug fermentations to shake flasks. This mutant had a knockout of the cwh1 gene (SACE_1598), encoding a cell-wall-associated hydrolase. The cwh1 knockout produced visible growth and morphological defects on solid medium. This study demonstrated that random transposon mutagenesis uncovers strain improvement-related genes potentially useful for strain engineering. PMID:26468041

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.

Impact of increased mutagenesis on adaptation to high temperature in bacteriophage Qβ.

Science.gov (United States)

Arribas, María; Cabanillas, Laura; Kubota, Kirina; Lázaro, Ester

2016-10-01

RNA viruses replicate with very high error rates, which makes them more sensitive to additional increases in this parameter. This fact has inspired an antiviral strategy named lethal mutagenesis, which is based on the artificial increase of the error rate above a threshold incompatible with virus infectivity. A relevant issue concerning lethal mutagenesis is whether incomplete treatments might enhance the adaptive possibilities of viruses. We have addressed this question by subjecting an RNA virus, the bacteriophage Qβ, to different transmission regimes in the presence or the absence of sublethal concentrations of the mutagenic nucleoside analogue 5-azacytidine (AZC). Populations obtained were subsequently exposed to a non-optimal temperature and analyzed to determine their consensus sequences. Our results show that previously mutagenized populations rapidly fixed a specific set of mutations upon propagation at the new temperature, suggesting that the expansion of the mutant spectrum caused by AZC has an influence on later evolutionary behavior. Copyright © 2016 Elsevier Inc. All rights reserved.

A mouse model of hereditary coproporphyria identified in an ENU mutagenesis screen

Directory of Open Access Journals (Sweden)

Ashlee J. Conway

2017-08-01

Full Text Available A genome-wide ethyl-N-nitrosourea (ENU mutagenesis screen in mice was performed to identify novel regulators of erythropoiesis. Here, we describe a mouse line, RBC16, which harbours a dominantly inherited mutation in the Cpox gene, responsible for production of the haem biosynthesis enzyme, coproporphyrinogen III oxidase (CPOX. A premature stop codon in place of a tryptophan at amino acid 373 results in reduced mRNA expression and diminished protein levels, yielding a microcytic red blood cell phenotype in heterozygous mice. Urinary and faecal porphyrins in female RBC16 heterozygotes were significantly elevated compared with that of wild-type littermates, particularly coproporphyrinogen III, whereas males were biochemically normal. Attempts to induce acute porphyric crises were made using fasting and phenobarbital treatment on females. While fasting had no biochemical effect on RBC16 mice, phenobarbital caused significant elevation of faecal coproporphyrinogen III in heterozygous mice. This is the first known investigation of a mutagenesis mouse model with genetic and biochemical parallels to hereditary coproporphyria.

Strength and stiffness reduction factors for infilled frames with openings

Science.gov (United States)

Decanini, Luis D.; Liberatore, Laura; Mollaioli, Fabrizio

2014-09-01

Framed structures are usually infilled with masonry walls. They may cause a significant increase in both stiffness and strength, reducing the deformation demand and increasing the energy dissipation capacity of the system. On the other hand, irregular arrangements of the masonry panels may lead to the concentration of damage in some regions, with negative effects; for example soft story mechanisms and shear failures in short columns. Therefore, the presence of infill walls should not be neglected, especially in regions of moderate and high seismicity. To this aim, simple models are available for solid infills walls, such as the diagonal no-tension strut model, while infilled frames with openings have not been adequately investigated. In this study, the effect of openings on the strength and stiffness of infilled frames is investigated by means of about 150 experimental and numerical tests. The main parameters involved are identified and a simple model to take into account the openings in the infills is developed and compared with other models proposed by different researchers. The model, which is based on the use of strength and stiffness reduction factors, takes into account the opening dimensions and presence of reinforcing elements around the opening. An example of an application of the proposed reduction factors is also presented.

Power to the frame: bringing sociology back to frame analysis

NARCIS (Netherlands)

Vliegenthart, R.; van Zoonen, L.

2011-01-01

This article critically reviews current frame and framing research in media and communication studies. It is first argued that most authors fail to distinguish between ‘frame’ and ‘framing’ and therewith produce a conceptual confusion and imprecision that is not conducive to the field. Second, it is

Efficient Mutagenesis Independent of Ligation (EMILI).

Science.gov (United States)

Füzik, Tibor; Ulbrich, Pavel; Ruml, Tomáš

2014-11-01

Site-directed mutagenesis is one of the most widely used techniques in life sciences. Here we describe an improved and simplified method for introducing mutations at desired sites. It consists of an inverse PCR using a plasmid template and two partially complementary primers. The synthesis step is followed by annealing of the PCR product's sticky ends, which are generated by exonuclease digestion. This method is fast, extremely efficient and cost-effective. It can be used to introduce large insertions and deletions, but also for multiple point mutations in a single step. To show the principle and to prove the efficiency of the method, we present a series of basic mutations (insertions, deletions, point mutations) on pUC19 plasmid DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

49 CFR 393.201 - Frames.

Science.gov (United States)

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false Frames. 393.201 Section 393.201 Transportation... SAFE OPERATION Frames, Cab and Body Components, Wheels, Steering, and Suspension Systems § 393.201 Frames. (a) The frame or chassis of each commercial motor vehicle shall not be cracked, loose, sagging or...

Desire or Disease? Framing Obesity to Influence Attributions of Responsibility and Policy Support.

Science.gov (United States)

McGlynn, Joseph; McGlone, Matthew S

2018-02-01

The way we describe health threats affects perceptions of severity and preferred solutions to reduce risk. Most people agree obesity is a problem, but differ in how they attribute responsibility for development and decline of the disease. We explored effects of message framing on attributions of responsibility and support for public obesity policies using a 3 × 2 factorial design. Participants read one of six versions of a health message describing the negative effects of obesity. Message frames influenced respondent attributions and their support for policies to reduce obesity. Those who read a message that assigned agency to the disease (e.g., Obesity causes health problems) endorsed genetics as the cause to a greater degree than those who read a semantically equivalent message that instead assigned agency to people (e.g., Obese people develop health problems). In contrast, assigning agency to people rather than to the disease prompted higher attributions of individual responsibility and support for public policies. Explicit message frames that directly connected responsibility for obesity to either individual or societal factors had no effect on respondent perceptions. Findings suggest explicit arguments may be less effective in shifting perceptions of health threats than arguments embedded in agentic message frames. The results demonstrate specific message features that influence how people attribute responsibility for the onset and solution of obesity.

Dragging of inertial frames.

Science.gov (United States)

Ciufolini, Ignazio

2007-09-06

The origin of inertia has intrigued scientists and philosophers for centuries. Inertial frames of reference permeate our daily life. The inertial and centrifugal forces, such as the pull and push that we feel when our vehicle accelerates, brakes and turns, arise because of changes in velocity relative to uniformly moving inertial frames. A classical interpretation ascribed these forces to acceleration relative to some absolute frame independent of the cosmological matter, whereas an opposite view related them to acceleration relative to all the masses and 'fixed stars' in the Universe. An echo and partial realization of the latter idea can be found in Einstein's general theory of relativity, which predicts that a spinning mass will 'drag' inertial frames along with it. Here I review the recent measurements of frame dragging using satellites orbiting Earth.

[Effect of shifting sand burial on evaporation reduction and salt restraint under saline water irrigation in extremely arid region].

Science.gov (United States)

Zhang, Jian-Guo; Zhao, Ying; Xu, Xin-Wen; Lei, Jia-Qiang; Li, Sheng-Yu; Wang, Yong-Dong

2014-05-01

The Taklimakan Desert Highway Shelterbelt is drip-irrigated with high saline groundwater (2.58-29.70 g x L(-1)), and shifting sand burial and water-salt stress are most common and serious problems in this region. So it is of great importance to study the effect of shifting sand burial on soil moisture evaporation, salt accumulation and their distribution for water saving, salinity restraint, and suitable utilization of local land and water resources. In this study, Micro-Lysimeters (MLS) were used to investigate dynamics of soil moisture and salt under different thicknesses of sand burial (1, 2, 3, 4, and 5 cm), and field control experiments of drip-irrigation were also carried out to investigate soil moisture and salt distribution under different thicknesses of shifting sand burial (5, 10, 15, 20, 25, 30, 35, and 40 cm). The soil daily and cumulative evaporation decreased with the increase of sand burial thickness in MLS, cumulative evaporation decreased by 2.5%-13.7% compared with control. And evaporative inhibiting efficiency increased with sand burial thickness, evaporative inhibiting efficiency of 1-5 cm sand burial was 16.7%-79.0%. Final soil moisture content beneath the interface of sand burial increased with sand burial thickness, and it increased by 2.5%-13.7% than control. The topsoil EC of shifting sand in MLS decreased by 1.19-6.00 mS x cm(-1) with the increasing sand burial thickness, whereas soil salt content beneath the interface in MLS increased and amplitude of the topsoil salt content was higher than that of the subsoil. Under drip-irrigation with saline groundwater, average soil moisture beneath the interface of shifting sand burial increased by 0.4% -2.0% compare with control, and the highest value of EC was 7.77 mS x cm(-1) when the sand burial thickness was 10 cm. The trend of salt accumulation content at shifting sand surface increased firstly, and then decreased with the increasing sand burial thickness. Soil salt contents beneath the

Frames and extension problems I

DEFF Research Database (Denmark)

Christensen, Ole

2014-01-01

In this article we present a short survey of frame theory in Hilbert spaces. We discuss Gabor frames and wavelet frames and set the stage for a discussion of various extension principles; this will be presented in the article Frames and extension problems II (joint with H.O. Kim and R.Y. Kim)....

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

International Nuclear Information System (INIS)

Valdivia, L.

1979-01-01

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 10 0 C). 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

Language Shift – The Case of Punjabi in Sargodha Region of Pakistan

Directory of Open Access Journals (Sweden)

Barirah NAZIR

2013-12-01

Full Text Available This paper examines the linguistic scenario of Punjabi (second major language in Pakistan after Urdu in Sargodha and the social mechanism which poses threat to the sustainability of Punjabi on a broader scale. It deals with the attitudes, causes and effects of the language shift from Punjabi to other languages due to prestige, modernity and social mobility issues. Triangulation (Questionnaires from n=80 and In-depth interviews from n=3 was used in order to observe the trends of shift. The findings exhibit that Punjabi speakers are not so loyal to their language, Punjabi language shift is a real not perceived phenomenon and a day may not be far away when Punjabi will be considered endangered language in Pakistan.  

A note on the standard dual frame of a wavelet frame with three-scale

International Nuclear Information System (INIS)

Chen Qingjiang; Wei Zongtian; Feng Jinshun

2009-01-01

In this paper, it is shown that there exist wavelet frames generated by two functions which have good dual wavelet frames, but for which the standard dual wavelet frame does not consist of wavelets. That is to say, the standard dual wavelet frame cannot be generated by the translations and dilations of a single function. Relation to some physical theories such as entropy and E-infinity theory is also discussed.

Measuring the quality of a quantum reference frame: The relative entropy of frameness

International Nuclear Information System (INIS)

Gour, Gilad; Marvian, Iman; Spekkens, Robert W.

2009-01-01

In the absence of a reference frame for transformations associated with group G, any quantum state that is noninvariant under the action of G may serve as a token of the missing reference frame. We here present a measure of the quality of such a token: the relative entropy of frameness. This is defined as the relative entropy distance between the state of interest and the nearest G-invariant state. Unlike the relative entropy of entanglement, this quantity is straightforward to calculate, and we find it to be precisely equal to the G-asymmetry, a measure of frameness introduced by Vaccaro et al. It is shown to provide an upper bound on the mutual information between the group element encoded into the token and the group element that may be extracted from it by measurement. In this sense, it quantifies the extent to which the token successfully simulates a full reference frame. We also show that despite a suggestive analogy from entanglement theory, the regularized relative entropy of frameness is zero and therefore does not quantify the rate of interconversion between the token and some standard form of quantum reference frame. Finally, we show how these investigations yield an approach to bounding the relative entropy of entanglement.

Mutagenesis of the somaclones in vitro of cut roses by 60Co γ-rays irradiation

International Nuclear Information System (INIS)

Qu Suping; Su Yan; Wang Lihua; Tang Kaixue; Wang Jihua; Zhang Hao

2009-01-01

Mutagenesis of cut rose in vitro irradiated by 60 Co γ-rays was studied. The callus of leaves and regenerations adventitious bud was used as the explants for mutagenesis. Effect of 60 Co γ-rays irradiation on the callus's regeneration rate, adventitious bud's multiplication rate and vegetal status were studied. The results showed that the regeneration frequency of callus was decreased by 60 Co γ-rays irradiation. The regenerations adventitious bud was the better experimental materials compared with the callus of leaves. The lethal dose was 122 Gy and the semi-lethal dose was 76 Gy according to the regression equation. The appropriate dose on adventitious bud by irradiation rays was 50-60 Gy. (authors)

Competitive Framing

OpenAIRE

Ran Spiegler

2014-01-01

I present a simple framework for modeling two-firm market competition when consumer choice is "frame-dependent", and firms use costless "marketing messages" to influence the consumer's frame. This framework embeds several recent models in the "behavioral industrial organization" literature. I identify a property that consumer choice may satisfy, which extends the concept of Weighted Regularity due to Piccione and Spiegler (2012), and provide a characterization of Nash equilibria under this pr...

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

International Nuclear Information System (INIS)

Azhar Mohamad; Sobri Hussein; Abdul Rahim Harun

2010-01-01

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 LD 50 , 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 LD 50 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)

Radiation mutagenesis in selection of apple trees

International Nuclear Information System (INIS)

Kolontaev, V.M.; Kolontaev, Yu.V.

1977-01-01

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

The effect of abstract versus concrete framing on judgments of biological and psychological bases of behavior.

Science.gov (United States)

Kim, Nancy S; Johnson, Samuel G B; Ahn, Woo-Kyoung; Knobe, Joshua

2017-01-01

Human behavior is frequently described both in abstract, general terms and in concrete, specific terms. We asked whether these two ways of framing equivalent behaviors shift the inferences people make about the biological and psychological bases of those behaviors. In five experiments, we manipulated whether behaviors are presented concretely (i.e. with reference to a specific person, instantiated in the particular context of that person's life) or abstractly (i.e. with reference to a category of people or behaviors across generalized contexts). People judged concretely framed behaviors to be less biologically based and, on some dimensions, more psychologically based than the same behaviors framed in the abstract. These findings held true for both mental disorders (Experiments 1 and 2) and everyday behaviors (Experiments 4 and 5), and yielded downstream consequences for the perceived efficacy of disorder treatments (Experiment 3). Implications for science educators, students of science, and members of the lay public are discussed.

Message framing in social networking sites.

Science.gov (United States)

Kao, Danny Tengti; Chuang, Shih-Chieh; Wang, Sui-Min; Zhang, Lei

2013-10-01