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Sample records for random mutagenesis strategy

  1. Generation of genetically modified rodents using random ENU mutagenesis

    NARCIS (Netherlands)

    van Boxtel, R.; Cuppen, E.

    2011-01-01

    The generation of genetically modified animals using N-ethyl-N-nitrosourea (ENU) mutagenesis is a fast and highly effective method. The technique is based on treating male animals with the supermutagen ENU, which randomly introduces mutations in the spermatogonial stem cells. By breeding these

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

    NARCIS (Netherlands)

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

    2016-01-01

    Random mutagenesis and genome shuffling was applied to improve solvent tolerance and isopropanol/butanol/ethanol (IBE) production in the strictly anaerobic bacteria Clostridium beijerinckii DSM 6423. Following chemical mutagenesis with N-methyl-N-nitro-N-nitrosoguanidine (NTG), screening of

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

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    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.

  4. Random mutagenesis of human serine racemase reveals residues important for the enzymatic activity

    Czech Academy of Sciences Publication Activity Database

    Hoffman, Hillary Elizabeth; Jirásková, Jana; Zvelebil, M.; Konvalinka, Jan

    2010-01-01

    Roč. 75, č. 1 (2010), s. 59-79 ISSN 0010-0765 R&D Projects: GA MŠk 1M0508 Institutional research plan: CEZ:AV0Z40550506 Keywords : D-serine * serine racemase * random mutagenesis Subject RIV: CE - Biochemistry Impact factor: 0.853, year: 2010

  5. Use of the Photoactic Ability of a Bacterium to Teach the Genetic Principles of Random Mutagenesis & Mutant Screening

    Science.gov (United States)

    Din, Neena; Bird, Terry H.; Berleman, James E.

    2007-01-01

    In this article, the authors present a laboratory activity that relies on the use of a very versatile bacterial system to introduce the concept of how mutagenesis can be used for molecular and genetic analysis of living organisms. They have used the techniques of random mutagenesis and selection/screening to obtain strains of the organism "R.…

  6. Random mutagenesis MAPPIT analysis identifies binding sites for Vif and Gag in both cytidine deaminase domains of Apobec3G.

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    Isabel Uyttendaele

    Full Text Available The mammalian two-hybrid system MAPPIT allows the detection of protein-protein interactions in intact human cells. We developed a random mutagenesis screening strategy based on MAPPIT to detect mutations that disrupt the interaction of one protein with multiple protein interactors simultaneously. The strategy was used to detect residues of the human cytidine deaminase Apobec3G that are important for its homodimerization and its interaction with the HIV-1 Gag and Vif proteins. The strategy is able to identify the previously described head-to-head homodimerization interface in the N-terminal domain of Apobec3G. Our analysis further detects two new potential interaction surfaces in the N-and C-terminal domain of Apobec3G for interaction with Vif and Gag or for Apobec3G dimerization.

  7. Random transposon mutagenesis of the Saccharopolyspora erythraea genome reveals additional genes influencing erythromycin biosynthesis.

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    Fedashchin, Andrij; Cernota, William H; Gonzalez, Melissa C; Leach, Benjamin I; Kwan, Noelle; Wesley, Roy K; Weber, J Mark

    2015-11-01

    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. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  8. Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

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    Leonard, Cory A.; Brown, Stacy D.; Hayman, J. Russell

    2013-01-01

    Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA) in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS). Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system. PMID:23983696

  9. Random Mutagenesis of the Aspergillus oryzae Genome Results in Fungal Antibacterial Activity

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    Cory A. Leonard

    2013-01-01

    Full Text Available Multidrug-resistant bacteria cause severe infections in hospitals and communities. Development of new drugs to combat resistant microorganisms is needed. Natural products of microbial origin are the source of most currently available antibiotics. We hypothesized that random mutagenesis of Aspergillus oryzae would result in secretion of antibacterial compounds. To address this hypothesis, we developed a screen to identify individual A. oryzae mutants that inhibit the growth of Methicillin-resistant Staphylococcus aureus (MRSA in vitro. To randomly generate A. oryzae mutant strains, spores were treated with ethyl methanesulfonate (EMS. Over 3000 EMS-treated A. oryzae cultures were tested in the screen, and one isolate, CAL220, exhibited altered morphology and antibacterial activity. Culture supernatant from this isolate showed antibacterial activity against Methicillin-sensitive Staphylococcus aureus, MRSA, and Pseudomonas aeruginosa, but not Klebsiella pneumonia or Proteus vulgaris. The results of this study support our hypothesis and suggest that the screen used is sufficient and appropriate to detect secreted antibacterial fungal compounds resulting from mutagenesis of A. oryzae. Because the genome of A. oryzae has been sequenced and systems are available for genetic transformation of this organism, targeted as well as random mutations may be introduced to facilitate the discovery of novel antibacterial compounds using this system.

  10. Molecular evolution of Fome lignosus laccase by ethyl methane sulfonate-based random mutagenesis in vitro.

    Science.gov (United States)

    Hu, Mei-Rong; Chao, Ya-Peng; Zhang, Guo-Qing; Yang, Xiu-Qing; Xue, Zhi-Quan; Qian, Shi-Jun

    2007-12-01

    In order to improve the laccase activity, mutant libraries are constructed through ethyl methane sulfonate-based (EMS) random mutagenesis. Mutagenesis improved expression 3.7-fold to 144 mgl(-1) laccase in yeast, together with a 1.4-fold increase in K(cat). Thus, the total activity is enhanced 5-fold for 2,2'-azino-bis 3-ethylbenzothiaoline-6-sulfonic acid (ABTS). In the presence of 0.6mM copper, the highest activity value reached 30 Uml(-1) after a 3-day cultivation at a temperature of 30 degrees C(.) In comparison with the wild type, the best mutant enzymatic properties (K(m) for ABTS and guaiacol, thermo- and pH stability, optimal pH) are not changed. Moreover, amino acid sequence analysis indicates that there are four substitutions in the best mutant laccase (Gly160Asp, Ala167Thr, Gly174Asp, and Glu234Gly). The best mutant laccase model showed that the Gly160 and Ala167 are to be found near the water channel; especially the distance of Ala167 to the Cu3a is 14.46 A. This implies that it is likely involved in the formation of water channel and that it helps facilitate the easy incoming and outgoing of water.

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

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    Chen-Ji Huang

    2011-01-01

    Full Text Available In order to enhance the sensitivity of diagnosis, a recombinant clone containing domain I of HCV core (amino acid residues 1 to 123 was subjected to random mutagenesis. Five mutants with higher sensitivity were obtained by colony screening of 616 mutants using reverse ELISA. Sequence analysis of these mutants revealed alterations focusing on W84, P95, P110, or V129. The inclusion bodies of these recombinant proteins overexpressed in E. coli BL21(DE3 were subsequently dissolved using 6 M urea and then refolded by stepwise dialysis. Compared to the unfolded wild-type antigen, the refolded M3b antigen (W84S, P110S and V129L exhibited an increase of 66% antigenicity with binding capacity of 0.96 and affinity of 113 μM−1. Moreover, the 33% decrease of the production demand suggests that M3b is a potential substitute for anti-HCV antibody detection.

  12. Casting epPCR (cepPCR): A simple random mutagenesis method to generate high quality mutant libraries.

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    Yang, Jianhua; Ruff, Anna J; Arlt, Marcus; Schwaneberg, Ulrich

    2017-09-01

    During the last decade, directed evolution has become a standard protein engineering strategy to reengineer proteins for industrial applications under high stress conditions (e.g., high temperature, extreme pH, ionic liquids, or organic solvents). The most commonly employed method for diversity generation to improve biocatalysts for these properties is random mutagenesis by error-prone polymerase chain reaction (epPCR). However, recent reports show that epPCR often fails to produce >70% of beneficial positions/amino acid exchanges which improve enzyme properties such as organic solvent or ionic liquid resistance. In this report, bsla (543 bp, small lipase gene from Bacillus subtilis) was divided into three fragments (147, 192, 204 bp). Each fragment was subjected to an epPCR with a high mutation load (22, 31, and 33 mutations per kb) in order to increase the number of identified beneficial positions while maintaining a fraction of active population which can efficiently be screened in agar plate or microtiter plate format. The use of this "casting epPCR" process termed as (cepPCR), doubles the number of identified beneficial positions (from 14% to 29%), when compared to standard epPCR for the BSLA enzyme model. A further increase to 39% of beneficial positions is obtainable through combination of cepPCR with the transversion biased sequence saturation mutagenesis (SeSaM) method. Furthermore, sequencing of up to 600 mutations per fragment provided valuable insights into the correlation of total throughput and number of identified beneficial positions as well as how an efficient balance of screening efforts to obtainable results can be achieved in directed evolution campaigns. Biotechnol. Bioeng. 2017;114: 1921-1927. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  13. Random mutagenesis of bacterial luciferase: critical role of Glu175 in the control of luminescence decay

    Science.gov (United States)

    2004-01-01

    Bacterial luciferases (LuxAB) can be readily classed as slow or fast decay luciferases based on their rates of luminescence decay in a single turnover assay. Luciferases from Vibrio harveyi and Xenorhabdus (Photorhabdus) luminescens have slow decay rates, and those from the Photobacterium genus, such as Photobacterium fisheri, P. phosphoreum and P. leiognathi, have rapid decay rates. By substitution of a 67-amino-acid stretch of P. phosphoreum LuxA in the central region of the LuxA subunit, the ‘slow’ X. luminescens luciferase was converted into a chimaeric luciferase with a significantly more rapid decay rate [Valkova, Szittner and Meighen (1999) Biochemistry 38, 13820–13828]. To understand better the role of specific residues in the classification of luciferases as slow and fast decay, we have conducted random mutagenesis on this region. One of the mutants generated by a single mutation on LuxA at position 175 [E175G (Glu175→Gly)] resulted in the ‘slow decay’ X. luminescens luciferase being converted into a luciferase with a significantly more rapid decay rate. These results indicate the importance of Glu175 in LuxA as a critical residue for differentiating between ‘slow’ and ‘fast’ luciferases and show that this distinction is primarily due to differences in aldehyde affinity and in the decomposition of the luciferase–flavin–oxygen intermediate. PMID:15352872

  14. Structural insights from random mutagenesis of Campylobacter jejuni oligosaccharyltransferase PglB

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    Ihssen Julian

    2012-09-01

    Full Text Available Abstract Background Protein glycosylation is of fundamental importance in many biological systems. The discovery of N-glycosylation in bacteria and the functional expression of the N-oligosaccharyltransferase PglB of Campylobacter jejuni in Escherichia coli enabled the production of engineered glycoproteins and the study of the underlying molecular mechanisms. A particularly promising application for protein glycosylation in recombinant bacteria is the production of potent conjugate vaccines where polysaccharide antigens of pathogenic bacteria are covalently bound to immunogenic carrier proteins. Results In this study capsular polysaccharides of the clinically relevant pathogen Staphylococcus aureus serotype 5 (CP5 were expressed in Escherichia coli and linked in vivo to a detoxified version of Pseudomonas aeruginosa exotoxin (EPA. We investigated which amino acids of the periplasmic domain of PglB are crucial for the glycosylation reaction using a newly established 96-well screening system enabling the relative quantification of glycoproteins by enzyme-linked immunosorbent assay. A random mutant library was generated by error-prone PCR and screened for inactivating amino acid substitutions. In addition to 15 inactive variants with amino acid changes within the previously known, strictly conserved WWDYG motif of N-oligosaccharyltransferases, 8 inactivating mutations mapped to a flexible loop in close vicinity of the amide nitrogen atom of the acceptor asparagine as revealed in the crystal structure of the homologous enzyme C. lari PglB. The importance of the conserved loop residue H479 for glycosylation was confirmed by site directed mutagenesis, while a change to alanine of the adjacent, non-conserved L480 had no effect. In addition, we investigated functional requirements in the so-called MIV motif of bacterial N-oligosaccharyltransferases. Amino acid residues I571 and V575, which had been postulated to interact with the acceptor peptide, were

  15. Random mutagenesis reveals residues of JAK2 critical in evading inhibition by a tyrosine kinase inhibitor.

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    Michael R Marit

    Full Text Available The non-receptor tyrosine kinase JAK2 is implicated in a group of myeloproliferative neoplasms including polycythemia vera, essential thrombocythemia, and primary myelofibrosis. JAK2-selective inhibitors are currently being evaluated in clinical trials. Data from drug-resistant chronic myeloid leukemia patients demonstrate that treatment with a small-molecule inhibitor generates resistance via mutation or amplification of BCR-ABL. We hypothesize that treatment with small molecule inhibitors of JAK2 will similarly generate inhibitor-resistant mutants in JAK2.In order to identify inhibitor-resistant JAK2 mutations a priori, we utilized TEL-JAK2 to conduct an in vitro random mutagenesis screen for JAK2 alleles resistant to JAK Inhibitor-I. Isolated mutations were evaluated for their ability to sustain cellular growth, stimulate downstream signaling pathways, and phosphorylate a novel JAK2 substrate in the presence of inhibitor.Mutations were found exclusively in the kinase domain of JAK2. The panel of mutations conferred resistance to high concentrations of inhibitor accompanied by sustained activation of the Stat5, Erk1/2, and Akt pathways. Using a JAK2 substrate, enhanced catalytic activity of the mutant JAK2 kinase was observed in inhibitor concentrations 200-fold higher than is inhibitory to the wild-type protein. When testing the panel of mutations in the context of the Jak2 V617F allele, we observed that a subset of mutations conferred resistance to inhibitor, validating the use of TEL-JAK2 in the initial screen. These results demonstrate that small-molecule inhibitors select for JAK2 inhibitor-resistant alleles, and the design of next-generation JAK2 inhibitors should consider the location of mutations arising in inhibitor-resistant screens.

  16. Enhancement of Lutein Production in Chlorella sorokiniana (Chorophyta by Improvement of Culture Conditions and Random Mutagenesis

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    Maria Angeles Vargas

    2011-09-01

    Full Text Available Chlorella sorokiniana has been selected for lutein production, after a screening of thirteen species of microalgae, since it showed both a high content in this carotenoid and a high growth rate. The effects of several nutritional and environmental factors on cell growth and lutein accumulation have been studied. Maximal specific growth rate and lutein content were attained at 690 µmol photons m−2 s−1, 28 °C, 2 mM NaCl, 40 mM nitrate and under mixotrophic conditions. In general, optimal conditions for the growth of this strain also lead to maximal lutein productivity. High lutein yielding mutants of C. sorokiniana have been obtained by random mutagenesis, using N-methyl-N′-nitro-nitrosoguanidine (MNNG as a mutagen and selecting mutants by their resistance to the inhibitors of the carotenogenic pathway nicotine and norflurazon. Among the mutants resistant to the herbicides, those exhibiting both high content in lutein and high growth rate were chosen. Several mutants exhibited higher contents in this carotenoid than the wild type, showing, in addition, either a similar or higher growth rate than the latter strain. The mutant MR-16 exhibited a 2.0-fold higher volumetric lutein content than that of the wild type, attaining values of 42.0 mg L−1 and mutants DMR-5 and DMR-8 attained a lutein cellular content of 7.0 mg g−1 dry weight. The high lutein yield exhibited by C. sorokiniana makes this microalga an excellent candidate for the production of this commercially interesting pigment.

  17. Enhancement of Lutein Production in Chlorella sorokiniana (Chorophyta) by Improvement of Culture Conditions and Random Mutagenesis

    Science.gov (United States)

    Cordero, Baldo F.; Obraztsova, Irina; Couso, Inmaculada; Leon, Rosa; Vargas, Maria Angeles; Rodriguez, Herminia

    2011-01-01

    Chlorella sorokiniana has been selected for lutein production, after a screening of thirteen species of microalgae, since it showed both a high content in this carotenoid and a high growth rate. The effects of several nutritional and environmental factors on cell growth and lutein accumulation have been studied. Maximal specific growth rate and lutein content were attained at 690 μmol photons m−2 s−1, 28 °C, 2 mM NaCl, 40 mM nitrate and under mixotrophic conditions. In general, optimal conditions for the growth of this strain also lead to maximal lutein productivity. High lutein yielding mutants of C. sorokiniana have been obtained by random mutagenesis, using N-methyl-N′-nitro-nitrosoguanidine (MNNG) as a mutagen and selecting mutants by their resistance to the inhibitors of the carotenogenic pathway nicotine and norflurazon. Among the mutants resistant to the herbicides, those exhibiting both high content in lutein and high growth rate were chosen. Several mutants exhibited higher contents in this carotenoid than the wild type, showing, in addition, either a similar or higher growth rate than the latter strain. The mutant MR-16 exhibited a 2.0-fold higher volumetric lutein content than that of the wild type, attaining values of 42.0 mg L−1 and mutants DMR-5 and DMR-8 attained a lutein cellular content of 7.0 mg g−1 dry weight. The high lutein yield exhibited by C. sorokiniana makes this microalga an excellent candidate for the production of this commercially interesting pigment. PMID:22131961

  18. Structure-Based and Random Mutagenesis Approaches Increase the Organophosphate-Degrading Activity of a Phosphotriesterase Homologue from Deinococcus radiodurans

    Energy Technology Data Exchange (ETDEWEB)

    Hawwa, Renda; Larsen, Sonia D.; Ratia, Kiira; Mesecar, Andrew D.; (UIC)

    2010-11-09

    An enzyme from the amidohydrolase family from Deinococcus radiodurans (Dr-OPH) with homology to phosphotriesterase has been shown to exhibit activity against both organophosphate (OP) and lactone compounds. We have characterized the physical properties of Dr-OPH and have found it to be a highly thermostable enzyme, remaining active after 3 h of incubation at 60 C and withstanding incubation at temperatures up to 70 C. In addition, it can withstand concentrations of at least 200 mg/mL. These properties make Dr-OPH a promising candidate for development in commercial applications. However, compared to the most widely studied OP-degrading enzyme, that from Pseudomonas diminuta, Dr-OPH has low hydrolytic activity against certain OP substrates. Therefore, we sought to improve the OP-degrading activity of Dr-OPH, specifically toward the pesticides ethyl and methyl paraoxon, using structure-based and random approaches. Site-directed mutagenesis, random mutagenesis, and site-saturation mutagenesis were utilized to increase the OP-degrading activity of Dr-OPH. Out of a screen of more than 30,000 potential mutants, a total of 26 mutant enzymes were purified and characterized kinetically. Crystal structures of w.t. Dr-OPH, of Dr-OPH in complex with a product analog, and of 7 mutant enzymes were determined to resolutions between 1.7 and 2.4 {angstrom}. Information from these structures directed the design and production of 4 additional mutants for analysis. In total, our mutagenesis efforts improved the catalytic activity of Dr-OPH toward ethyl and methyl paraoxon by 126- and 322-fold and raised the specificity for these two substrates by 557- and 183-fold, respectively. Our work highlights the importance of an iterative approach to mutagenesis, proving that large rate enhancements are achieved when mutations are made in already active mutants. In addition, the relationship between the kinetic parameters and the introduced mutations has allowed us to hypothesize on those

  19. 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...

  20. Random mutagenesis of Luciola mingrelica firefly luciferase. Mutant enzymes with bioluminescence spectra showing low pH sensitivity.

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    Koksharov, M I; Ugarova, N N

    2008-08-01

    Most firefly luciferases demonstrate a strong pH-dependence of bioluminescence spectra. Gene region encoding first 225 residues of Luciola mingrelica luciferase was subjected to random mutagenesis, and four mutants with altered pH-sensitivity of bioluminescence spectra were isolated. F16L substitution showed distinctly lower pH-dependence of bioluminescence spectra, and Y35N,H and F16L/A40S substitutions resulted in the enzymes with bioluminescence spectra virtually independent from pH in the range of 6.0-7.8. The structural explanation is proposed for the effect of mutations on pH-sensitivity of bioluminescence spectra.

  1. A Practical Strategy to Discover New Antitumor Compounds by Activating Silent Metabolite Production in Fungi by Diethyl Sulphate Mutagenesis

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    Shi-Ming Fang

    2014-03-01

    Full Text Available Many fungal biosynthetic pathways are silent in standard culture conditions, and activation of the silent pathways may enable access to new metabolites with antitumor activities. The aim of the present study was to develop a practical strategy for microbial chemists to access silent metabolites in fungi. We demonstrated this strategy using a marine-derived fungus Penicillium purpurogenum G59 and a modified diethyl sulphate mutagenesis procedure. Using this strategy, we discovered four new antitumor compounds named penicimutanolone (1, penicimutanin A (2, penicimutanin B (3, and penicimutatin (4. Structures of the new compounds were elucidated by spectroscopic methods, especially extensive 2D NMR analysis. Antitumor activities were assayed by the MTT method using human cancer cell lines. Bioassays and HPLC-photodiode array detector (PDAD-UV and HPLC-electron spray ionization (ESI-MS analyses were used to estimate the activated secondary metabolite production. Compounds 2 and 3 had novel structures, and 1 was a new compound belonging to a class of very rare natural products from which only four members are so far known. Compounds 1–3 inhibited several human cancer cell lines with IC50 values lower than 20 μM, and 4 inhibited the cell lines to some extent. These results demonstrated the effectiveness of this strategy to discover new compounds by activating silent fungal metabolic pathways. These discoveries provide rationale for the increased use of chemical mutagenesis strategies in silent fungal metabolite studies.

  2. Tailoring of global transcription sigma D factor by random mutagenesis to improve Escherichia coli tolerance towards low-pHs.

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    Gao, Xi; Jiang, Ling; Zhu, Liying; Xu, Qing; Xu, Xian; Huang, He

    2016-04-20

    Bioconversion processes of organic acid or acid hydrolysis of raw material for microbial metabolism often suffer limitations as a result of microbial sensitivity in low-pH conditions. We adopted a three-step method called RAndom Insertional-deletional Strand Exchange mutagenesis (RAISE) to engineer the components of global regulator Sigma D factor (RpoD) of Escherichia coli to improve its acid tolerance. The best strain Mutant VII was identified from random mutagenesis libraries based on the growth performance, which exhibited much higher growth rate than the control (0.22h(-1) vs. 0.15h(-1)) at pH as low as 3.17. Combined transcriptome and phenome analysis of E. coli was carried out to better understand the global effects of RpoD on the regulatory networks. Our analysis showed that 95 (2.1%) of all E. coli genes were induced and 178 (4.0%) genes were repressed, including those for trehalose biosynthesis, nucleotides biosynthesis, carbon metabolism, amino acid utilization, except for acid resistance. Also regulated were the master regulators (ArcA, EvgA, H-NS and RpoS) and gene/operon-specific transcription factors (GadX, GadW, AppY, YdeO, KdgR). These results demonstrated that RpoD acts as global regulator in the growth phase of E. coli and consequently improves acid tolerances. Copyright © 2016 Elsevier B.V. All rights reserved.

  3. An inducible tool for random mutagenesis in Aspergillus niger based on the transposon Vader.

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    Paun, Linda; Nitsche, Benjamin; Homan, Tim; Ram, Arthur F; Kempken, Frank

    2016-07-01

    The ascomycete Aspergillus niger is widely used in the biotechnology, for instance in producing most of the world's citric acid. It is also known as a major food and feed contaminant. While generation of gene knockouts for functional genomics has become feasible in ku70 mutants, analyzing gene functions or metabolic pathways remains a laborious task. An unbiased transposon-based mutagenesis approach may aid this process of analyzing gene functions by providing mutant libraries in a short time. The Vader transposon is a non-autonomous DNA-transposon, which is activated by the homologous tan1-transposase. However, in the most commonly used lab strain of A. niger (N400 strain and derivatives), we found that the transposase, encoded by the tan1 gene, is mutated and inactive. To establish a Vader transposon-based mutagenesis system in the N400 background, we expressed the functional transposase of A. niger strain CBS 513.88 under the control of an inducible promoter based on the Tet-on system, which is activated in the presence of the antibiotic doxycycline (DOX). Increasing amounts of doxycycline lead to higher Vader excision frequencies, whereas little to none activity of Vader was observed without addition of doxycycline. Hence, this system appears to be suitable for producing stable mutants in the A. niger N400 background.

  4. Agrobacterium-mediated transformation of Guignardia citricarpa: an efficient tool to gene transfer and random mutagenesis.

    Science.gov (United States)

    Rodrigues, Maria Beatriz Calderan; Fávaro, Léia Cecília de Lima; Pallu, Ana Paula de Souza; Ferreira, Anderson; Sebastianes, Fernanda de Souza; Rodrigues, Maria Juliana Calderan; Spósito, Marcel Bellato; de Araújo, Welington Luiz; Pizzirani-Kleiner, Aline Aparecida

    2013-01-01

    Guignardia citricarpa is the causal agent of Citrus Black Spot (CBS), an important disease in Citriculture. Due to the expressive value of this activity worldwide, especially in Brazil, understanding more about the functioning of this fungus is of utmost relevance, making possible the elucidation of its infection mechanisms, and providing tools to control CBS. This work describes for the first time an efficient and successful methodology for genetic transformation of G. citricarpa mycelia, which generated transformants expressing the gene encoding for the gfp (green fluorescent protein) and also their interaction with citrus plant. Mycelia of G. citricarpa were transformed via Agrobacterium tumefaciens, which carried the plasmid pFAT-gfp, contains the genes for hygromycin resistance (hph) as well as gfp. The optimization of the agrotransformation protocol was performed testing different conditions (type of membrane; inductor agent concentration [acetosyringone - AS] and cocultivation time). Results demonstrated that the best condition occurred with the utilization of cellulose's ester membrane; 200 μM of AS and 96 h as cocultivation time. High mitotic stability (82 %) was displayed by transformants using Polymerase Chain Reaction (PCR) technique to confirm the hph gene insertion. In addition, the presence of gfp was observed inside mycelia by epifluorescence optical microscopy. This technique easy visualization of the behaviour of the pathogen interacting with the plant for the first time, allowing future studies on the pathogenesis of this fungus. The establishment of a transformation method for G. citricarpa opens a range of possibilities and facilitates the study of insertional mutagenesis and genetic knockouts, in order to identify the most important genes involved in the pathogenesis mechanisms and plant-pathogen interaction. Copyright © 2013 The British Mycological Society. Published by Elsevier Ltd. All rights reserved.

  5. Use of an EZ-Tn5-based random mutagenesis system to identify a novel toxin regulatory locus in Clostridium perfringens strain 13.

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    Jorge E Vidal

    2009-07-01

    Full Text Available Although useful for probing bacterial pathogenesis and physiology, current random mutagenesis systems suffer limitations for studying the toxin-producing bacterium Clostridium perfringens.An EZ-Tn5-based random mutagenesis approach was developed for use in C. perfringens. This mutagenesis system identified a new regulatory locus controlling toxin production by strain 13, a C. perfringens type A strain. The novel locus, encoding proteins with homology to the AgrB and AgrD components of the Agr quorum sensing system of Staphylococcus aureus and two hypothetical proteins, was found to regulate early production of both alpha toxin and perfringolysin O (PFO by strain 13. PFO production by the strain 13 DeltaagrB mutant could be restored by genetic complementation or by physical complementation, i.e. by co-culture of the strain 13 DeltaagrB mutant with a pfoA mutant of either strain 13 or C. perfringens type C CN3685. A similar AgrB- and AgrD-encoding locus is identifiable in all sequenced C. perfringens strains, including type B, C, D, and E isolates, suggesting this regulatory locus contributes to toxin regulation by most C. perfringens strains. In strain 13, the agrB and agrD genes were found to be co-transcribed in an operon with two upstream genes encoding hypothetical proteins.The new Tn5-based random mutagenesis system developed in this study is more efficient and random than previously reported C. perfringens random mutagenesis approaches. It allowed identification of a novel C. perfringens toxin regulatory locus with homology to the Agr system of S. aureus and which functions as expected of an Agr-like quorum sensing system. Since previous studies have shown that alpha toxin and perfringolysin O are responsible for strain 13-induced clostridial myonecrosis in the mouse model, the new agr regulatory locus may have importance for strain 13 virulence.

  6. Chimeric cytochromes P450 engineered by domain swapping and random mutagenesis for producing human metabolites of drugs.

    Science.gov (United States)

    Kang, Ji-Yeon; Ryu, Sang Hoon; Park, Sun-Ha; Cha, Gun Su; Kim, Dong-Hyun; Kim, Keon-Hee; Hong, Austin W; Ahn, Taeho; Pan, Jae-Gu; Joung, Young Hee; Kang, Hyung-Sik; Yun, Chul-Ho

    2014-07-01

    Human drug metabolites produced by cytochrome P450 enzymes are critical for safety testing and may themselves act as drugs or leads in the drug discovery and development process. Here, highly active chimeric fusion proteins (chimeras) were obtained by reductase domain swapping of mutants at key catalytic residues of the heme domain with that of a natural variant (CYP102A1.2) of P450 BM3 (CYP102A1.1) from Bacillus megaterium. Random mutagenesis at the heme domain of the chimera was also used to generate chimeric mutants that were more active and diverse than the chimeras themselves. To determine whether the chimeras and several mutants of the highly active chimera displayed enhanced catalytic activity and, more importantly, whether they acquired activities of biotechnological importance, we measured the oxidation activities of the chimeras and chimeric mutants toward human P450 substrates, mainly drugs. Some of the chimeric mutants showed high activity toward typical human P450 substrates including drugs. Statin leads, especially chiral products, with inhibitory effects toward HMG-CoA reductase could be obtained from metabolites of statin drugs generated using these chimeric mutants. This study reveals the critical role of the reductase domain for the activity of P450 BM3 and shows that chimeras generated by domain swapping can be used to develop industrial enzymes for the synthesis of human metabolites from drugs and drug leads. © 2014 Wiley Periodicals, Inc.

  7. Agrobacterium tumefaciens-Mediated Transformation of Valsa mali: An Efficient Tool for Random Insertion Mutagenesis

    Directory of Open Access Journals (Sweden)

    Caixia Wang

    2013-01-01

    Full Text Available Valsa mali is a causal agent of apple and pear trees canker disease, which is a destructive disease that causes serious economic losses in eastern Asia, especially in China. The lack of an efficient transformation system for Valsa mali retards its investigation, which poses difficulties to control the disease. In this research, a transformation system for this pathogen was established for the first time using A. tumefaciens-mediated transformation (ATMT, with the optimal transformation conditions as follows: 106/mL conidia suspension, cocultivation temperature 22°C, cocultivation time 72 hours, and 200 μM acetosyringone (AS in the inductive medium. The average transformation efficiency was 1015.00 ± 37.35 transformants per 106 recipient conidia. Thirty transformants were randomly selected for further confirmation and the results showed the presence of T-DNA in all hygromycin B resistant transformants and also revealed random and single gene integration with genetic stability. Compared with wild-type strain, those transformants exhibited various differences in morphology, conidia production, and conidia germination ability. In addition, pathogenicity assays revealed that 14 transformants had mitigated pathogenicity, while one had enhanced infection ability. The results suggest that ATMT of V. mali is a useful tool to gain novel insight into this economically important pathogen at molecular levels.

  8. Enhancement of thermostability of kojibiose phosphorylase from Thermoanaerobacter brockii ATCC35047 by random mutagenesis.

    Science.gov (United States)

    Yamamoto, Takuo; Mukai, Kazuhisa; Yamashita, Hiroshi; Kubota, Michio; Fukuda, Shigeharu; Kurimoto, Masashi; Tsujisaka, Yoshio

    2005-08-01

    Random mutation by error-prone PCR was introduced into kojibiose phosphorylase from Thermoanaerobacter brockii ATCC35047. One thermostable mutant enzyme, D513N, was isolated. The D513N mutant enzyme showed an optimum temperature of 67.5-70 degrees C (the wild type, 65 degrees C), and thermostability up to 67.5 degrees C (the wild type, up to 60 degrees C). The half-lives of D513N were estimated to be 135 h at 60 degrees C, 110 min at 70 degrees C and 6 min at 75 degrees C, respectively. They were about 1.6-fold, 7-fold and 6-fold longer than those of the wild-type enzyme, respectively.

  9. MEGAWHOP cloning: a method of creating random mutagenesis libraries via megaprimer PCR of whole plasmids.

    Science.gov (United States)

    Miyazaki, Kentaro

    2011-01-01

    MEGAWHOP allows for the cloning of DNA fragments into a vector and is used for conventional restriction digestion/ligation-based procedures. In MEGAWHOP, the DNA fragment to be cloned is used as a set of complementary primers that replace a homologous region in a template vector through whole-plasmid PCR. After synthesis of a nicked circular plasmid, the mixture is treated with DpnI, a dam-methylated DNA-specific restriction enzyme, to digest the template plasmid. The DpnI-treated mixture is then introduced into competent Escherichia coli cells to yield plasmids carrying replaced insert fragments. Plasmids produced by the MEGAWHOP method are virtually free of contamination by species without any inserts or with multiple inserts, and also the parent. Because the fragment is usually long enough to not interfere with hybridization to the template, various types of fragments can be used with mutations at any site (either known or unknown, random, or specific). By using fragments having homologous sequences at the ends (e.g., adaptor sequence), MEGAWHOP can also be used to recombine nonhomologous sequences mediated by the adaptors, allowing rapid creation of novel constructs and chimeric genes. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Forward and reverse mutagenesis in C. elegans.

    Science.gov (United States)

    Kutscher, Lena M; Shaham, Shai

    2014-01-17

    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.

  11. Three New and Eleven Known Unusual C25 Steroids: Activated Production of Silent Metabolites in a Marine-Derived Fungus by Chemical Mutagenesis Strategy using Diethyl Sulphate

    Directory of Open Access Journals (Sweden)

    Ming-Wen Xia

    2014-03-01

    Full Text Available Three new (1–3 and 11 known (4–14 C25 steroids with an unusual bicyclo[4.4.1]A/B ring system were isolated by tracing newly produced metabolites in the EtOAc extract of an antitumor mutant AD-1-2 obtained by the diethyl sulphate (DES mutagenesis of a marine-derived Penicillium purpurogenum G59. HPLC-PDAD-UV and HPLC-ESI-MS analyses indicated that the G59 strain did not produce these metabolites and the production of 1–14 in the mutant AD-1-2 extract was caused by the activation of silent metabolites in the original G59 strain by DES mutagenesis. The structures of the new compounds, named antineocyclocitrinols A (1 and B (2 and 23-O-methylantineocyclocitrinol (3, including their absolute configurations were determined by various spectroscopic methods, especially the NMR and Mo2-induced CD analyses. Compounds 1–3 provide the first examples of the C25 bicyclo[4.4.1]A/B ring steroids with the Z-configuration of 20,22-double bond. All of 1–14 weakly inhibited several human cancer cell lines to varying extents. These results provided additional examples for the successful application of the chemical mutagenesis strategy using DES to discover new compounds by activating silent metabolites in fungal isolates and supported also the effectiveness and usefulness of this new strategy.

  12. Three new and eleven known unusual C25 steroids: activated production of silent metabolites in a marine-derived fungus by chemical mutagenesis strategy using diethyl sulphate.

    Science.gov (United States)

    Xia, Ming-Wen; Cui, Cheng-Bin; Li, Chang-Wei; Wu, Chang-Jing

    2014-03-13

    Three new (1-3) and 11 known (4-14) C25 steroids with an unusual bicyclo[4.4.1]A/B ring system were isolated by tracing newly produced metabolites in the EtOAc extract of an antitumor mutant AD-1-2 obtained by the diethyl sulphate (DES) mutagenesis of a marine-derived Penicillium purpurogenum G59. HPLC-PDAD-UV and HPLC-ESI-MS analyses indicated that the G59 strain did not produce these metabolites and the production of 1-14 in the mutant AD-1-2 extract was caused by the activation of silent metabolites in the original G59 strain by DES mutagenesis. The structures of the new compounds, named antineocyclocitrinols A (1) and B (2) and 23-O-methylantineocyclocitrinol (3), including their absolute configurations were determined by various spectroscopic methods, especially the NMR and Mo2-induced CD analyses. Compounds 1-3 provide the first examples of the C25 bicyclo[4.4.1]A/B ring steroids with the Z-configuration of 20,22-double bond. All of 1-14 weakly inhibited several human cancer cell lines to varying extents. These results provided additional examples for the successful application of the chemical mutagenesis strategy using DES to discover new compounds by activating silent metabolites in fungal isolates and supported also the effectiveness and usefulness of this new strategy.

  13. Protein Engineering by Random Mutagenesis and Structure-Guided Consensus of Geobacillus stearothermophilus Lipase T6 for Enhanced Stability in Methanol

    Science.gov (United States)

    Dror, Adi; Shemesh, Einav; Dayan, Natali

    2014-01-01

    The abilities of enzymes to catalyze reactions in nonnatural environments of organic solvents have opened new opportunities for enzyme-based industrial processes. However, the main drawback of such processes is that most enzymes have a limited stability in polar organic solvents. In this study, we employed protein engineering methods to generate a lipase for enhanced stability in methanol, which is important for biodiesel production. Two protein engineering approaches, random mutagenesis (error-prone PCR) and structure-guided consensus, were applied in parallel on an unexplored lipase gene from Geobacillus stearothermophilus T6. A high-throughput colorimetric screening assay was used to evaluate lipase activity after an incubation period in high methanol concentrations. Both protein engineering approaches were successful in producing variants with elevated half-life values in 70% methanol. The best variant of the random mutagenesis library, Q185L, exhibited 23-fold-improved stability, yet its methanolysis activity was decreased by one-half compared to the wild type. The best variant from the consensus library, H86Y/A269T, exhibited 66-fold-improved stability in methanol along with elevated thermostability (+4.3°C) and a 2-fold-higher fatty acid methyl ester yield from soybean oil. Based on in silico modeling, we suggest that the Q185L substitution facilitates a closed lid conformation that limits access for both the methanol and substrate excess into the active site. The enhanced stability of H86Y/A269T was a result of formation of new hydrogen bonds. These improved characteristics make this variant a potential biocatalyst for biodiesel production. PMID:24362426

  14. Promoter analysis by saturation mutagenesis

    Directory of Open Access Journals (Sweden)

    Baliga Nitin

    2001-01-01

    Full Text Available Gene expression and regulation are mediated by DNA sequences, in most instances, directly upstream to the coding sequences by recruiting transcription factors, regulators, and a RNA polymerase in a spatially defined fashion. Few nucleotides within a promoter make contact with the bound proteins. The minimal set of nucleotides that can recruit a protein factor is called a cis-acting element. This article addresses a powerful mutagenesis strategy that can be employed to define cis-acting elements at a molecular level. Technical details including primer design, saturation mutagenesis, construction of promoter libraries, phenotypic analysis, data analysis, and interpretation are discussed.

  15. Construction of "small-intelligent" focused mutagenesis libraries using well-designed combinatorial degenerate primers.

    Science.gov (United States)

    Tang, Lixia; Gao, Hui; Zhu, Xuechen; Wang, Xiong; Zhou, Ming; Jiang, Rongxiang

    2012-03-01

    Site-saturation mutagenesis is a powerful tool for protein optimization due to its efficiency and simplicity. A degenerate codon NNN or NNS (K) is often used to encode the 20 standard amino acids, but this will produce redundant codons and cause uneven distribution of amino acids in the constructed library. Here we present a novel "small-intelligent" strategy to construct mutagenesis libraries that have a minimal gene library size without inherent amino acid biases, stop codons, or rare codons of Escherichia coli by coupling well-designed combinatorial degenerate primers with suitable PCR-based mutagenesis methods. The designed primer mixture contains exactly one codon per amino acid and thus allows the construction of small-intelligent mutagenesis libraries with one gene per protein. In addition, the software tool DC-Analyzer was developed to assist in primer design according to the user-defined randomization scheme for library construction. This small-intelligent strategy was successfully applied to the randomization of halohydrin dehalogenases with one or two randomized sites. With the help of DC-Analyzer, the strategy was proven to be as simple as NNS randomization and could serve as a general tool to efficiently randomize target genes at positions of interest.

  16. Improvement of enzyme activity and soluble expression of an alkaline protease isolated from oil-polluted mud flat metagenome by random mutagenesis.

    Science.gov (United States)

    Gong, Bo-Liang; Mao, Run-Qian; Xiao, Yue; Jia, Mei-Lu; Zhong, Xiao-Lin; Liu, Yan; Xu, Pei-Lin; Li, Gang

    2017-11-01

    A new protease gene (pro1437)was separated from an oil-polluted Mud flat metagenomic library. Pro1437 belongs to a peptidase M48 superfamily according to the results of sequence analysis, and it showed very low identities compared to other known proteases or peptidases. The error-prone PCR was used to introduce random mutations and improve the expression of pro1437. After two rounds of mutagenesis and screening, a mutant (Pro2T21) with a 6.6-fold higher activity and a 4.8-fold higher expression level than Pro1437 was obtained. Sequence analysis found three amino acid substitutions (A54V, L192H, F224L) in Pro2T21. 3D structure modelling analysis indicated A54V and L192H probably played a crucial role in the improvement of enzymatic activity and soluble expression level of Pro2T21. Furthermore, Pro2T21opti displayed a 5.8-fold higher expression level than the wild type under optimal pH 8.0 at 50°C after codon-optimization. Also, Pro2T21opti represented robust compatibility with several popular laundry detergents, and blood stains on white cloth pieces were completely washed away when endogenous protease-inactivated Tide and Pro2T21opti were used together. Therefore, Pro2T21opti has great potential for use as an additive in detergents after further study. Copyright © 2017. Published by Elsevier Inc.

  17. Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway

    Directory of Open Access Journals (Sweden)

    Gaigalat Lars

    2006-08-01

    essential L-histidinol-phosphate phosphatase (EC 3.1.3.15 in C. glutamicum. The cg0910 gene, renamed hisN, and its encoded enzyme have putative orthologs in almost all Actinobacteria, including mycobacteria and streptomycetes. Conclusion The absence of regional and sequence preferences of IS6100-transposition demonstrate that the established system is suitable for efficient genome-scale random mutagenesis in the sequenced type strain C.glutamicum ATCC 13032. The identification of the hisN gene encoding histidinol-phosphate phosphatase in C. glutamicum closed the last gap in histidine synthesis in the Actinobacteria. The system might be a valuable genetic tool also in other bacteria due to the broad host-spectrum of IS6100.

  18. Functional mapping of the fission yeast DNA polymerase δ B-subunit Cdc1 by site-directed and random pentapeptide insertion mutagenesis

    Directory of Open Access Journals (Sweden)

    Gray Fiona C

    2009-08-01

    Full Text Available Abstract Background DNA polymerase δ plays an essential role in chromosomal DNA replication in eukaryotic cells, being responsible for synthesising the bulk of the lagging strand. In fission yeast, Pol δ is a heterotetrameric enzyme comprising four evolutionarily well-conserved proteins: the catalytic subunit Pol3 and three smaller subunits Cdc1, Cdc27 and Cdm1. Pol3 binds directly to the B-subunit, Cdc1, which in turn binds the C-subunit, Cdc27. Human Pol δ comprises the same four subunits, and the crystal structure was recently reported of a complex of human p50 and the N-terminal domain of p66, the human orthologues of Cdc1 and Cdc27, respectively. Results To gain insights into the structure and function of Cdc1, random and directed mutagenesis techniques were used to create a collection of thirty alleles encoding mutant Cdc1 proteins. Each allele was tested for function in fission yeast and for binding of the altered protein to Pol3 and Cdc27 using the two-hybrid system. Additionally, the locations of the amino acid changes in each protein were mapped onto the three-dimensional structure of human p50. The results obtained from these studies identify amino acid residues and regions within the Cdc1 protein that are essential for interaction with Pol3 and Cdc27 and for in vivo function. Mutations specifically defective in Pol3-Cdc1 interactions allow the identification of a possible Pol3 binding surface on Cdc1. Conclusion In the absence of a three-dimensional structure of the entire Pol δ complex, the results of this study highlight regions in Cdc1 that are vital for protein function in vivo and provide valuable clues to possible protein-protein interaction surfaces on the Cdc1 protein that will be important targets for further study.

  19. Spectral tuning of photoproteins by partnering site-directed mutagenesis strategies with the incorporation of chromophore analogs.

    Science.gov (United States)

    Rowe, L; Rothert, A; Logue, C; Ensor, C M; Deo, S K; Daunert, S

    2008-02-01

    Aequorin and obelin are photoproteins whose calcium controlled bioluminescent light emission is used for labeling in assays, for the determination of calcium concentrations in vivo, and as a reporter in cellular imaging. Both of these photoproteins emit blue light from a 2-hydroperoxycoelenterazine chromophore, which is non-covalently bound in the hydrophobic core of the proteins. In an effort to produce aequorin and obelin variants with improved analytical properties, such as alternative emission colors and altered decay kinetics, seven mutants of aequorin and obelin were prepared and combined with 10 different coelenterazine analogs. These semi-synthetic photoprotein mutants exhibited shifts in bioluminescent properties when compared with wild-type proteins. The bioluminescent parameters determined for these semi-synthetic photoprotein mutants included specific activity, emission spectra and decay half-life time. This spectral tuning strategy resulted in semi-synthetic photoprotein mutants that had significantly altered bioluminescent properties. The largest emission maxima shift obtained was 44 nm, and the largest decay half-life difference was 23.91 s.

  20. Efficient sampling of complex network with modified random walk strategies

    Science.gov (United States)

    Xie, Yunya; Chang, Shuhua; Zhang, Zhipeng; Zhang, Mi; Yang, Lei

    2018-02-01

    We present two novel random walk strategies, choosing seed node (CSN) random walk and no-retracing (NR) random walk. Different from the classical random walk sampling, the CSN and NR strategies focus on the influences of the seed node choice and path overlap, respectively. Three random walk samplings are applied in the Erdös-Rényi (ER), Barabási-Albert (BA), Watts-Strogatz (WS), and the weighted USAir networks, respectively. Then, the major properties of sampled subnets, such as sampling efficiency, degree distributions, average degree and average clustering coefficient, are studied. The similar conclusions can be reached with these three random walk strategies. Firstly, the networks with small scales and simple structures are conducive to the sampling. Secondly, the average degree and the average clustering coefficient of the sampled subnet tend to the corresponding values of original networks with limited steps. And thirdly, all the degree distributions of the subnets are slightly biased to the high degree side. However, the NR strategy performs better for the average clustering coefficient of the subnet. In the real weighted USAir networks, some obvious characters like the larger clustering coefficient and the fluctuation of degree distribution are reproduced well by these random walk strategies.

  1. Microspore induced doubled haploids production from ethyl methanesulfonate (EMS) soaked flower buds is an efficient strategy for mutagenesis in Chinese cabbage

    NARCIS (Netherlands)

    Lu, Yin; Dai, Shuangyan; Gu, Aixia; Liu, Mengyang; Wang, Yanhua; Luo, Shuangxia; Zhao, Yujing; Wang, Shan; Xuan, Shuxin; Chen, Xueping; Li, Xiaofeng; Bonnema, Guusje; Zhao, Jianjun; Shen, Shuxing

    2016-01-01

    Chinese cabbage buds were soaked with Ethyl methanesulfonate (EMS) to induce mutagenesis. The influence of different EMS concentrations and treatment durations on microspore development, embryo production rate and seedling rate were evaluated in five Chinese cabbage genotypes. Mutations in four

  2. Massively parallel single-amino-acid mutagenesis.

    Science.gov (United States)

    Kitzman, Jacob O; Starita, Lea M; Lo, Russell S; Fields, Stanley; Shendure, Jay

    2015-03-01

    Random mutagenesis methods only partially cover the mutational space and are constrained by DNA synthesis length limitations. Here we demonstrate programmed allelic series (PALS), a single-volume, site-directed mutagenesis approach using microarray-programmed oligonucleotides. We created libraries including nearly every missense mutation as singleton events for the yeast transcription factor Gal4 (99.9% coverage) and human tumor suppressor p53 (93.5%). PALS-based comprehensive missense mutational scans may aid structure-function studies, protein engineering, and the interpretation of variants identified by clinical sequencing.

  3. Massively Parallel Single Amino Acid Mutagenesis

    Science.gov (United States)

    Kitzman, Jacob O.; Starita, Lea M.; Lo, Russell S.; Fields, Stanley; Shendure, Jay

    2014-01-01

    Random mutagenesis methods only partially cover the mutational space, and are constrained by DNA synthesis length limitations. Here, we demonstrate PALS, a single-volume, site-directed mutagenesis approach using microarray-programmed oligonucleotides. We created libraries including nearly every missense mutation as singleton events for the yeast transcription factor Gal4 (99.9% coverage) and human tumor suppressor p53 (93.5%). PALS-based comprehensive missense mutational scans may aid structure-function studies, protein engineering, and the interpretation of variants identified by clinical sequencing. PMID:25559584

  4. 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.

  5. Strategies in localization proofs for one-dimensional random ...

    Indian Academy of Sciences (India)

    R. Narasimhan (Krishtel eMaging) 1461 1996 Oct 15 13:05:22

    Strategies in localization proofs for one-dimensional random. Schrödinger operators. G ¨UNTER STOLZ. Department of Mathematics, University of Alabama at Birmingham, Birmingham, AL. 35294-1170, USA. E-mail: stolz@math.uab.edu. Abstract. Recent results on localization, both exponential and dynamical, for various.

  6. Coevolution of quantum and classical strategies on evolving random networks.

    Directory of Open Access Journals (Sweden)

    Qiang Li

    Full Text Available We study the coevolution of quantum and classical strategies on weighted and directed random networks in the realm of the prisoner's dilemma game. During the evolution, agents can break and rewire their links with the aim of maximizing payoffs, and they can also adjust the weights to indicate preferences, either positive or negative, towards their neighbors. The network structure itself is thus also subject to evolution. Importantly, the directionality of links does not affect the accumulation of payoffs nor the strategy transfers, but serves only to designate the owner of each particular link and with it the right to adjust the link as needed. We show that quantum strategies outperform classical strategies, and that the critical temptation to defect at which cooperative behavior can be maintained rises, if the network structure is updated frequently. Punishing neighbors by reducing the weights of their links also plays an important role in maintaining cooperation under adverse conditions. We find that the self-organization of the initially random network structure, driven by the evolutionary competition between quantum and classical strategies, leads to the spontaneous emergence of small average path length and a large clustering coefficient.

  7. Are random trading strategies more successful than technical ones?

    Directory of Open Access Journals (Sweden)

    Alessio Emanuele Biondo

    Full Text Available In this paper we explore the specific role of randomness in financial markets, inspired by the beneficial role of noise in many physical systems and in previous applications to complex socio-economic systems. After a short introduction, we study the performance of some of the most used trading strategies in predicting the dynamics of financial markets for different international stock exchange indexes, with the goal of comparing them to the performance of a completely random strategy. In this respect, historical data for FTSE-UK, FTSE-MIB, DAX, and S & P500 indexes are taken into account for a period of about 15-20 years (since their creation until today.

  8. Combining rational and random strategies in β-glucosidase Zm-p60.1 protein library construction.

    Directory of Open Access Journals (Sweden)

    Dušan Turek

    Full Text Available Saturation mutagenesis is a cornerstone technique in protein engineering because of its utility (in conjunction with appropriate analytical techniques for assessing effects of varying residues at selected positions on proteins' structures and functions. Site-directed mutagenesis with degenerate primers is the simplest and most rapid saturation mutagenesis technique. Thus, it is highly appropriate for assessing whether or not variation at certain sites is permissible, but not necessarily the most time- and cost-effective technique for detailed assessment of variations' effects. Thus, in the presented study we applied the technique to randomize position W373 in β-glucosidase Zm-p60.1, which is highly conserved among β-glucosidases. Unexpectedly, β-glucosidase activity screening of the generated variants showed that most variants were active, although they generally had significantly lower activity than the wild type enzyme. Further characterization of the library led us to conclude that a carefully selected combination of randomized codon-based saturation mutagenesis and site-directed mutagenesis may be most efficient, particularly when constructing and investigating randomized libraries with high fractions of positive hits.

  9. Classical mutagenesis in higher plants

    NARCIS (Netherlands)

    Koornneef, M.

    2002-01-01

    For a long time, mutagenesis research in plants focused on crop improvement and, especially for crop plants, opimised protocols were developed with barley being one of the favourite species. However, the interest in mutagenesis has shifted to basic plant research in the last 20 years, when the power

  10. 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....

  11. New approach for fish breeding by chemical mutagenesis: establishment of TILLING method in fugu (Takifugu rubripes) with ENU mutagenesis.

    Science.gov (United States)

    Kuroyanagi, Miwa; Katayama, Takashi; Imai, Tadashi; Yamamoto, Yoshihisa; Chisada, Shin-ichi; Yoshiura, Yasutoshi; Ushijima, Tomokazu; Matsushita, Tomonao; Fujita, Masashi; Nozawa, Aoi; Suzuki, Yuzuru; Kikuchi, Kiyoshi; Okamoto, Hiroyuki

    2013-11-13

    In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetics strategy that combines random chemical mutagenesis with high-throughput discovery technologies for screening the induced mutations in target genes. Although the chemical mutagenesis has been used widely in a variety of model species and also genetic breeding of microorganisms and crops, the application of the mutagenesis in fish breeding has been only rarely reported. In this study, we developed the TILLING method in fugu with ENU mutagenesis and high-resolution melting (HRM) analysis to detect base pair changes in target sequences. Fugu males were treated 3 times at weekly intervals with various ENU concentrations, and then the collected sperm after the treatment was used to fertilize normal female for generating the mutagenized population (F1). The fertilization and the hatching ratios were similar to those of the control and did not reveal a dose dependency of ENU. Genomic DNA from the harvested F1 offspring was used for the HRM analysis. To obtain a fish exhibiting a useful phenotype (e.g. high meat production and rapid growth), fugu myostatin (Mstn) gene was examined as a target gene, because it has been clarified that the mstn deficient medaka exhibited double-muscle phenotype in common with MSTN knockout mice and bovine MSTN mutant. As a result, ten types of ENU-induced mutations were identified including a nonsense mutation in the investigated region with HRM analysis. In addition, the average mutation frequency in fugu Mstn gene was 1 mutant per 297 kb, which is similar to values calculated for zebrafish and medaka TILLING

  12. Antimicrobials, stress and mutagenesis.

    Directory of Open Access Journals (Sweden)

    Alexandro Rodríguez-Rojas

    2014-10-01

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

  13. MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites

    National Research Council Canada - National Science Library

    Tang, Lixia; Wang, Xiong; Ru, Beibei; Sun, Hengfei; Huang, Jian; Gao, Hui

    2014-01-01

    ...) for the automated design of intelligent mutagenesis libraries that can completely cover user-defined randomized sequences, especially when multiple contiguous and/or adjacent sites are targeted...

  14. Classical mutagenesis in higher plants

    OpenAIRE

    Koornneef, M.

    2002-01-01

    For a long time, mutagenesis research in plants focused on crop improvement and, especially for crop plants, opimised protocols were developed with barley being one of the favourite species. However, the interest in mutagenesis has shifted to basic plant research in the last 20 years, when the power of mutant approaches in combination with molecular techniques to investigate the molecular nature of the genes became fully appreciated

  15. Sleeping Beauty Transposon Mutagenesis as a Tool for Gene Discovery in the NOD Mouse Model of Type 1 Diabetes.

    Science.gov (United States)

    Elso, Colleen M; Chu, Edward P F; Alsayb, May A; Mackin, Leanne; Ivory, Sean T; Ashton, Michelle P; Bröer, Stefan; Silveira, Pablo A; Brodnicki, Thomas C

    2015-10-04

    A number of different strategies have been used to identify genes for which genetic variation contributes to type 1 diabetes (T1D) pathogenesis. Genetic studies in humans have identified >40 loci that affect the risk for developing T1D, but the underlying causative alleles are often difficult to pinpoint or have subtle biological effects. A complementary strategy to identifying "natural" alleles in the human population is to engineer "artificial" alleles within inbred mouse strains and determine their effect on T1D incidence. We describe the use of the Sleeping Beauty (SB) transposon mutagenesis system in the nonobese diabetic (NOD) mouse strain, which harbors a genetic background predisposed to developing T1D. Mutagenesis in this system is random, but a green fluorescent protein (GFP)-polyA gene trap within the SB transposon enables early detection of mice harboring transposon-disrupted genes. The SB transposon also acts as a molecular tag to, without additional breeding, efficiently identify mutated genes and prioritize mutant mice for further characterization. We show here that the SB transposon is functional in NOD mice and can produce a null allele in a novel candidate gene that increases diabetes incidence. We propose that SB transposon mutagenesis could be used as a complementary strategy to traditional methods to help identify genes that, when disrupted, affect T1D pathogenesis. Copyright © 2015 Elso et al.

  16. Sleeping Beauty Transposon Mutagenesis as a Tool for Gene Discovery in the NOD Mouse Model of Type 1 Diabetes

    Science.gov (United States)

    Elso, Colleen M.; Chu, Edward P. F.; Alsayb, May A.; Mackin, Leanne; Ivory, Sean T.; Ashton, Michelle P.; Bröer, Stefan; Silveira, Pablo A.; Brodnicki, Thomas C.

    2015-01-01

    A number of different strategies have been used to identify genes for which genetic variation contributes to type 1 diabetes (T1D) pathogenesis. Genetic studies in humans have identified >40 loci that affect the risk for developing T1D, but the underlying causative alleles are often difficult to pinpoint or have subtle biological effects. A complementary strategy to identifying “natural” alleles in the human population is to engineer “artificial” alleles within inbred mouse strains and determine their effect on T1D incidence. We describe the use of the Sleeping Beauty (SB) transposon mutagenesis system in the nonobese diabetic (NOD) mouse strain, which harbors a genetic background predisposed to developing T1D. Mutagenesis in this system is random, but a green fluorescent protein (GFP)-polyA gene trap within the SB transposon enables early detection of mice harboring transposon-disrupted genes. The SB transposon also acts as a molecular tag to, without additional breeding, efficiently identify mutated genes and prioritize mutant mice for further characterization. We show here that the SB transposon is functional in NOD mice and can produce a null allele in a novel candidate gene that increases diabetes incidence. We propose that SB transposon mutagenesis could be used as a complementary strategy to traditional methods to help identify genes that, when disrupted, affect T1D pathogenesis. PMID:26438296

  17. Long-distance effects of insertional mutagenesis.

    Directory of Open Access Journals (Sweden)

    Ruchi Singhal

    2011-01-01

    Full Text Available Most common systems of genetic engineering of mammalian cells are associated with insertional mutagenesis of the modified cells. Insertional mutagenesis is also a popular approach to generate random alterations for gene discovery projects. A better understanding of the interaction of the structural elements within an insertional mutagen and the ability of such elements to influence host genes at various distances away from the insertion site is a matter of considerable practical importance.We observed that, in the context of a lentiviral construct, a transcript, which is initiated at an internal CMV promoter/enhancer region and incorporates a splice donor site, is able to extend past a collinear viral LTR and trap exons of host genes, while the polyadenylation signal, which is naturally present in the LTR, is spliced out. Unexpectedly, when a vector, which utilizes this phenomenon, was used to produce mutants with elevated activity of NF-κB, we found mutants, which owed their phenotype to the effect of the insert on a gene located tens or even hundreds of kilobases away from the insertion site. This effect did not result from a CMV-driven transcript, but was sensitive to functional suppression of the insert. Interestingly, despite the long-distance effect, expression of loci most closely positioned to the insert appeared unaffected.We concluded that a polyadenylation signal in a retroviral LTR, when occurring within an intron, is an inefficient barrier against the formation of a hybrid transcript, and that a vector containing a strong enhancer may selectively affect the function of genes far away from its insertion site. These phenomena have to be considered when experimental or therapeutic transduction is performed. In particular, the long-distance effects of insertional mutagenesis bring into question the relevance of the lists of disease-associated retroviral integration targets, which did not undergo functional validation.

  18. 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…

  19. Strategies in localization proofs for one-dimensional random ...

    Indian Academy of Sciences (India)

    Recent results on localization, both exponential and dynamical, for various models of one-dimensional, continuum, random Schrödinger operators are reviewed. This includes Anderson models with indefinite single site potentials, the Bernoulli–Anderson model, the Poisson model, and the random displacement model.

  20. SOME SYSTEMATIC SAMPLING STRATEGIES USING MULTIPLE RANDOM STARTS

    Directory of Open Access Journals (Sweden)

    Sampath Sundaram

    2010-09-01

    Full Text Available In this paper an attempt is made to extend linear systematic sampling using multiple random starts due to Gautschi(1957for various types of systematic sampling schemes available in literature, namely(i  Balanced Systematic Sampling (BSS of  Sethi (1965 and (ii Modified Systematic Sampling (MSS of Singh, Jindal, and Garg  (1968. Further, the proposed methods were compared with Yates corrected estimator developed with reference to Gautschi’s Linear systematic sampling (LSS with two random starts using appropriate super population models with the  help of R package for statistical computing.

  1. Combinatorial Mutagenesis and Selection to Understand and Improve Yeast Promoters

    Directory of Open Access Journals (Sweden)

    Laila Berg

    2013-01-01

    Full Text Available Microbial promoters are important targets both for understanding the global gene expression and developing genetic tools for heterologous expression of proteins and complex biosynthetic pathways. Previously, we have developed and used combinatorial mutagenesis methods to analyse and improve bacterial expression systems. Here, we present for the first time an analogous strategy for yeast. Our model promoter is the strong and inducible promoter in methylotrophic Pichia pastoris. The Zeocin resistance gene was applied as a valuable reporter for mutant promoter activity, and we used an episomal plasmid vector to ensure a constant reporter gene dosage in the yeast host cells. This novel design enabled direct selection for colonies of recombinant cells with altered Zeocin tolerance levels originating solely from randomly introduced point mutations in the promoter DNA sequence. We demonstrate that this approach can be used to select for promoter variants with abolished glucose repression in large mutant libraries. We also selected promoter variants with elevated expression level under induced conditions. The properties of the selected promoter variants were confirmed by expressing luciferase as an alternative reporter gene. The tools developed here should be useful for effective screening, characterization, and improvement of any yeast promoters.

  2. Optimal strategy analysis based on robust predictive control for inventory system with random demand

    Science.gov (United States)

    Saputra, Aditya; Widowati, Sutrisno

    2017-12-01

    In this paper, the optimal strategy for a single product single supplier inventory system with random demand is analyzed by using robust predictive control with additive random parameter. We formulate the dynamical system of this system as a linear state space with additive random parameter. To determine and analyze the optimal strategy for the given inventory system, we use robust predictive control approach which gives the optimal strategy i.e. the optimal product volume that should be purchased from the supplier for each time period so that the expected cost is minimal. A numerical simulation is performed with some generated random inventory data. We simulate in MATLAB software where the inventory level must be controlled as close as possible to a set point decided by us. From the results, robust predictive control model provides the optimal strategy i.e. the optimal product volume that should be purchased and the inventory level was followed the given set point.

  3. The Beneficial Role of Random Strategies in Social and Financial Systems

    Science.gov (United States)

    Biondo, Alessio Emanuele; Pluchino, Alessandro; Rapisarda, Andrea

    2013-05-01

    In this paper we focus on the beneficial role of random strategies in social sciences by means of simple mathematical and computational models. We briefly review recent results obtained by two of us in previous contributions for the case of the Peter principle and the efficiency of a Parliament. Then, we develop a new application of random strategies to the case of financial trading and discuss in detail our findings about forecasts of markets dynamics.

  4. SOME SYSTEMATIC SAMPLING STRATEGIES USING MULTIPLE RANDOM STARTS

    OpenAIRE

    Sampath Sundaram; Ammani Sivaraman

    2010-01-01

    In this paper an attempt is made to extend linear systematic sampling using multiple random starts due to Gautschi(1957)for various types of systematic sampling schemes available in literature, namely(i)  Balanced Systematic Sampling (BSS) of  Sethi (1965) and (ii) Modified Systematic Sampling (MSS) of Singh, Jindal, and Garg  (1968). Further, the proposed methods were compared with Yates corrected estimator developed with reference to Gautschi’s Linear systematic samplin...

  5. Genome-wide transposon mutagenesis in Saccharomyces cerevisiae and Candida albicans.

    Science.gov (United States)

    Xu, Tao; Bharucha, Nikë; Kumar, Anuj

    2011-01-01

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

  6. Comparing a stratified treatment strategy with the standard treatment in randomized clinical trials

    DEFF Research Database (Denmark)

    Sun, Hong; Bretz, Frank; Gerke, Oke

    2016-01-01

    The increasing emergence of predictive markers for different treatments in the same patient population allows us to define stratified treatment strategies. We consider randomized clinical trials that compare a standard treatment with a new stratified treatment strategy that divides the study...... population into subgroups receiving different treatments. Because the new strategy may not be beneficial in all subgroups, we consider in this paper an intermediate approach that establishes a treatment effect in a subset of patients built by joining several subgroups. The approach is based on the simple...

  7. Multisite Randomized Controlled Trial Examining Intelligent Tutoring of Structure Strategy for Fifth-Grade Readers

    Science.gov (United States)

    Wijekumar, Kausalai; Meyer, Bonnie J. F.; Lei, Pui-Wa; Lin, Yu-Chu; Johnson, Lori A.; Spielvogel, James A.; Shurmatz, Kathryn M.; Ray, Melissa; Cook, Michael

    2014-01-01

    This article reports on a large scale randomized controlled trial to study the efficacy of a web-based intelligent tutoring system for the structure strategy designed to improve content area reading comprehension. The research was conducted with 128 fifth-grade classrooms within 12 school districts in rural and suburban settings. Classrooms within…

  8. Supplemental Reading Strategy Instruction for Adolescents: A Randomized Trial and Follow-up Study

    Science.gov (United States)

    Cantrell, Susan Chambers; Almasi, Janice F.; Rintamaa, Margaret; Carter, Janis C.

    2016-01-01

    In this study, the authors examine the impact of a yearlong supplemental reading course involving daily instruction in the learning strategies curriculum on lower achieving adolescent students' reading achievement and motivation. Using a multiple-cohort randomized treatment-control group design over 4 years, they compared achievement and…

  9. Sequential causal inference: application to randomized trials of adaptive treatment strategies.

    Science.gov (United States)

    Dawson, Ree; Lavori, Philip W

    2008-05-10

    Clinical trials that randomize subjects to decision algorithms, which adapt treatments over time according to individual response, have gained considerable interest as investigators seek designs that directly inform clinical decision making. We consider designs in which subjects are randomized sequentially at decision points, among adaptive treatment options under evaluation. We present a sequential method to estimate the comparative effects of the randomized adaptive treatments, which are formalized as adaptive treatment strategies. Our causal estimators are derived using Bayesian predictive inference. We use analytical and empirical calculations to compare the predictive estimators to (i) the 'standard' approach that allocates the sequentially obtained data to separate strategy-specific groups as would arise from randomizing subjects at baseline; (ii) the semi-parametric approach of marginal mean models that, under appropriate experimental conditions, provides the same sequential estimator of causal differences as the proposed approach. Simulation studies demonstrate that sequential causal inference offers substantial efficiency gains over the standard approach to comparing treatments, because the predictive estimators can take advantage of the monotone structure of shared data among adaptive strategies. We further demonstrate that the semi-parametric asymptotic variances, which are marginal 'one-step' estimators, may exhibit significant bias, in contrast to the predictive variances. We show that the conditions under which the sequential method is attractive relative to the other two approaches are those most likely to occur in real studies.

  10. 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.

  11. Comparing cost effects of two quality strategies to improve test ordering in primary care: a randomized trial.

    NARCIS (Netherlands)

    Verstappen, W.H.; Merode, F. van; Grimshaw, J.; Dubois, W.; Grol, R.P.T.M.; Weijden, T. van der

    2004-01-01

    OBJECTIVE: To determine the costs and cost reductions of an innovative strategy aimed at improving test ordering routines of primary care physicians, compared with a traditional strategy. DESIGN: Multicenter randomized controlled trial with randomization at the local primary care physicians group

  12. Language-specific strategy for programming hearing aids - A double-blind randomized controlled crossover study.

    Science.gov (United States)

    Matsumoto, Nozomu; Suzuki, Nobuyoshi; Iwasaki, Satoshi; Ishikawa, Kazuha; Tsukiji, Hiroki; Higashino, Yoshie; Tabuki, Tomoko; Nakagawa, Takashi

    2017-11-17

    Voice-aligned compression (VAC) is a method used in Oticon's hearing aids to provide more comfortable hearing without sacrificing speech discrimination. The complex, non-linear compression curve for the VAC strategy is designed based on the frequency profile of certain spoken Western languages. We hypothesized that hearing aids could be further customized for Japanese-speaking users by modifying the compression curve using the frequency profile of spoken Japanese. A double-blind randomized controlled crossover study was performed to determine whether or not Oticon's modified amplification strategy (VAC-J) provides subjectively preferable hearing aids for Japanese-speaking hearing aid users compared to the same company's original amplification strategy (VAC). The participants were randomized to two groups. The VAC-first group received a pair of hearing aids programmed using the VAC strategy and wore them for three weeks, and then received a pair of hearing aids programmed using VAC-J strategy and wore them for three weeks. The VAC-J-first group underwent the same study, but they received hearing aids in the reverse sequence. A Speech, Spatial and Qualities (SSQ) questionnaire was administered before beginning to use the hearing aids, at the end of using the first pair of hearing aids, and at the end of using the second pair of hearing aids. Twenty-five participants that met the inclusion/exclusion criteria from January 1 to October 31, 2016, were randomized to two groups. Twenty-two participants completed the study. There were no statistically significant differences in the increment of SSQ scores between the participants when using the VAC- or the VAC-J-programmed hearing aids. However, participants preferred the VAC-J strategy to the VAC strategy at the end of the study, and this difference was statistically significant. Japanese-speaking hearing aid users preferred using hearing aids that were fitted with the VAC-J strategy. Our results show that the VAC strategy

  13. Comparing three knowledge communication strategies - Diffusion, Dissemination and Translation - through randomized controlled studies.

    Science.gov (United States)

    Lane, Joseph P; Stone, Vathsala I

    2015-01-01

    This paper describes a series of three randomized controlled case studies comparing the effectiveness of three strategies for communicating new research-based knowledge (Diffusion, Dissemination, Translation), to different Assistive Technology (AT) stakeholder groups. Pre and post intervention measures for level of knowledge use (unaware, aware, interested, using) via the LOKUS instrument, assessed the relative effectiveness of the three strategies. The latter two approaches were both more effective than diffusion but also equally effective. The results question the value added by tailoring research findings to specific audiences, and instead supports the critical yet neglected role for relevance in determining knowledge use by stakeholders.

  14. Randomized dynamical decoupling strategies and improved one-way key rates for quantum cryptography

    Energy Technology Data Exchange (ETDEWEB)

    Kern, Oliver

    2009-05-25

    The present thesis deals with various methods of quantum error correction. It is divided into two parts. In the first part, dynamical decoupling methods are considered which have the task of suppressing the influence of residual imperfections in a quantum memory. Such imperfections might be given by couplings between the finite dimensional quantum systems (qudits) constituting the quantum memory, for instance. The suppression is achieved by altering the dynamics of an imperfect quantum memory with the help of a sequence of local unitary operations applied to the qudits. Whereas up to now the operations of such decoupling sequences have been constructed in a deterministic fashion, strategies are developed in this thesis which construct the operations by random selection from a suitable set. Formulas are derived which estimate the average performance of such strategies. As it turns out, randomized decoupling strategies offer advantages and disadvantages over deterministic ones. It is possible to benefit from the advantages of both kind of strategies by designing combined strategies. Furthermore, it is investigated if and how the discussed decoupling strategies can be employed to protect a quantum computation running on the quantum memory. It is shown that a purely randomized decoupling strategy may be used by applying the decoupling operations and adjusted gates of the quantum algorithm in an alternating fashion. Again this method can be enhanced by the means of deterministic methods in order to obtain a combined decoupling method for quantum computations analogously to the combining strategies for quantum memories. The second part of the thesis deals with quantum error-correcting codes and protocols for quantum key distribution. The focus is on the BB84 and the 6-state protocol making use of only one-way communication during the error correction and privacy amplification steps. It is shown that by adding additional errors to the preliminary key (a process called

  15. Robust Network Architecture Against Random Threats in WMD Environments: Theoretical Limits and Recovery Strategies

    Science.gov (United States)

    2017-08-01

    help us understand how a social environment evolves so that we are able to make predictions about its impact. Moreover, we might even learn how to...Mika, B. Schlkopf, and R. Williamson, “ Regularized principal manifolds,” Journal of Machine Learning Research,, vol. 1, pp. 179–209, June 2001. [74] H...Architecture Against Random Threats in WMD Environments : Theoretical Limits and Recovery Strategies Distribution Statement A. Approved for public

  16. Randomized comparison of conservative versus aggressive strategy for provisional side branch intervention in coronary bifurcation lesions: results from the SMART-STRATEGY (Smart Angioplasty Research Team-Optimal Strategy for Side Branch Intervention in Coronary Bifurcation Lesions) randomized trial.

    Science.gov (United States)

    Song, Young Bin; Hahn, Joo-Yong; Song, Pil-Sang; Yang, Jeong Hoon; Choi, Jin-Ho; Choi, Seung-Hyuk; Lee, Sang Hoon; Gwon, Hyeon-Cheol

    2012-11-01

    The authors sought to compare conservative and aggressive strategies for provisional side branch (SB) intervention in coronary bifurcation lesions. The optimal provisional approach for coronary bifurcation lesions has not been established. In this prospective randomized trial, 258 patients with a coronary bifurcation lesion treated with drug-eluting stents were randomized to a conservative (n = 128) or aggressive (n = 130) SB intervention strategy. The criteria for SB intervention after main vessel stenting differed between the conservative and aggressive groups; Thrombolysis In Myocardial Infarction flow grade 75% for non-left main bifurcations and diameter stenosis >75% versus diameter stenosis >50% for left main bifurcations. The primary endpoint was target vessel failure (cardiac death, myocardial infarction, or target vessel revascularization) at 12 months. Left main bifurcation lesions were noted in 114 patients (44%) and true bifurcation lesions in 171 patients (66%). SB ballooning after main vessel stenting and SB stenting after SB ballooning were performed less frequently in the conservative group than in the aggressive group (25.8% vs. 68.5%, p strategy was associated with a lower incidence of procedure-related myocardial necrosis compared with the aggressive strategy (5.5% vs. 17.7%, p = 0.002). At 12 months, the incidence of target vessel failure was similar in both groups (9.4% in the conservative group vs. 9.2% in the aggressive group, p = 0.97). Compared with the aggressive strategy, the conservative strategy for provisional SB intervention was associated with similar long-term clinical outcomes and a lower incidence of procedure-related myocardial necrosis. (Optimal Strategy for Side Branch Stenting in Coronary Bifurcation Lesions [SMART-STRATEGY]; NCT00794014). Copyright © 2012 American College of Cardiology Foundation. Published by Elsevier Inc. All rights reserved.

  17. School-based strategies for oral health education of adolescents- a cluster randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Haleem Abdul

    2012-12-01

    Full Text Available Abstract Background Oral health education (OHE in schools has largely been imparted by dental professionals. Considering the substantial cost of this expert-led approach, the strategies relying on teachers, peer-leaders and learners themselves have also been utilized. However the evidence for comparative effectiveness of these strategies is lacking in the dental literature. The present study was conducted to compare the effectiveness of dentist-led, teacher-led, peer-led and self-learning strategies of oral health education. Methods A two-year cluster randomized controlled trial following a parallel design was conducted. It involved five groups of adolescents aged 10-11 years at the start of the study. The trial involved process as well as four outcome evaluations. The present paper discusses the findings of the study pertaining to the baseline and final outcome evaluation, both comprising of a self-administered questionnaire, a structured interview and clinical oral examination. The data were analyzed using Generalized Estimating Equations. Results All the three educator-led strategies of OHE had statistically higher mean oral health knowledge (OHK, oral health behavior (OHB, oral hygiene status (OHS and combined knowledge, behavior and oral hygiene status (KBS scores than the self-learning and control groups (p Conclusions The dentist-led, teacher-led and peer-led strategies of oral health education are equally effective in improving the oral health knowledge and oral hygiene status of adolescents. The peer-led strategy, however, is almost as effective as the dentist-led strategy and comparatively more effective than the teacher-led and self-learning strategies in improving their oral health behavior. Trail registration SRCTN39391017

  18. School-based strategies for oral health education of adolescents- a cluster randomized controlled trial

    Science.gov (United States)

    2012-01-01

    Background Oral health education (OHE) in schools has largely been imparted by dental professionals. Considering the substantial cost of this expert-led approach, the strategies relying on teachers, peer-leaders and learners themselves have also been utilized. However the evidence for comparative effectiveness of these strategies is lacking in the dental literature. The present study was conducted to compare the effectiveness of dentist-led, teacher-led, peer-led and self-learning strategies of oral health education. Methods A two-year cluster randomized controlled trial following a parallel design was conducted. It involved five groups of adolescents aged 10-11 years at the start of the study. The trial involved process as well as four outcome evaluations. The present paper discusses the findings of the study pertaining to the baseline and final outcome evaluation, both comprising of a self-administered questionnaire, a structured interview and clinical oral examination. The data were analyzed using Generalized Estimating Equations. Results All the three educator-led strategies of OHE had statistically higher mean oral health knowledge (OHK), oral health behavior (OHB), oral hygiene status (OHS) and combined knowledge, behavior and oral hygiene status (KBS) scores than the self-learning and control groups (poral health education are equally effective in improving the oral health knowledge and oral hygiene status of adolescents. The peer-led strategy, however, is almost as effective as the dentist-led strategy and comparatively more effective than the teacher-led and self-learning strategies in improving their oral health behavior. Trail registration SRCTN39391017 PMID:23249443

  19. Strategies to improve recruitment and retention of older stroke survivors to a randomized clinical exercise trial.

    Science.gov (United States)

    Taylor-Piliae, Ruth E; Boros, Daniella; Coull, Bruce M

    2014-03-01

    Relatively few exercise randomized clinical trials (RCTs) among stroke survivors have reported the effectiveness of recruitment and retention strategies, despite its central importance to study integrity. Our objective is to examine recruitment and retention strategies used among a group of older community-dwelling stroke survivors for an exercise RCT. Recruitment strategies were multidimensional using both paid (ie, newspaper, radio and, television) and unpaid advertisements (ie, staff visits, flyers, and brochures placed at outpatient rehabilitation centers, physician offices, and community facilities working with older adults; free media coverage of the study, presentations at stroke support groups, relatives/friends, and study Web site) to obtain referrals. Retention strategies centered on excellent communication, the study participants' needs, and having dedicated study staff. Attrition rates and adherence to the intervention were used to examine the effectiveness of these retention strategies. A total of 393 referrals were received, 233 persons were screened, and 145 stroke survivors enrolled in the study. During 3 years of study recruitment, we achieved 97% of our enrollment target. We enrolled 62% of those screened. Study enrollment from paid advertising was 21.4% (n = 31), whereas unpaid advertisements resulted in 78.6% (n = 114) of our participants. Attrition was 10% (n = 14 dropouts), and adherence to the intervention was 85%. Recruitment and retention of participants in an exercise RCT are time and labor intensive. Multiple recruitment and retention strategies are required to ensure an adequate sample of community-dwelling stroke survivors. Many of these strategies are also relevant for exercise RCTs among adults with other chronic illnesses. Copyright © 2014 National Stroke Association. Published by Elsevier Inc. All rights reserved.

  20. Implications of structural genomics target selection strategies: Pfam5000, whole genome, and random approaches

    Energy Technology Data Exchange (ETDEWEB)

    Chandonia, John-Marc; Brenner, Steven E.

    2004-07-14

    The structural genomics project is an international effort to determine the three-dimensional shapes of all important biological macromolecules, with a primary focus on proteins. Target proteins should be selected according to a strategy which is medically and biologically relevant, of good value, and tractable. As an option to consider, we present the Pfam5000 strategy, which involves selecting the 5000 most important families from the Pfam database as sources for targets. We compare the Pfam5000 strategy to several other proposed strategies that would require similar numbers of targets. These include including complete solution of several small to moderately sized bacterial proteomes, partial coverage of the human proteome, and random selection of approximately 5000 targets from sequenced genomes. We measure the impact that successful implementation of these strategies would have upon structural interpretation of the proteins in Swiss-Prot, TrEMBL, and 131 complete proteomes (including 10 of eukaryotes) from the Proteome Analysis database at EBI. Solving the structures of proteins from the 5000 largest Pfam families would allow accurate fold assignment for approximately 68 percent of all prokaryotic proteins (covering 59 percent of residues) and 61 percent of eukaryotic proteins (40 percent of residues). More fine-grained coverage which would allow accurate modeling of these proteins would require an order of magnitude more targets. The Pfam5000 strategy may be modified in several ways, for example to focus on larger families, bacterial sequences, or eukaryotic sequences; as long as secondary consideration is given to large families within Pfam, coverage results vary only slightly. In contrast, focusing structural genomics on a single tractable genome would have only a limited impact in structural knowledge of other proteomes: a significant fraction (about 30-40 percent of the proteins, and 40-60 percent of the residues) of each proteome is classified in small

  1. 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.

  2. Implementation of client versus care-provider strategies to improve external cephalic version rates: a cluster randomized controlled trial

    NARCIS (Netherlands)

    Vlemmix, F.; Rosman, A.N.; Rijnders, M.E.; Beuckens, A.; Opmeer, B.C.; Mol, B.W.J.; Kok, M.; Fleuren, M.A.H.

    2015-01-01

    Onjective: To determine the effectiveness of a client or care-provider strategy to improve the implementation of external cephalic version. Design: Cluster randomized controlled trial.Setting: Twenty-five clusters; hospitals and their referring midwifery practices randomly selected in the

  3. Randomized Trial of MST and ARC in a Two-Level Evidence-Based Treatment Implementation Strategy

    Science.gov (United States)

    Glisson, Charles; Schoenwald, Sonja K.; Hemmelgarn, Anthony; Green, Philip; Dukes, Denzel; Armstrong, Kevin S.; Chapman, Jason E.

    2010-01-01

    Objective: A randomized trial assessed the effectiveness of a 2-level strategy for implementing evidence-based mental health treatments for delinquent youth. Method: A 2 x 2 design encompassing 14 rural Appalachian counties included 2 factors: (a) the random assignment of delinquent youth within each county to a multisystemic therapy (MST) program…

  4. MDC-Analyzer: a novel degenerate primer design tool for the construction of intelligent mutagenesis libraries with contiguous sites.

    Science.gov (United States)

    Tang, Lixia; Wang, Xiong; Ru, Beibei; Sun, Hengfei; Huang, Jian; Gao, Hui

    2014-06-01

    Recent computational and bioinformatics advances have enabled the efficient creation of novel biocatalysts by reducing amino acid variability at hot spot regions. To further expand the utility of this strategy, we present here a tool called Multi-site Degenerate Codon Analyzer (MDC-Analyzer) for the automated design of intelligent mutagenesis libraries that can completely cover user-defined randomized sequences, especially when multiple contiguous and/or adjacent sites are targeted. By initially defining an objective function, the possible optimal degenerate PCR primer profiles could be automatically explored using the heuristic approach of Greedy Best-First-Search. Compared to the previously developed DC-Analyzer, MDC-Analyzer allows for the existence of a small amount of undesired sequences as a tradeoff between the number of degenerate primers and the encoded library size while still providing all the benefits of DC-Analyzer with the ability to randomize multiple contiguous sites. MDC-Analyzer was validated using a series of randomly generated mutation schemes and experimental case studies on the evolution of halohydrin dehalogenase, which proved that the MDC methodology is more efficient than other methods and is particularly well-suited to exploring the sequence space of proteins using data-driven protein engineering strategies.

  5. REPLACR-mutagenesis, a one-step method for site-directed mutagenesis by recombineering

    National Research Council Canada - National Science Library

    Trehan, Ashutosh; Kiełbus, Michał; Czapinski, Jakub; Stepulak, Andrzej; Huhtaniemi, Ilpo; Rivero-Müller, Adolfo

    2016-01-01

    .... Most of the current methods for mutagenesis involve multiple step procedures. One of the most accurate methods for genetically altering DNA is recombineering, which uses bacteria expressing viral recombination proteins...

  6. Strategies to enhance venous thromboprophylaxis in hospitalized medical patients (SENTRY: a pilot cluster randomized trial

    Directory of Open Access Journals (Sweden)

    Pai Menaka

    2013-01-01

    Full Text Available Abstract Background Venous thromboembolism (VTE is a common preventable cause of mortality in hospitalized medical patients. Despite rigorous randomized trials generating strong recommendations for anticoagulant use to prevent VTE, nearly 40% of medical patients receive inappropriate thromboprophylaxis. Knowledge-translation strategies are needed to bridge this gap. Methods We conducted a 16-week pilot cluster randomized controlled trial (RCT to determine the proportion of medical patients that were appropriately managed for thromboprophylaxis (according to the American College of Chest Physician guidelines within 24 hours of admission, through the use of a multicomponent knowledge-translation intervention. Our primary goal was to determine the feasibility of conducting this study on a larger scale. The intervention comprised clinician education, a paper-based VTE risk assessment algorithm, printed physicians’ orders, and audit and feedback sessions. Medical wards at six hospitals (representing clusters in Ontario, Canada were included; three were randomized to the multicomponent intervention and three to usual care (i.e., no active strategies for thromboprophylaxis in place. Blinding was not used. Results A total of 2,611 patients (1,154 in the intervention and 1,457 in the control group were eligible and included in the analysis. This multicomponent intervention did not lead to a significant difference in appropriate VTE prophylaxis rates between intervention and control hospitals (appropriate management rate odds ratio = 0.80; 95% confidence interval: 0.50, 1.28; p = 0.36; intra-class correlation coefficient: 0.022, and thus was not considered feasible. Major barriers to effective knowledge translation were poor attendance by clinical staff at education and feedback sessions, difficulty locating preprinted orders, and lack of involvement by clinical and administrative leaders. We identified several factors that may increase uptake of a VTE

  7. Mariner-based transposon mutagenesis for Bacteroides species.

    Science.gov (United States)

    Ichimura, Minoru; Uchida, Keiko; Nakayama-Imaohji, Haruyuki; Hirakawa, Hideki; Tada, Tomoyo; Morita, Hidetoshi; Yasutomo, Koji; Okazaki, Katsuichiro; Kuwahara, Tomomi

    2014-06-01

    Bacteroides is one of the most predominant groups of human gut microbiota. Recent metagenomic analyses and studies on gnotobiotic mice demonstrated the tight association of Bacteroides with epithelial function, the gut immune system and systemic metabolism in the host. The mariner family transposon shows relatively low target site specificity and has hosts ranging from prokaryotes to eukaryotes. Thereby, random mutagenesis using the mariner family transposon is expected to identify key molecules for human-Bacteroides symbiosis. In this study, we constructed the plasmid pMI07 to deliver the gene cassette (ermF/ITR), which harbors the erythromycin resistant marker (ermF) and the inverted repeat sequences (ITRs) recognized by Himar1 transposase, to Bacteroides via electrotransformation. pMI07 successfully delivered ermF/ITR to the Bacteroides genomes and generated thousands of insertion mutants/μg of pMI07 in B. thetaiotaomicron, B. fragilis, B. ovatus, and also, although to a lesser extent, B. vulgatus. Analyses of the ermF/ITR insertion sites in B. thetaiotaomicron and B. vulgatus revealed that the cassette targeted the dinucleotide TA and integrated into the genomes in an unbiased manner. The data reported here will provide useful information for transposon mutagenesis in Bacteroides species, which will enable identification of the genes responsible for their unique phenotypes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Implementing school nursing strategies to reduce LGBTQ adolescent suicide: a randomized cluster trial study protocol.

    Science.gov (United States)

    Willging, Cathleen E; Green, Amy E; Ramos, Mary M

    2016-10-22

    Reducing youth suicide in the United States (U.S.) is a national public health priority, and lesbian, gay, bisexual, transgender, and queer or questioning (LGBTQ) youth are at elevated risk. The Centers for Disease Control and Prevention (CDC) endorses six evidence-based (EB) strategies that center on meeting the needs of LGBTQ youth in schools; however, fewer than 6 % of U.S. schools implement all of them. The proposed intervention model, "RLAS" (Implementing School Nursing Strategies to Reduce LGBTQ Adolescent Suicide), builds on the Exploration, Preparation, Implementation, and Sustainment (EPIS) conceptual framework and the Dynamic Adaptation Process (DAP) to implement EB strategies in U.S. high schools. The DAP accounts for the multilevel context of school settings and uses Implementation Resource Teams (IRTs) to facilitate appropriate expertise, advise on acceptable adaptations, and provide data feedback to make schools implementation ready and prepared to sustain changes. Mixed methods will be used to examine individual, school, and community factors influencing both implementation process and youth outcomes. A cluster randomized controlled trial will assess whether LGBTQ students and their peers in RLAS intervention schools (n = 20) report reductions in suicidality, depression, substance use, bullying, and truancy related to safety concerns compared to those in usual care schools (n = 20). Implementation progress and fidelity for each EB strategy in RLAS intervention schools will be examined using a modified version of the Stages of Implementation Completion checklist. During the implementation and sustainment phases, annual focus groups will be conducted with the 20 IRTs to document their experiences identifying and advancing adaptation supports to facilitate use of EB strategies and their perceptions of the DAP. The DAP represents a data-informed, collaborative, multiple stakeholder approach to progress from exploration to sustainment and obtain

  9. Implementing school nursing strategies to reduce LGBTQ adolescent suicide: a randomized cluster trial study protocol

    Directory of Open Access Journals (Sweden)

    Cathleen E. Willging

    2016-10-01

    Full Text Available Abstract Background Reducing youth suicide in the United States (U.S. is a national public health priority, and lesbian, gay, bisexual, transgender, and queer or questioning (LGBTQ youth are at elevated risk. The Centers for Disease Control and Prevention (CDC endorses six evidence-based (EB strategies that center on meeting the needs of LGBTQ youth in schools; however, fewer than 6 % of U.S. schools implement all of them. The proposed intervention model, “RLAS” (Implementing School Nursing Strategies to Reduce LGBTQ Adolescent Suicide, builds on the Exploration, Preparation, Implementation, and Sustainment (EPIS conceptual framework and the Dynamic Adaptation Process (DAP to implement EB strategies in U.S. high schools. The DAP accounts for the multilevel context of school settings and uses Implementation Resource Teams (IRTs to facilitate appropriate expertise, advise on acceptable adaptations, and provide data feedback to make schools implementation ready and prepared to sustain changes. Methods/Design Mixed methods will be used to examine individual, school, and community factors influencing both implementation process and youth outcomes. A cluster randomized controlled trial will assess whether LGBTQ students and their peers in RLAS intervention schools (n = 20 report reductions in suicidality, depression, substance use, bullying, and truancy related to safety concerns compared to those in usual care schools (n = 20. Implementation progress and fidelity for each EB strategy in RLAS intervention schools will be examined using a modified version of the Stages of Implementation Completion checklist. During the implementation and sustainment phases, annual focus groups will be conducted with the 20 IRTs to document their experiences identifying and advancing adaptation supports to facilitate use of EB strategies and their perceptions of the DAP. Discussion The DAP represents a data-informed, collaborative, multiple stakeholder

  10. A Cluster-Randomized Trial of Two Strategies to Improve Antibiotic Use for Patients with a Complicated Urinary Tract Infection

    NARCIS (Netherlands)

    Spoorenberg, Veroniek; Hulscher, Marlies E. J. L.; Geskus, Ronald B.; de Reijke, Theo M.; Opmeer, Brent C.; Prins, Jan M.; Geerlings, Suzanne E.

    2015-01-01

    Up to 50% of hospital antibiotic use is inappropriate and therefore improvement strategies are urgently needed. We compared the effectiveness of two strategies to improve the quality of antibiotic use in patients with a complicated urinary tract infection (UTI). In a multicentre, cluster-randomized

  11. The Effect of Different Types of Monitoring Strategies on Weight Loss: A Randomized Controlled Trial.

    Science.gov (United States)

    Jospe, Michelle R; Roy, Melyssa; Brown, Rachel C; Williams, Sheila M; Osborne, Hamish R; Meredith-Jones, Kim A; McArthur, Jenny R; Fleming, Elizabeth A; Taylor, Rachael W

    2017-09-01

    To determine the effectiveness of various monitoring strategies on weight loss, body composition, blood markers, exercise, and psychosocial indices in adults with overweight and obesity following a 12-month weight loss program. Two hundred fifty adults with BMI ≥ 27 were randomized to brief, monthly, individual consults, daily self-monitoring of weight, self-monitoring of diet using MyFitnessPal, self-monitoring of hunger, or control over 12 months. All groups received diet and exercise advice, and 171 participants (68.4%) remained at 12 months. No significant differences in weight, body composition, blood markers, exercise, or eating behavior were apparent between those in the four monitoring groups and the control condition at 12 months (all P ≥ 0.053). Weight differences between groups ranged from -1.1 kg (-3.8 to 1.6) to 2.2 kg (-1.0 to 5.3). However, brief support and hunger training groups reported significantly lower scores for depression (difference [95% CI]: -3.16 [-5.70 to -0.62] and -3.05 [-5.61 to -0.50], respectively) and anxiety (-1.84, [-3.67 to -0.02]) scores than control participants. Although adding a monitoring strategy to diet and exercise advice did not further increase weight loss, no adverse effects on eating behavior were observed, and some monitoring strategies may even benefit mental health. © 2017 The Obesity Society.

  12. Equilibrium Model of Discrete Dynamic Supply Chain Network with Random Demand and Advertisement Strategy

    Directory of Open Access Journals (Sweden)

    Guitao Zhang

    2014-01-01

    Full Text Available The advertisement can increase the consumers demand; therefore it is one of the most important marketing strategies in the operations management of enterprises. This paper aims to analyze the impact of advertising investment on a discrete dynamic supply chain network which consists of suppliers, manufactures, retailers, and demand markets associated at different tiers under random demand. The impact of advertising investment will last several planning periods besides the current period due to delay effect. Based on noncooperative game theory, variational inequality, and Lagrange dual theory, the optimal economic behaviors of the suppliers, the manufactures, the retailers, and the consumers in the demand markets are modeled. In turn, the supply chain network equilibrium model is proposed and computed by modified project contraction algorithm with fixed step. The effectiveness of the model is illustrated by numerical examples, and managerial insights are obtained through the analysis of advertising investment in multiple periods and advertising delay effect among different periods.

  13. Cerebral collateral therapeutics in acute ischemic stroke: A randomized preclinical trial of four modulation strategies.

    Science.gov (United States)

    Beretta, Simone; Versace, Alessandro; Carone, Davide; Riva, Matteo; Dell'Era, Valentina; Cuccione, Elisa; Cai, Ruiyao; Monza, Laura; Pirovano, Silvia; Padovano, Giada; Stiro, Fabio; Presotto, Luca; Paternò, Giovanni; Rossi, Emanuela; Giussani, Carlo; Sganzerla, Erik P; Ferrarese, Carlo

    2017-10-01

    Cerebral collaterals are dynamically recruited after arterial occlusion and highly affect tissue outcome in acute ischemic stroke. We investigated the efficacy and safety of four pathophysiologically distinct strategies for acute modulation of collateral flow (collateral therapeutics) in the rat stroke model of transient middle cerebral artery (MCA) occlusion. A composed randomization design was used to assign rats (n = 118) to receive phenylephrine (induced hypertension), polygeline (intravascular volume load), acetazolamide (cerebral arteriolar vasodilation), head down tilt (HDT) 15° (cerebral blood flow diversion), or no treatment, starting 30 min after MCA occlusion. Compared to untreated animals, treatment with collateral therapeutics was associated with lower infarct volumes (62% relative mean difference; 51.57 mm3 absolute mean difference; p therapy.

  14. Evaluation of vaccination strategies for SIR epidemics on random networks incorporating household structure

    CERN Document Server

    Ball, Frank

    2016-01-01

    This paper is concerned with the analysis of vaccination strategies in a stochastic SIR (susceptible $\\to$ infected $\\to$ removed) model for the spread of an epidemic amongst a population of individuals with a random network of social contacts that is also partitioned into households. Under various vaccine action models, we consider both household-based vaccination schemes, in which the way in which individuals are chosen for vaccination depends on the size of the households in which they reside, and acquaintance vaccination, which targets individuals of high degree in the social network. For both types of vaccination scheme, assuming a large population with few initial infectives, we derive a threshold parameter which determines whether or not a large outbreak can occur and also the probability and fraction of the population infected by such an outbreak. The performance of these schemes is studied numerically, focusing on the influence of the household size distribution and the degree distribution of the soc...

  15. Relevant feature set estimation with a knock-out strategy and random forests

    DEFF Research Database (Denmark)

    Ganz, Melanie; Greve, Douglas N; Fischl, Bruce

    2015-01-01

    Group analysis of neuroimaging data is a vital tool for identifying anatomical and functional variations related to diseases as well as normal biological processes. The analyses are often performed on a large number of highly correlated measurements using a relatively smaller number of samples...... unintuitive and difficult to determine. In this article, we propose a novel MVPA method for group analysis of high-dimensional data that overcomes the drawbacks of the current techniques. Our approach explicitly aims to identify all relevant variations using a "knock-out" strategy and the Random Forest...... algorithm. In evaluations with synthetic datasets the proposed method achieved substantially higher sensitivity and accuracy than the state-of-the-art MVPA methods, and outperformed the univariate approach when the effect size is low. In experiments with real datasets the proposed method identified regions...

  16. A cluster randomized trial of decision support strategies for reducing antibiotic use in acute bronchitis.

    Science.gov (United States)

    Gonzales, Ralph; Anderer, Tammy; McCulloch, Charles E; Maselli, Judith H; Bloom, Frederick J; Graf, Thomas R; Stahl, Melissa; Yefko, Michelle; Molecavage, Julie; Metlay, Joshua P

    2013-02-25

    National quality indicators show little change in the overuse of antibiotics for uncomplicated acute bronchitis. We compared the effect of 2 decision support strategies on antibiotic treatment of uncomplicated acute bronchitis. We conducted a 3-arm cluster randomized trial among 33 primary care practices belonging to an integrated health care system in central Pennsylvania. The printed decision support intervention sites (11 practices) received decision support for acute cough illness through a print-based strategy, the computer-assisted decision support intervention sites (11 practices) received decision support through an electronic medical record-based strategy, and the control sites (11 practices) served as a control arm. Both intervention sites also received clinician education and feedback on prescribing practices, as well as patient education brochures at check-in. Antibiotic prescription rates for uncomplicated acute bronchitis in the winter period (October 1, 2009, through March 31, 2010) following introduction of the intervention were compared with the previous 3 winter periods in an intent-to-treat analysis. Compared with the baseline period, the percentage of adolescents and adults prescribed antibiotics during the intervention period decreased at the printed decision support intervention sites (from 80.0% to 68.3%) and at the computer-assisted decision support intervention sites (from 74.0% to 60.7%) but increased slightly at the control sites (from 72.5% to 74.3%). After controlling for patient and clinician characteristics, as well as clustering of observations by clinician and practice site, the differences for the intervention sites were statistically significant from the control sites (P = .003 for control sites vs printed decision support intervention sites and P = .01 for control sites vs computer-assisted decision support intervention sites) but not between themselves (P = .67 for printed decision support intervention sites vs computer

  17. A randomized controlled trial evaluating the impact of knowledge translation and exchange strategies

    Directory of Open Access Journals (Sweden)

    O'Mara Linda

    2009-09-01

    Full Text Available Abstract Context Significant resources and time are invested in the production of research knowledge. The primary objective of this randomized controlled trial was to evaluate the effectiveness of three knowledge translation and exchange strategies in the incorporation of research evidence into public health policies and programs. Methods This trial was conducted with a national sample of public health departments in Canada from 2004 to 2006. The three interventions, implemented over one year in 2005, included access to an online registry of research evidence; tailored messaging; and a knowledge broker. The primary outcome assessed the extent to which research evidence was used in a recent program decision, and the secondary outcome measured the change in the sum of evidence-informed healthy body weight promotion policies or programs being delivered at health departments. Mixed-effects models were used to test the hypotheses. Findings One hundred and eight of 141 (77% health departments participated in this study. No significant effect of the intervention was observed for primary outcome (p e.g., value placed on research evidence in decision making. Conclusion The results of this study suggest that under certain conditions tailored, targeted messages are more effective than knowledge brokering and access to an online registry of research evidence. Greater emphasis on the identification of organizational factors is needed in order to implement strategies that best meet the needs of individual organizations. Trial Registration The trial registration number and title are as follows: ISRCTN35240937 -- Is a knowledge broker more effective than other strategies in promoting evidence-based physical activity and healthy body weight programming?

  18. Anaesthesiological strategies in elective craniotomy: randomized, equivalence, open trial – The NeuroMorfeo trial

    Directory of Open Access Journals (Sweden)

    Guzzetti Stefano

    2009-04-01

    Full Text Available Abstract Background Many studies have attempted to determine the "best" anaesthetic technique for neurosurgical procedures in patients without intracranial hypertension. So far, no study comparing intravenous (IA with volatile-based neuroanaesthesia (VA has been able to demonstrate major outcome differences nor a superiority of one of the two strategies in patients undergoing elective supratentorial neurosurgery. Therefore, current practice varies and includes the use of either volatile or intravenous anaesthetics in addition to narcotics. Actually the choice of the anaestesiological strategy depends only on the anaesthetists' preferences or institutional policies. This trial, named NeuroMorfeo, aims to assess the equivalence between volatile and intravenous anaesthetics for neurosurgical procedures. Methods/Design NeuroMorfeo is a multicenter, randomized, open label, controlled trial, based on an equivalence design. Patients aged between 18 and 75 years, scheduled for elective craniotomy for supratentorial lesion without signs of intracranial hypertension, in good physical state (ASA I-III and Glasgow Coma Scale (GCS equal to 15, are randomly assigned to one of three anaesthesiological strategies (two VA arms, sevoflurane + fentanyl or sevoflurane + remifentanil, and one IA, propofol + remifentanil. The equivalence between intravenous and volatile-based neuroanaesthesia will be evaluated by comparing the intervals required to reach, after anaesthesia discontinuation, a modified Aldrete score ≥ 9 (primary end-point. Two statistical comparisons have been planned: 1 sevoflurane + fentanyl vs. propofol + remifentanil; 2 sevoflurane + remifentanil vs. propofol + remifentanil. Secondary end-points include: an assessment of neurovegetative stress based on (a measurement of urinary catecholamines and plasma and urinary cortisol and (b estimate of sympathetic/parasympathetic balance by power spectrum analyses of electrocardiographic tracings recorded

  19. 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

    2017-01-01

    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. DOI: http://dx.doi.org/10.7554/eLife.26248.001 PMID:28639938

  20. Condition-Based Conveyor Belt Replacement Strategy in Lignite Mines with Random Belt Deterioration

    Science.gov (United States)

    Blazej, Ryszard; Jurdziak, Leszek

    2017-12-01

    In Polish lignite surface mines, condition-based belt replacement strategies are applied in order to assure profitable refurbishment of worn out belts performed by external firms specializing in belt maintenance. In two of three lignite mines, staff asses belt condition subjectively during visual inspections. Only one mine applies specialized diagnostic device (HRDS) allowing objective magnetic evaluation of belt core condition in order to choose the most profitable moment for the dismantling of worn out belt segments from conveyors and sending them to the maintenance firm which provides their refurbishment. This article describes the advantages of a new diagnostic device called DiagBelt. It was developed at the Faculty of Geoengineering, Mining and Geology, Wroclaw University of Science and Technology. Economic gains from its application are calculated for the lignite mine and for the belt maintenance firm, taking into account random life (durability) of new and reconditioned belts (after the 1st and the 2nd refurbishment). Recursive calculations for following years allow the estimation of the length and costs of replaced, reconditioned and purchased belts on an annual basis, while the use of the Monte Carlo method allows the estimation of their variability caused by random deterioration of belts. Savings are obtained due to better selection of moments (times) for the replacement of belt segments and die to the possibility to qualify worn out belts for refurbishment without the need to remove their covers. In effect, increased belt durability and lowered share of waste belts (which were not qualified for reconditioning) create savings which can quickly cover expenditures on new diagnostic tools and regular belt inspections in the mine.

  1. Renal Insufficiency Following Contrast Media Administration Trial (REMEDIAL): a randomized comparison of 3 preventive strategies.

    Science.gov (United States)

    Briguori, Carlo; Airoldi, Flavio; D'Andrea, Davide; Bonizzoni, Erminio; Morici, Nuccia; Focaccio, Amelia; Michev, Iassen; Montorfano, Matteo; Carlino, Mauro; Cosgrave, John; Ricciardelli, Bruno; Colombo, Antonio

    2007-03-13

    Volume supplementation by saline infusion combined with N-acetylcysteine (NAC) represents an effective strategy to prevent contrast agent-induced nephrotoxicity (CIN). Preliminary data support the concept that sodium bicarbonate and ascorbic acid also may be effective in preventing CIN. Three hundred twenty-six consecutive patients with chronic kidney disease, referred to our institutions for coronary and/or peripheral procedures, were randomly assigned to prophylactic administration of 0.9% saline infusion plus NAC (n=111), sodium bicarbonate infusion plus NAC (n=108), and 0.9% saline plus ascorbic acid plus NAC (n=107). All enrolled patients had serum creatinine > or = 2.0 mg/dL and/or estimated glomerular filtration rate or = 25% in the creatinine concentration 48 hours after the procedure (CIN). The amount of contrast media administered (179+/-102, 169+/-92, and 169+/-94 mL, respectively; P=0.69) and risk scores (9.1+/-3.4, 9.5+/-3.6, and 9.3+/-3.6; P=0.21) were similar in the 3 groups. CIN occurred in 11 of 111 patients (9.9%) in the saline plus NAC group, in 2 of 108 (1.9%) in the bicarbonate plus NAC group (P=0.019 by Fisher exact test versus saline plus NAC group), and in 11 of 107 (10.3%) in the saline plus ascorbic acid plus NAC group (P=1.00 versus saline plus NAC group). The strategy of volume supplementation by sodium bicarbonate plus NAC seems to be superior to the combination of normal saline with NAC alone or with the addition of ascorbic acid in preventing CIN in patients at medium to high risk.

  2. Randomized Controlled Trial Evaluating a Standardized Strategy for Uveitis Etiologic Diagnosis (ULISSE).

    Science.gov (United States)

    de Parisot, Audrey; Kodjikian, Laurent; Errera, Marie-Hélène; Sedira, Neila; Heron, Emmanuel; Pérard, Laurent; Cornut, Pierre-Loïc; Schneider, Christelle; Rivière, Sophie; Ollé, Priscille; Pugnet, Grégory; Cathébras, Pascal; Manoli, Pierre; Bodaghi, Bahram; Saadoun, David; Baillif, Stéphanie; Tieulie, Nathalie; Andre, Marc; Chiambaretta, Frédéric; Bonin, Nicolas; Bielefeld, Philip; Bron, Alain; Mouriaux, Frédéric; Bienvenu, Boris; Vicente, Stéphanie; Bin, Sylvie; Broussolle, Christiane; Decullier, Evelyne; Sève, Pascal

    2017-06-01

    To prospectively assess the efficiency of a standardized diagnostic approach, compared to an open strategy, for the etiologic diagnosis of uveitis. Noninferiority, prospective, multicenter, clustered randomized controlled trial. Consecutive patients with uveitis, who visited 1 of the participating departments of ophthalmology, were included. In the standardized group, all patients had a minimal evaluation regardless of the type of uveitis (complete blood count, erythrocyte sedimentation rate, C-reactive protein, tuberculin skin test, syphilis serology, and chest radiograph) followed by more complex investigations according to ophthalmologic findings. In the open group, the ophthalmologist could order any type of investigation. Main outcome was the percentage of etiologic diagnoses at 6 months. Nine hundred and three patients with uveitis were included from January 2010 to May 2013 and the per-protocol population comprised 676 patients (open 373; standardized 303). Mean age at diagnosis was 46 years. Anatomic distribution of uveitis was as follows: anterior (60.8% and 72.3%, P = .0017), intermediate (11.7% and 12.3%, P = .8028), posterior (17.8% and 8.2%, P = .0004), and panuveitis (15.3% and 15.2%, P = .9596). An etiologic diagnosis was established in 54.4% of cases in the open group and 49.5% in the standardized group (P = .2029). The difference between both strategies (standardized minus open) was -4.9% (95% CI [-12.5%; 2.6%]). There were more investigations in the open group than in the standardized group (5371 vs 3759, P uveitis, although its noninferiority cannot be proved. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Perspective on mutagenesis and repair: the standard model and alternate modes of mutagenesis.

    Science.gov (United States)

    Miller, Jeffrey H

    2005-01-01

    The basic ideas of replication, mutagenesis, and repair have outlined a picture of how point mutations occur that has provided a valuable framework for theory and experiment, much as the Standard Model of particle physics has done for our concept of fundamental particles. However, alternative modes of mutagenesis are being defined that are changing our perspective of the "Standard Model" of mutagenesis, requiring an expanded model. The genome is now envisioned as being in dynamic equilibrium between a multitude of forces for mutational change and forces that counteract such change. By maintaining a delicate balance between these forces, cells avoid unwanted or excessive mutations. Yet, cells allow mutagenesis to occur under certain conditions. We can define an emerging paradigm. Namely, mechanisms exist that can direct point mutations to specific designated genes or regions of genes. In some cases, this is achieved by specific enzymes, and in other cases high mutability is programmed into the sequence of certain genes to help generate diversity. In yet additional cases, general mutability is increased under stress, and selective forces allow the recovery of favorable mutants.

  4. Metaphor use and health literacy: a pilot study of strategies to explain randomization in cancer clinical trials.

    Science.gov (United States)

    Krieger, Janice L; Parrott, Roxanne L; Nussbaum, Jon F

    2011-01-01

    Patients often have difficulty understanding what randomization is and why it is needed in Phase III clinical trials. Physicians commonly report using metaphorical language to convey the role of chance in being assignment to treatment; however, the effectiveness of this strategy as an educational tool has not been explored. Guided by W. McGuire's (1972) information-processing model, the purpose of this pilot study was to explore effects of metaphors to explain randomization on message acceptance and behavioral intention to participate in a Phase III clinical trial among a sample of low-income, rural women (N = 64). Participants were randomly assigned to watch a video that explained randomization using 1 of 3 message strategies: a low-literacy definition, standard metaphor (i.e., flip of a coin), or a culturally derived metaphor (i.e., sex of a baby). The influence of attention on behavioral intentions to participate in clinical trials was partially moderated by message strategy. Under conditions of low attention, participants in the culturally derived metaphor condition experienced significantly higher intentions to participate in clinical trials compared with participants in the standard metaphor condition. However, as attention increased, differences in intentions among the conditions diminished. Having a positive affective response to the randomization message was a strong, positive predictor of behavioral intentions to participate in clinical trials. The authors discuss the theoretical and practical implications of these findings.

  5. Efficacy of the Lexicon Pirate Strategy Therapy for Improving Lexical Learning in School-Age Children: A Randomized Controlled Trial

    Science.gov (United States)

    Motsch, Hans-Joachim; Marks, Dana-Kristin

    2015-01-01

    Lexicon Pirate was originally developed as a strategy intervention programme to treat lexical disorders of pre-school children. To evaluate the therapy's effectiveness for school-age students, a randomized controlled trial (RCT, N = 157) was conducted. Based on a pre--post-test design, the programme's impacts were compared with a control group…

  6. A randomized controlled trial of two primary school intervention strategies to prevent early onset tobacco smoking.

    Science.gov (United States)

    Storr, Carla L; Ialongo, Nicholas S; Kellam, Sheppard G; Anthony, James C

    2002-03-01

    In this article, we examine the impact of two universal, grade 1 preventive interventions on the onset of tobacco smoking as assessed in early adolescence. The classroom-centered (CC) intervention was designed to reduce the risk for tobacco smoking by enhancing teachers' behavior management skills in first grade and, thereby, reducing child attention problems and aggressive and shy behavior-known risk behaviors for later substance use. The family-school partnership (FSP) intervention targeted these early risk behaviors via improvements in parent-teacher communication and parents' child behavior management strategies. A cohort of 678 urban, predominately African-American, public school students were randomly assigned to one of three Grade 1 classrooms at entrance to primary school (age 6). One classroom featured the CC intervention, a second the FSP intervention, and the third served as a control classroom. Six years later, 81% of the students completed audio computer-assisted self-interviews. Relative to controls, a modest attenuation in the risk of smoking initiation was found for students who had been assigned to either the CC or FSP intervention classrooms (26% versus 33%) (adjusted relative risk for CC/control contrast=0.57, 95% confidence interval (CI), 0.34-0.96; adjusted relative risk for FSP/control contrast=0.69, 95% CI, 0.50-0.97). Results lend support to targeting the early antecedent risk behaviors for tobacco smoking.

  7. From classical mutagenesis to nuclease-based breeding - directing natural DNA repair for a natural end-product.

    Science.gov (United States)

    Pacher, Michael; Puchta, Holger

    2017-05-01

    Production of mutants of crop plants by the use of chemical or physical genotoxins has a long tradition. These factors induce the natural DNA repair machinery to repair damage in an error-prone way. In the case of radiation, multiple double-strand breaks (DSBs) are induced randomly in the genome, leading in very rare cases to a desirable phenotype. In recent years the use of synthetic, site-directed nucleases (SDNs) - also referred to as sequence-specific nucleases - like the CRISPR/Cas system has enabled scientists to use exactly the same naturally occurring DNA repair mechanisms for the controlled induction of genomic changes at pre-defined sites in plant genomes. As these changes are not necessarily associated with the permanent integration of foreign DNA, the obtained organisms per se cannot be regarded as genetically modified as there is no way to distinguish them from natural variants. This applies to changes induced by DSBs as well as single-strand breaks, and involves repair by non-homologous end-joining and homologous recombination. The recent development of SDN-based 'DNA-free' approaches makes mutagenesis strategies in classical breeding indistinguishable from SDN-derived targeted genome modifications, even in regard to current regulatory rules. With the advent of new SDN technologies, much faster and more precise genome editing becomes available at reasonable cost, and potentially without requiring time-consuming deregulation of newly created phenotypes. This review will focus on classical mutagenesis breeding and the application of newly developed SDNs in order to emphasize similarities in the context of the regulatory situation for genetically modified crop plants. © 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

  8. Efficacy of a Maternal Depression Prevention Strategy in Head Start: A Randomized Clinical Trial.

    Science.gov (United States)

    Silverstein, Michael; Diaz-Linhart, Yaminette; Cabral, Howard; Beardslee, William; Hegel, Mark; Haile, Winta; Sander, Jenna; Patts, Gregory; Feinberg, Emily

    2017-08-01

    Low-income and minority mothers experience a disproportionate incidence of depression and lack access to treatment services. Development of prevention strategies in accessible community-based venues is a potentially important public health strategy. To determine the efficacy of a depression prevention strategy embedded in Head Start. This randomized clinical trial was performed from February 15, 2011, through May 9, 2016, at 6 Head Start agencies serving families at or below the federal poverty level. Participants included mothers with depressed mood, anhedonia, or depression history but who were not in a current major depressive episode. Participants were followed up for 12 months with masked outcome assessments. Final follow-up was completed on May 9, 2016. Participants were randomized to a problem-solving education (PSE) intervention (n = 111) or usual Head Start services (n = 119). Primary outcomes were problem-solving skills and depressive symptoms. To capture the chronicity and intensity of symptoms, the Quick Inventory of Depressive Symptoms was administered bimonthly, and rates of clinically significant symptom elevations were compared across groups. Secondarily, the presence of a major depressive episode was assessed using the Structured Clinical Interview for DSM-IV Axis I Disorders. Among the 230 participants, 152 (66.1%) were Hispanic, with a mean (SD) age of 31.4 (7.3) years. An intention-to-treat analysis among 223 participants contributing follow-up data found no differences in problem-solving skills across groups. The mean (SD) number of depressive symptom elevations among the PSE participants was 0.84 (1.39) compared with 1.12 (1.47) among the usual service participants (adjusted incident rate ratio [aIRR], 0.60; 95% CI, 0.41-0.90). In analyses stratified according to baseline depressive symptoms, PSE exerted a preventive effect among those with lower-level baseline symptoms, with a mean (SD) of 0.39 (0.84) elevations among PSE participants

  9. Best strategies to implement clinical pathways in an emergency department setting: study protocol for a cluster randomized controlled trial.

    Science.gov (United States)

    Jabbour, Mona; Curran, Janet; Scott, Shannon D; Guttman, Astrid; Rotter, Thomas; Ducharme, Francine M; Lougheed, M Diane; McNaughton-Filion, M Louise; Newton, Amanda; Shafir, Mark; Paprica, Alison; Klassen, Terry; Taljaard, Monica; Grimshaw, Jeremy; Johnson, David W

    2013-05-22

    The clinical pathway is a tool that operationalizes best evidence recommendations and clinical practice guidelines in an accessible format for 'point of care' management by multidisciplinary health teams in hospital settings. While high-quality, expert-developed clinical pathways have many potential benefits, their impact has been limited by variable implementation strategies and suboptimal research designs. Best strategies for implementing pathways into hospital settings remain unknown. This study will seek to develop and comprehensively evaluate best strategies for effective local implementation of externally developed expert clinical pathways. We will develop a theory-based and knowledge user-informed intervention strategy to implement two pediatric clinical pathways: asthma and gastroenteritis. Using a balanced incomplete block design, we will randomize 16 community emergency departments to receive the intervention for one clinical pathway and serve as control for the alternate clinical pathway, thus conducting two cluster randomized controlled trials to evaluate this implementation intervention. A minimization procedure will be used to randomize sites. Intervention sites will receive a tailored strategy to support full clinical pathway implementation. We will evaluate implementation strategy effectiveness through measurement of relevant process and clinical outcomes. The primary process outcome will be the presence of an appropriately completed clinical pathway on the chart for relevant patients. Primary clinical outcomes for each clinical pathway include the following: Asthma--the proportion of asthmatic patients treated appropriately with corticosteroids in the emergency department and at discharge; and Gastroenteritis--the proportion of relevant patients appropriately treated with oral rehydration therapy. Data sources include chart audits, administrative databases, environmental scans, and qualitative interviews. We will also conduct an overall process

  10. Cloning and mutagenesis of a herpesvirus genome as an infectious bacterial artificial chromosome

    OpenAIRE

    Messerle, Martin; Crnkovic, Irena; Hammerschmidt, Wolfgang; Ziegler, Heike; Koszinowski, Ulrich H

    1997-01-01

    A strategy for cloning and mutagenesis of an infectious herpesvirus genome is described. The mouse cytomegalovirus genome was cloned and maintained as a 230 kb bacterial artificial chromosome (BAC) in E. coli. Transfection of the BAC plasmid into eukaryotic cells led to a productive virus infection. The feasibility to introduce targeted mutations into the BAC cloned virus genome was shown by mutation of the immediate-early 1 gene and generation of a mutant virus. Thus, the complete constructi...

  11. A cluster randomized controlled trial of the Promoting Alternative Thinking Strategies (PATHS) curriculum.

    Science.gov (United States)

    Humphrey, Neil; Barlow, Alexandra; Wigelsworth, Michael; Lendrum, Ann; Pert, Kirsty; Joyce, Craig; Stephens, Emma; Wo, Lawrence; Squires, Garry; Woods, Kevin; Calam, Rachel; Turner, Alex

    2016-10-01

    This randomized controlled trial (RCT) evaluated the efficacy of the Promoting Alternative Thinking Strategies curriculum (PATHS; Kusche & Greenberg, 1994) as a means to improve children's social-emotional competence (assessed via the Social Skills Improvement System (SSIS); Gresham & Elliot, 2008) and mental health outcomes (assessed via the Strengths and Difficulties Questionnaire (SDQ); Goodman, 1997). Forty-five schools in Greater Manchester, England, were randomly assigned to treatment and control groups. Allocation was balanced by proportions of children eligible for free school meals and speaking English as an additional language via minimization. Children (N=4516) aged 7-9years at baseline in the participating schools were the target cohort. During the two-year trial period, teachers of this cohort in schools allocated to the intervention group delivered the PATHS curriculum, while their counterparts in the control group continued their usual provision. Teachers in PATHS schools received initial training and on-going support and assistance from trained coaches. Hierarchical linear modeling of outcome data was undertaken to identify both primary (e.g., for all children) and secondary (e.g., for children classified as "at-risk") intervention effects. A primary effect of the PATHS curriculum was found, demonstrating increases in teacher ratings of changes in children's social-emotional competence. Additionally, secondary effects of PATHS were identified, showing reductions in teacher ratings of emotional symptoms and increases in pro-social behavior and child ratings of engagement among children identified as at-risk at baseline. However, our analyses also identified primary effects favoring the usual provision group, showing reductions in teacher ratings of peer problems and emotional symptoms, and secondary effects demonstrating reductions in teacher ratings of conduct problems and child ratings of co-operation among at-risk children. Effect sizes were small

  12. Biomarker-based strategy for early discontinuation of empirical antifungal treatment in critically ill patients: a randomized controlled trial.

    Science.gov (United States)

    Rouzé, Anahita; Loridant, Séverine; Poissy, Julien; Dervaux, Benoit; Sendid, Boualem; Cornu, Marjorie; Nseir, Saad

    2017-11-01

    The aim of this study was to determine the impact of a biomarker-based strategy on early discontinuation of empirical antifungal treatment. Prospective randomized controlled single-center unblinded study, performed in a mixed ICU. A total of 110 patients were randomly assigned to a strategy in which empirical antifungal treatment duration was determined by (1,3)-β-D-glucan, mannan, and anti-mannan serum assays, performed on day 0 and day 4; or to a routine care strategy, based on international guidelines, which recommend 14 days of treatment. In the biomarker group, early stop recommendation was determined using an algorithm based on the results of biomarkers. The primary outcome was the percentage of survivors discontinuing empirical antifungal treatment early, defined as a discontinuation strictly before day 7. A total of 109 patients were analyzed (one patient withdraw consent). Empirical antifungal treatment was discontinued early in 29 out of 54 patients in the biomarker strategy group, compared with one patient out of 55 in the routine strategy group [54% vs 2%, p empirical antifungal treatment among critically ill patients with suspected invasive Candida infection. These results confirm previous findings suggesting that early discontinuation of empirical antifungal treatment had no negative impact on outcome. However, further studies are needed to confirm the safety of this strategy. This trial was registered at ClinicalTrials.gov, NCT02154178.

  13. Testing the implementation and sustainment facilitation (ISF strategy as an effective adjunct to the Addiction Technology Transfer Center (ATTC strategy: study protocol for a cluster randomized trial

    Directory of Open Access Journals (Sweden)

    Bryan R. Garner

    2017-11-01

    Full Text Available Abstract Background Improving the extent to which evidence-based practices (EBPs—treatments that have been empirically shown to be efficacious or effective—are integrated within routine practice is a well-documented challenge across numerous areas of health. In 2014, the National Institute on Drug Abuse funded a type 2 effectiveness–implementation hybrid trial titled the substance abuse treatment to HIV Care (SAT2HIV Project. Aim 1 of the SAT2HIV Project tests the effectiveness of a motivational interviewing-based brief intervention (MIBI for substance use as an adjunct to usual care within AIDS service organizations (ASOs as part of its MIBI Experiment. Aim 2 of the SAT2HIV Project tests the effectiveness of implementation and sustainment facilitation (ISF as an adjunct to the Addiction Technology Transfer Center (ATTC model for training staff in motivational interviewing as part of its ISF Experiment. The current paper describes the study protocol for the ISF Experiment. Methods Using a cluster randomized design, case management and leadership staff from 39 ASOs across the United States were randomized to receive either the ATTC strategy (control condition or the ATTC + ISF strategy (experimental condition. The ATTC strategy is staff-focused and includes 10 discrete strategies (e.g., provide centralized technical assistance, conduct educational meetings, provide ongoing consultation. The ISF strategy is organization-focused and includes seven discrete strategies (e.g., use an implementation advisor, organize implementation team meetings, conduct cyclical small tests of change. Building upon the exploration–preparation–implementation–sustainment (EPIS framework, the effectiveness of the ISF strategy is examined via three staff-level measures: (1 time-to-proficiency (i.e., preparation phase outcome, (2 implementation effectiveness (i.e., implementation phase outcome, and (3 level of sustainment (i.e., sustainment phase outcome

  14. Testing the implementation and sustainment facilitation (ISF) strategy as an effective adjunct to the Addiction Technology Transfer Center (ATTC) strategy: study protocol for a cluster randomized trial.

    Science.gov (United States)

    Garner, Bryan R; Zehner, Mark; Roosa, Mathew R; Martino, Steve; Gotham, Heather J; Ball, Elizabeth L; Stilen, Patricia; Speck, Kathryn; Vandersloot, Denna; Rieckmann, Traci R; Chaple, Michael; Martin, Erika G; Kaiser, David; Ford, James H

    2017-11-17

    Improving the extent to which evidence-based practices (EBPs)-treatments that have been empirically shown to be efficacious or effective-are integrated within routine practice is a well-documented challenge across numerous areas of health. In 2014, the National Institute on Drug Abuse funded a type 2 effectiveness-implementation hybrid trial titled the substance abuse treatment to HIV Care (SAT2HIV) Project. Aim 1 of the SAT2HIV Project tests the effectiveness of a motivational interviewing-based brief intervention (MIBI) for substance use as an adjunct to usual care within AIDS service organizations (ASOs) as part of its MIBI Experiment. Aim 2 of the SAT2HIV Project tests the effectiveness of implementation and sustainment facilitation (ISF) as an adjunct to the Addiction Technology Transfer Center (ATTC) model for training staff in motivational interviewing as part of its ISF Experiment. The current paper describes the study protocol for the ISF Experiment. Using a cluster randomized design, case management and leadership staff from 39 ASOs across the United States were randomized to receive either the ATTC strategy (control condition) or the ATTC + ISF strategy (experimental condition). The ATTC strategy is staff-focused and includes 10 discrete strategies (e.g., provide centralized technical assistance, conduct educational meetings, provide ongoing consultation). The ISF strategy is organization-focused and includes seven discrete strategies (e.g., use an implementation advisor, organize implementation team meetings, conduct cyclical small tests of change). Building upon the exploration-preparation-implementation-sustainment (EPIS) framework, the effectiveness of the ISF strategy is examined via three staff-level measures: (1) time-to-proficiency (i.e., preparation phase outcome), (2) implementation effectiveness (i.e., implementation phase outcome), and (3) level of sustainment (i.e., sustainment phase outcome). Although not without limitations, the ISF

  15. Personalized versus standardized dosing strategies for the treatment of childhood amblyopia: study protocol for a randomized controlled trial.

    Science.gov (United States)

    Moseley, Merrick J; Wallace, Michael P; Stephens, David A; Fielder, Alistair R; Smith, Laura C; Stewart, Catherine E

    2015-04-25

    Amblyopia is the commonest visual disorder of childhood in Western societies, affecting, predominantly, spatial visual function. Treatment typically requires a period of refractive correction ('optical treatment') followed by occlusion: covering the nonamblyopic eye with a fabric patch for varying daily durations. Recent studies have provided insight into the optimal amount of patching ('dose'), leading to the adoption of standardized dosing strategies, which, though an advance on previous ad-hoc regimens, take little account of individual patient characteristics. This trial compares the effectiveness of a standardized dosing strategy (that is, a fixed daily occlusion dose based on disease severity) with a personalized dosing strategy (derived from known treatment dose-response functions), in which an initially prescribed occlusion dose is modulated, in a systematic manner, dependent on treatment compliance. A total of 120 children aged between 3 and 8 years of age diagnosed with amblyopia in association with either anisometropia or strabismus, or both, will be randomized to receive either a standardized or a personalized occlusion dose regimen. To avoid confounding by the known benefits of refractive correction, participants will not be randomized until they have completed an optical treatment phase. The primary study objective is to determine whether, at trial endpoint, participants receiving a personalized dosing strategy require fewer hours of occlusion than those in receipt of a standardized dosing strategy. Secondary objectives are to quantify the relationship between observed changes in visual acuity (logMAR, logarithm of the Minimum Angle of Resolution) with age, amblyopia type, and severity of amblyopic visual acuity deficit. This is the first randomized controlled trial of occlusion therapy for amblyopia to compare a treatment arm representative of current best practice with an arm representative of an entirely novel treatment regimen based on statistical

  16. Test-Enhanced E-Learning Strategies in Postgraduate Medical Education: A Randomized Cohort Study.

    Science.gov (United States)

    DelSignore, Lisa A; Wolbrink, Traci A; Zurakowski, David; Burns, Jeffrey P

    2016-11-21

    The optimal design of pedagogical strategies for e-learning in graduate and postgraduate medical education remains to be determined. Video-based e-learning use is increasing, with initial research suggesting that taking short breaks while watching videos (independent of answering test questions) may improve learning by focusing attention on the content presented. Interspersed test questions may also improve knowledge acquisition and retention. To examine the effect of interspersed test questions and periodic breaks on immediate knowledge acquisition and retention at 6 months by pediatric residents engaged in video-based e-learning. First- and second-year pediatric residents were randomized to 1 of the following 3 groups: viewing the complete video uninterrupted (full video), viewing the video interrupted with unrelated logic puzzles (logic puzzles), or viewing the video interrupted with brief comprehension test questions (short answer questions). Residents answered pre- and post-tests before and after video viewing, followed by a retention test at 6 months. Primary outcome included comparison of the change in test scores between groups. A total of 49 residents completed the initial testing session. All 3 learning groups had comparable mean increases in immediate knowledge gain, but with no significant differences between groups (F2,46=0.35, P=.71). Thirty-five residents completed retention testing with comparable degrees of knowledge retention in the full video and short answer test questions groups (P<.001), but no significant change in the logic puzzles group (F1,32=2.44, P=.13). Improved knowledge gain was not demonstrated among residents answering interspersed questions or completing logic puzzles during interrupted online video viewing when compared with residents viewing uninterrupted video content. However, residents who either participated in uninterrupted video viewing or answered interspersed questions during interrupted video viewing demonstrated

  17. Control group selection in critical care randomized controlled trials evaluating interventional strategies: An ethical assessment.

    Science.gov (United States)

    Silverman, Henry J; Miller, Franklin G

    2004-03-01

    Ethical concern has been raised with critical care randomized controlled trials in which the standard of care reflects a broad range of clinical practices. Commentators have argued that trials without an unrestricted control group, in which standard practices are implemented at the discretion of the attending physician, lack the ability to redefine the standard of care and might expose subjects to excessive harms due to an inability to stop early. To develop a framework for analyzing control group selection for critical care trials. Ethical analysis. A key ethical variable in trial design is the extent with which the control group adequately reflects standard care practices. Such a control group might incorporate either the "unrestricted" practices of physicians or a protocol that specifies and restricts the parameters of standard practices. Control group selection should be determined with respect to the following ethical objectives of trial design: 1) clinical value, 2) scientific validity, 3) efficiency and feasibility, and 4) protection of human subjects. Because these objectives may conflict, control group selection will involve trade-offs and compromises. Trials using a protocolized rather than an unrestricted standard care control group will likely have enhanced validity. However, if the protocolized control group lacks representativeness to standard care practices, then trials that use such groups will offer less clinical value and could provide less assurance of protecting subjects compared with trials that use unrestricted control groups. For trials evaluating contrasting strategies that do not adequately represent standard practices, use of a third group that is more representative of standard practices will enhance clinical value and increase the ability to stop early if needed to protect subjects. These advantages might come at the expense of efficiency and feasibility. Weighing and balancing the competing ethical objectives of trial design should be

  18. Efficient multi-site-directed mutagenesis directly from genomic ...

    Indian Academy of Sciences (India)

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

  19. Transposon Tn5 mutagenesis of pseudomonas fluorescens to isolate mutants deficient in antibacterial activity.

    Science.gov (United States)

    Rajendran, N; Jahn, D; Jayaraman, K; Marahiel, M A

    1994-01-15

    Pseudomonas fluorescens was subjected to insertion mutagenesis studies using the transposon Tn5-GM to generate mutants deficient in antibacterial activity minus mutants. The transposon located on the temperature-sensitive plasmid pCHR84 was conjugally transferred into the non-pathogenic pseudomonad using the triparental mating procedure. Random integration of Tn5-GM into the chromosome of P. fluorescens was achieved by heat treatment of the transformed cells at 42 degrees C. Approximately 2% of transconjugants revealed an auxotrophic phenotype indicating efficient integration of the employed transposon into the chromosome of P. fluorescens. One transposon insertion mutant was obtained showing an antibacterial activity minus phenotype. This mutant (MM-7) was found to be defective in the production of an unidentified antibacterial compound against B. subtilis. These results introduce Tn5 transposon mutagenesis as a new useful tool for the molecular analysis of P. fluorescens.

  20. Prediction of enzyme mutant activity using computational mutagenesis and incremental transduction.

    Science.gov (United States)

    Basit, Nada; Wechsler, Harry

    2011-01-01

    Wet laboratory mutagenesis to determine enzyme activity changes is expensive and time consuming. This paper expands on standard one-shot learning by proposing an incremental transductive method (T2bRF) for the prediction of enzyme mutant activity during mutagenesis using Delaunay tessellation and 4-body statistical potentials for representation. Incremental learning is in tune with both eScience and actual experimentation, as it accounts for cumulative annotation effects of enzyme mutant activity over time. The experimental results reported, using cross-validation, show that overall the incremental transductive method proposed, using random forest as base classifier, yields better results compared to one-shot learning methods. T2bRF is shown to yield 90% on T4 and LAC (and 86% on HIV-1). This is significantly better than state-of-the-art competing methods, whose performance yield is at 80% or less using the same datasets.

  1. Prediction of Enzyme Mutant Activity Using Computational Mutagenesis and Incremental Transduction

    Directory of Open Access Journals (Sweden)

    Nada Basit

    2011-01-01

    Full Text Available Wet laboratory mutagenesis to determine enzyme activity changes is expensive and time consuming. This paper expands on standard one-shot learning by proposing an incremental transductive method (T2bRF for the prediction of enzyme mutant activity during mutagenesis using Delaunay tessellation and 4-body statistical potentials for representation. Incremental learning is in tune with both eScience and actual experimentation, as it accounts for cumulative annotation effects of enzyme mutant activity over time. The experimental results reported, using cross-validation, show that overall the incremental transductive method proposed, using random forest as base classifier, yields better results compared to one-shot learning methods. T2bRF is shown to yield 90% on T4 and LAC (and 86% on HIV-1. This is significantly better than state-of-the-art competing methods, whose performance yield is at 80% or less using the same datasets.

  2. 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.

  3. Randomized controlled trial comparing four strategies for delivering e-curriculum to health care professionals [ISRCTN88148532

    Directory of Open Access Journals (Sweden)

    Mitra Ananda

    2006-01-01

    Full Text Available Abstract Background Internet education is increasingly provided to health professionals, but little is known about the most effective strategies for delivering the content. The purpose of this study is to compare four strategies for delivering an Internet-based (e- curriculum on clinicians' knowledge (K, confidence (CONF, and communication (COMM about herbs and other dietary supplements (HDS. Methods This national randomized 2 × 2 factorial trial included physicians, pharmacists, nurses, nutritionists and trainees in these fields. Participants were randomly assigned to one of four curriculum delivery strategies for 40 brief modules about HDS: a delivering four (4 modules weekly over ten (10 weeks by email (drip-push; b modules accessible on web site with 4 reminders weekly for 10 weeks (drip-pull; c 40 modules delivered within 4 days by email (bolus-push; and d 40 modules available on the Internet with one email informing participants of availability (bolus-pull. Results Of the 1,267 enrollees, 25% were male; the average age was 40 years. The completion rate was 62%, without significant differences between delivery groups. There were statistically significant improvements in K, CONF and COMM scores after the course (P Conclusion All delivery strategies tested similarly improved K, CONF, COMM scores about HDS. Educators can use the strategy that is most convenient without diminishing effectiveness. Additional curricula may be necessary to make substantial changes in clinicians' communication practices.

  4. 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.

  5. Pictorial mnemonic-strategy interventions for children with special needs: Illustration of a multiply randomized single-case crossover design.

    Science.gov (United States)

    Hwang, Yooyeun; Levin, Joel R; Johnson, Evan W

    2016-01-25

    An innovative single-case crossover design containing multiple forms of randomization was implemented with eight participants in seven weekly sessions, during which instruction was given in the use of two different pictorial mnemonic (memory-enhancing) strategies: one designed to improve the children's learning of the dates of various inventions and the other designed to improve the children's acquisition of unfamiliar vocabulary items. A composite randomization statistical test revealed that when compared with the children's own preferred learning methods, the mnemonic-strategy approach produced the predicted facilitation effects. At the same time, it was evident that mnemonic instruction enhanced children's performance to a greater extent on the vocabulary task than on the inventions task. In-depth examination of both individual student performance profiles and the tasks/procedures were conducted, yielding recommendations and challenges for follow-up single-case intervention research on the topic.

  6. Optimizing Household Chlorination Marketing Strategies: A Randomized Controlled Trial on the Effect of Price and Promotion on Adoption in Haiti.

    Science.gov (United States)

    Ritter, Michael; Camille, Eveline; Velcine, Christophe; Guillaume, Rose-Kerline; Lantagne, Daniele

    2017-07-01

    Household water treatment can reduce diarrheal morbidity and mortality in developing countries, but adoption remains low and supply is often unreliable. To test effects of marketing strategies on consumers and suppliers, we randomized 1,798 households in rural Haiti and collected data on purchases of a household chlorination product for 4 months. Households received randomly selected prices ($0.11-$0.56 per chlorine bottle), and half received monthly visits from sales agents. Each $0.22 drop in price increased purchases by 0.10 bottles per household per month (P effective use of resources than household visits, though all marketing strategies tested offer cost-effective ways to achieve incremental health impact. Decisions about pricing and promotion for health products in developing countries affect health impact, cost recovery, and cost-effectiveness, and tradeoffs between these goals should be made explicit in program design.

  7. 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.

  8. Strategies for prevention of postoperative delirium: a systematic review and meta-analysis of randomized trials

    Science.gov (United States)

    2013-01-01

    Introduction The ideal measures to prevent postoperative delirium remain unestablished. We conducted this systematic review and meta-analysis to clarify the significance of potential interventions. Methods The PRISMA statement guidelines were followed. Two researchers searched MEDLINE, EMBASE, CINAHL and the Cochrane Library for articles published in English before August 2012. Additional sources included reference lists from reviews and related articles from 'Google Scholar'. Randomized clinical trials (RCTs) on interventions seeking to prevent postoperative delirium in adult patients were included. Data extraction and methodological quality assessment were performed using predefined data fields and scoring system. Meta-analysis was accomplished for studies that used similar strategies. The primary outcome measure was the incidence of postoperative delirium. We further tested whether interventions effective in preventing postoperative delirium shortened the length of hospital stay. Results We identified 38 RCTs with interventions ranging from perioperative managements to pharmacological, psychological or multicomponent interventions. Meta-analysis showed dexmedetomidine sedation was associated with less delirium compared to sedation produced by other drugs (two RCTs with 415 patients, pooled risk ratio (RR) = 0.39; 95% confidence interval (CI) = 0.16 to 0.95). Both typical (three RCTs with 965 patients, RR = 0.71; 95% CI = 0.54 to 0.93) and atypical antipsychotics (three RCTs with 627 patients, RR = 0.36; 95% CI = 0.26 to 0.50) decreased delirium occurrence when compared to placebos. Multicomponent interventions (two RCTs with 325 patients, RR = 0.71; 95% CI = 0.58 to 0.86) were effective in preventing delirium. No difference in the incidences of delirium was found between: neuraxial and general anesthesia (four RCTs with 511 patients, RR = 0.99; 95% CI = 0.65 to 1.50); epidural and intravenous analgesia (three RCTs with 167 patients, RR = 0.93; 95% CI = 0.61 to 1

  9. Study protocol: Couples Partnering for Lipid Enhancing Strategies (CouPLES – a randomized, controlled trial

    Directory of Open Access Journals (Sweden)

    Weinberger Morris

    2009-02-01

    Full Text Available Abstract Background Almost 50% of Americans have elevated low-density lipoprotein cholesterol (LDL-C. The behaviors required to lower LDL-C levels may be difficult to adhere to if they are inconsistent with spouses' health practices, and, alternatively, may be enhanced by enlisting support from the spouse. This trial extends previous trials by requiring spouse enrollment, teaching spouses how to provide emotional and instrumental support, allowing patients to decide which component of the intervention they would like to receive, and having patients determine their own goals and action plans. Methods Veteran outpatients with above-goal LDL-C (N = 250 and their spouses are randomized, as a couple, to receive printed education materials only or the materials plus an 11-month, nurse-delivered, telephone-based intervention. The intervention contains four modules: medication adherence, diet, exercise, and patient-physician communication. Patients decide which modules they complete and in which order; modules may be repeated or omitted. Telephone calls are to patients and spouses separately and occur monthly. During each patient telephone call, patients' progress is reviewed, and patients create goals and action plans for the upcoming month. During spouse telephone calls, which occur within one week of patient calls, spouses are informed of patients' goals and action plans and devise strategies to increase emotional and instrumental support. The primary outcome is patients' LDL-C, measured at baseline, 6 months, and 11 months. Linear mixed models will be used to test the primary hypothesis that an 11-month, telephone-based patient-spouse intervention will result in a greater reduction in LDL-C as compared to printed education materials. Various process measures, including social support, self-efficacy, medication adherence, dietary behavior, and exercise, are also assessed to explain any change, or lack thereof, in LDL-C. Discussion Given the social

  10. A Randomized Trial Examining Three Strategies for Supporting Health Insurance Decisions among the Uninsured.

    Science.gov (United States)

    Politi, Mary C; Kaphingst, Kimberly A; Liu, Jingxia Esther; Perkins, Hannah; Furtado, Karishma; Kreuter, Matthew W; Shacham, Enbal; McBride, Timothy

    2016-10-01

    The Affordable Care Act allows uninsured individuals to select health insurance from numerous private plans, a challenging decision-making process. This study examined the effectiveness of strategies to support health insurance decisions among the uninsured. Participants (N = 343) from urban, suburban, and rural areas were randomized to 1 of 3 conditions: 1) a plain language table; 2) a visual condition where participants chose what information to view and in what order; and 3) a narrative condition. We administered measures assessing knowledge (true/false responses about key features of health insurance), confidence in choices (uncertainty subscale of the Decisional Conflict Scale), satisfaction (items from the Health Information National Trends Survey), preferences for insurance features (measured on a Likert scale from not at all important to very important), and plan choice. Although we did not find significant differences in knowledge, confidence in choice, or satisfaction across condition, participants across conditions made value-consistent choices, selecting plans that aligned with their preferences for key insurance features. In addition, those with adequate health literacy skills as measured by the Rapid Estimate of Adult Literacy in Medicine-Short Form (REALM-SF) had higher knowledge overall ([Formula: see text] = 6.1 v. 4.8, P < 0.001) and preferred the plain language table to the visual (P = 0.04) and visual to narrative (P = 0.0002) conditions, while those with inadequate health literacy skills showed no preference for study condition. A similar pattern was seen for those with higher subjective numeracy skills and higher versus lower education with regard to health insurance knowledge. Individuals with higher income felt less confident in their choices ([Formula: see text] = 28.7 v. 10.0, where higher numbers indicate less confidence/more uncertainty; P = 0.004). Those developing materials about the health insurance marketplace to support health

  11. Strategies for prevention of postoperative delirium: a systematic review and meta-analysis of randomized trials.

    Science.gov (United States)

    Zhang, Hao; Lu, Yan; Liu, Meng; Zou, Zui; Wang, Long; Xu, Feng-Ying; Shi, Xue-Yin

    2013-03-18

    The ideal measures to prevent postoperative delirium remain unestablished. We conducted this systematic review and meta-analysis to clarify the significance of potential interventions. The PRISMA statement guidelines were followed. Two researchers searched MEDLINE, EMBASE, CINAHL and the Cochrane Library for articles published in English before August 2012. Additional sources included reference lists from reviews and related articles from 'Google Scholar'. Randomized clinical trials (RCTs) on interventions seeking to prevent postoperative delirium in adult patients were included. Data extraction and methodological quality assessment were performed using predefined data fields and scoring system. Meta-analysis was accomplished for studies that used similar strategies. The primary outcome measure was the incidence of postoperative delirium. We further tested whether interventions effective in preventing postoperative delirium shortened the length of hospital stay. We identified 38 RCTs with interventions ranging from perioperative managements to pharmacological, psychological or multicomponent interventions. Meta-analysis showed dexmedetomidine sedation was associated with less delirium compared to sedation produced by other drugs (two RCTs with 415 patients, pooled risk ratio (RR)=0.39; 95% confidence interval (CI)=0.16 to 0.95). Both typical (three RCTs with 965 patients, RR=0.71; 95% CI=0.54 to 0.93) and atypical antipsychotics (three RCTs with 627 patients, RR=0.36; 95% CI=0.26 to 0.50) decreased delirium occurrence when compared to placebos. Multicomponent interventions (two RCTs with 325 patients, RR=0.71; 95% CI=0.58 to 0.86) were effective in preventing delirium. No difference in the incidences of delirium was found between: neuraxial and general anesthesia (four RCTs with 511 patients, RR=0.99; 95% CI=0.65 to 1.50); epidural and intravenous analgesia (three RCTs with 167 patients, RR=0.93; 95% CI=0.61 to 1.43) or acetylcholinesterase inhibitors and placebo

  12. A mild ovarian stimulation strategy in women with poor ovarian reserve undergoing IVF: a multicenter randomized non-inferiority trial.

    Science.gov (United States)

    Youssef, M A; van Wely, M; Al-Inany, H; Madani, T; Jahangiri, N; Khodabakhshi, S; Alhalabi, M; Akhondi, M; Ansaripour, S; Tokhmechy, R; Zarandi, L; Rizk, A; El-Mohamedy, M; Shaeer, E; Khattab, M; Mochtar, M H; van der Veen, F

    2017-01-01

    In subfertile women with poor ovarian reserve undergoing IVF does a mild ovarian stimulation strategy lead to comparable ongoing pregnancy rates in comparison to a conventional ovarian stimulation strategy? A mild ovarian stimulation strategy in women with poor ovarian reserve undergoing IVF leads to similar ongoing pregnancy rates as a conventional ovarian stimulation strategy. Women diagnosed with poor ovarian reserve are treated with a conventional ovarian stimulation strategy consisting of high-dose gonadotropins and pituitary downregulation with a long mid-luteal start GnRH-agonist protocol. Previous studies comparing a conventional strategy with a mild ovarian stimulation strategy consisting of low-dose gonadotropins and pituitary downregulation with a GnRH-antagonist have been under powered and their effectiveness is inconclusive. This open label multicenter randomized trial was designed to compare one cycle of a mild ovarian stimulation strategy consisting of low-dose gonadotropins (150 IU FSH) and pituitary downregulation with a GnRH-antagonist to one cycle of a conventional ovarian stimulation strategy consisting of high-dose gonadotropins (450 IU HMG) and pituitary downregulation with a long mid-luteal GnRH-agonist in women of advanced maternal age and/or women with poor ovarian reserve undergoing IVF between May 2011 and April 2014. Couples seeking infertility treatment were eligible if they fulfilled the following inclusion criteria: female age ≥35 years, a raised basal FSH level >10 IU/ml irrespective of age, a low antral follicular count of ≤5 follicles or poor ovarian response or cycle cancellation during a previous IVF cycle irrespective of age. The primary outcome was ongoing pregnancy rate per woman randomized. Analyses were on an intention-to-treat basis. We randomly assigned 195 women to the mild ovarian stimulation strategy and 199 women to the conventional ovarian stimulation strategy. Ongoing pregnancy rate was 12.8% (25/195) for mild

  13. Different strategies for mechanical VENTilation during CardioPulmonary Bypass (CPBVENT 2014): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Bignami, Elena; Guarnieri, Marcello; Saglietti, Francesco; Maglioni, Enivarco Massimo; Scolletta, Sabino; Romagnoli, Stefano; De Paulis, Stefano; Paternoster, Gianluca; Trumello, Cinzia; Meroni, Roberta; Scognamiglio, Antonio; Budillon, Alessandro Maria; Pota, Vincenzo; Zangrillo, Alberto; Alfieri, Ottavio

    2017-06-07

    There is no consensus on which lung-protective strategies should be used in cardiac surgery patients. Sparse and small randomized clinical and animal trials suggest that maintaining mechanical ventilation during cardiopulmonary bypass is protective on the lungs. Unfortunately, such evidence is weak as it comes from surrogate and minor clinical endpoints mainly limited to elective coronary surgery. According to the available data in the academic literature, an unquestionable standardized strategy of lung protection during cardiopulmonary bypass cannot be recommended. The purpose of the CPBVENT study is to investigate the effectiveness of different strategies of mechanical ventilation during cardiopulmonary bypass on postoperative pulmonary function and complications. The CPBVENT study is a single-blind, multicenter, randomized controlled trial. We are going to enroll 870 patients undergoing elective cardiac surgery with planned use of cardiopulmonary bypass. Patients will be randomized into three groups: (1) no mechanical ventilation during cardiopulmonary bypass, (2) continuous positive airway pressure of 5 cmH2O during cardiopulmonary bypass, (3) respiratory rate of 5 acts/min with a tidal volume of 2-3 ml/Kg of ideal body weight and positive end-expiratory pressure of 3-5 cmH2O during cardiopulmonary bypass. The primary endpoint will be the incidence of a PaO2/FiO2 ratio bypass will have an impact on postoperative pulmonary complications and outcomes of patients undergoing cardiac surgery. ClinicalTrials.gov, ID: NCT02090205 . Registered on 8 March 2014.

  14. Improvement of sampling strategies for randomly distributed hotspots in soil applying a computerized simulation considering the concept of uncertainty.

    Science.gov (United States)

    Hildebrandt, Thomas; Pick, Denis; Einax, Jürgen W

    2012-02-01

    The pollution of soil and environment as a result of human activity is a major problem. Nowadays, the determination of local contaminations is of interest for environmental remediation. These hotspots can have various toxic effects on plants, animals, humans, and the whole ecological system. However, economical and juridical consequences are also possible, e.g., high costs for remediation measures. In this study three sampling strategies (simple random sampling, stratified sampling, and systematic sampling) were applied on randomly distributed hotspot contaminations to prove their efficiency in term of finding hotspots. The results were used for the validation of a computerized simulation. This application can simulate the contamination on a field, the sampling pattern, and a virtual sampling. A constant hit rate showed that none of the sampling patterns could reach better results than others. Furthermore, the uncertainty associated with the results is described by confidence intervals. It is to be considered that the uncertainty during sampling is enormous and will decrease slightly, even the number of samples applied was increased to an unreasonable amount. It is hardly possible to identify the exact number of randomly distributed hotspot contaminations by statistical sampling. But a range of possible results could be calculated. Depending on various parameters such as shape and size of the area, number of hotspots, and sample quantity, optimal sampling strategies could be derived. Furthermore, an estimation of bias arising from sampling methodology is possible. The developed computerized simulation is an innovative tool for optimizing sampling strategies in terrestrial compartments for hotspot distributions.

  15. Strategies to Reduce Injuries and Develop Confidence in Elders (STRIDE): A Cluster-Randomized Pragmatic Trial of a Multifactorial Fall Injury Prevention Strategy: Design and Methods.

    Science.gov (United States)

    Bhasin, Shalender; Gill, Thomas M; Reuben, David B; Latham, Nancy K; Gurwitz, Jerry H; Dykes, Patricia; McMahon, Siobhan; Storer, Thomas W; Duncan, Pamela W; Ganz, David A; Basaria, Shehzad; Miller, Michael E; Travison, Thomas G; Greene, Erich J; Dziura, James; Esserman, Denise; Allore, Heather; Carnie, Martha B; Fagan, Maureen; Hanson, Catherine; Baker, Dorothy; Greenspan, Susan L; Alexander, Neil; Ko, Fred; Siu, Albert L; Volpi, Elena; Wu, Albert W; Rich, Jeremy; Waring, Stephen C; Wallace, Robert; Casteel, Carri; Magaziner, Jay; Charpentier, Peter; Lu, Charles; Araujo, Katy; Rajeevan, Haseena; Margolis, Scott; Eder, Richard; McGloin, Joanne M; Skokos, Eleni; Wiggins, Jocelyn; Garber, Lawrence; Clauser, Steven B; Correa-De-Araujo, Rosaly; Peduzzi, Peter

    2017-10-14

    Fall injuries are a major cause of morbidity and mortality among older adults. We describe the design of a pragmatic trial to compare the effectiveness of an evidence-based, patient-centered multifactorial fall injury prevention strategy to an enhanced usual care. Strategies to Reduce Injuries and Develop Confidence in Elders (STRIDE) is a 40-month cluster-randomized, parallel-group, superiority, pragmatic trial being conducted at 86 primary care practices in 10 healthcare systems across USA. The 86 practices were randomized to intervention or control group using covariate-based constrained randomization, stratified by healthcare system. Participants are community-living persons, ≥70 years, at increased risk for serious fall injuries. The intervention is a co-management model in which a nurse Falls Care Manager performs multifactorial risk assessments, develops individualized care plans, which include surveillance, follow-up evaluation, and intervention strategies. Control group receives enhanced usual care, with clinicians and patients receiving evidence-based information on falls prevention. Primary outcome is serious fall injuries, operationalized as those leading to medical attention (non-vertebral fractures, joint dislocation, head injury, lacerations, and other major sequelae). Secondary outcomes include all fall injuries, all falls, and well-being (concern for falling; anxiety and depressive symptoms; physical function and disability). Target sample size was 5,322 participants to provide 90% power to detect 20% reduction in primary outcome rate relative to control. Trial enrolled 5451 subjects in 20 months. Intervention and follow-up are ongoing. The findings of the STRIDE study will have important clinical and policy implications for the prevention of fall injuries in older adults.

  16. A Cluster-Randomized Trial of Two Strategies to Improve Antibiotic Use for Patients with a Complicated Urinary Tract Infection.

    Science.gov (United States)

    Spoorenberg, Veroniek; Hulscher, Marlies E J L; Geskus, Ronald B; de Reijke, Theo M; Opmeer, Brent C; Prins, Jan M; Geerlings, Suzanne E

    2015-01-01

    Up to 50% of hospital antibiotic use is inappropriate and therefore improvement strategies are urgently needed. We compared the effectiveness of two strategies to improve the quality of antibiotic use in patients with a complicated urinary tract infection (UTI). In a multicentre, cluster-randomized trial 19 Dutch hospitals (departments Internal Medicine and Urology) were allocated to either a multi-faceted strategy including feedback, educational sessions, reminders and additional/optional improvement actions, or a competitive feedback strategy, i.e. providing professionals with non-anonymous comparative feedback on the department's appropriateness of antibiotic use. Retrospective baseline- and post-intervention measurements were performed in 2009 and 2012 in 50 patients per department, resulting in 1,964 and 2,027 patients respectively. Principal outcome measures were nine validated guideline-based quality indicators (QIs) that define appropriate antibiotic use in patients with a complicated UTI, and a QI sumscore that summarizes for each patient the appropriateness of antibiotic use. Performance scores on several individual QIs showed improvement from baseline to post-intervention measurements, but no significant differences were found between both strategies. The mean patient's QI sum score improved significantly in both strategy groups (multi-faceted: 61.7% to 65.0%, P = 0.04 and competitive feedback: 62.8% to 66.7%, P = 0.01). Compliance with the strategies was suboptimal, but better compliance was associated with more improvement. The effectiveness of both strategies was comparable and better compliance with the strategies was associated with more improvement. To increase effectiveness, improvement activities should be rigorously applied, preferably by a locally initiated multidisciplinary team. Nederlands Trial Register 1742.

  17. A Cluster-Randomized Trial of Two Strategies to Improve Antibiotic Use for Patients with a Complicated Urinary Tract Infection.

    Directory of Open Access Journals (Sweden)

    Veroniek Spoorenberg

    Full Text Available Up to 50% of hospital antibiotic use is inappropriate and therefore improvement strategies are urgently needed. We compared the effectiveness of two strategies to improve the quality of antibiotic use in patients with a complicated urinary tract infection (UTI.In a multicentre, cluster-randomized trial 19 Dutch hospitals (departments Internal Medicine and Urology were allocated to either a multi-faceted strategy including feedback, educational sessions, reminders and additional/optional improvement actions, or a competitive feedback strategy, i.e. providing professionals with non-anonymous comparative feedback on the department's appropriateness of antibiotic use. Retrospective baseline- and post-intervention measurements were performed in 2009 and 2012 in 50 patients per department, resulting in 1,964 and 2,027 patients respectively. Principal outcome measures were nine validated guideline-based quality indicators (QIs that define appropriate antibiotic use in patients with a complicated UTI, and a QI sumscore that summarizes for each patient the appropriateness of antibiotic use.Performance scores on several individual QIs showed improvement from baseline to post-intervention measurements, but no significant differences were found between both strategies. The mean patient's QI sum score improved significantly in both strategy groups (multi-faceted: 61.7% to 65.0%, P = 0.04 and competitive feedback: 62.8% to 66.7%, P = 0.01. Compliance with the strategies was suboptimal, but better compliance was associated with more improvement.The effectiveness of both strategies was comparable and better compliance with the strategies was associated with more improvement. To increase effectiveness, improvement activities should be rigorously applied, preferably by a locally initiated multidisciplinary team.Nederlands Trial Register 1742.

  18. A Fuzzy-Logic Power Management Strategy Based on Markov Random Prediction for Hybrid Energy Storage Systems

    Directory of Open Access Journals (Sweden)

    Yanzi Wang

    2016-01-01

    Full Text Available Over the last few years; issues regarding the use of hybrid energy storage systems (HESSs in hybrid electric vehicles have been highlighted by the industry and in academic fields. This paper proposes a fuzzy-logic power management strategy based on Markov random prediction for an active parallel battery-UC HESS. The proposed power management strategy; the inputs for which are the vehicle speed; the current electric power demand and the predicted electric power demand; is used to distribute the electrical power between the battery bank and the UC bank. In this way; the battery bank power is limited to a certain range; and the peak and average charge/discharge power of the battery bank and overall loss incurred by the whole HESS are also reduced. Simulations and scaled-down experimental platforms are constructed to verify the proposed power management strategy. The simulations and experimental results demonstrate the advantages; feasibility and effectiveness of the fuzzy-logic power management strategy based on Markov random prediction.

  19. Principles and strategies for monitoring data collection integrity in a multi-site randomized clinical trial of a behavioral intervention.

    Science.gov (United States)

    Phillips-Salimi, Celeste R; Donovan Stickler, Molly A; Stegenga, Kristin; Lee, Melissa; Haase, Joan E

    2011-08-01

    Although treatment fidelity strategies for enhancing the integrity of behavioral interventions have been well described, little has been written about monitoring data collection integrity. This article describes the principles and strategies developed to monitor data collection integrity of the "Stories and Music for Adolescent/Young Adult Resilience During Transplant" study (R01NR008583, U10CA098543, and U10CA095861)-a multi-site Children's Oncology Group randomized clinical trial of a music therapy intervention for adolescents and young adults undergoing stem cell transplant. The principles and strategies outlined in this article provide one model for development and evaluation of a data collection integrity monitoring plan for behavioral interventions that may be adapted by investigators and may be useful to funding agencies and grant application reviewers in evaluating proposals. Copyright © 2011 Wiley Periodicals, Inc.

  20. A new combined strategy to implement a community occupational therapy intervention: designing a cluster randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Adang Eddy

    2011-03-01

    Full Text Available Abstract Background Even effective interventions for people with dementia and their caregivers require specific implementation efforts. A pilot study showed that the highly effective community occupational therapy in dementia (COTiD program was not implemented optimally due to various barriers. To decrease these barriers and make implementation of the program more effective a combined implementation (CI strategy was developed. In our study we will compare the effectiveness of this CI strategy with the usual educational (ED strategy. Methods In this cluster randomized, single-blinded, controlled trial, each cluster consists of at least two occupational therapists, a manager, and a physician working at Dutch healthcare organizations that deliver community occupational therapy. Forty-five clusters, stratified by healthcare setting (nursing home, hospital, mental health service, have been allocated randomly to either the intervention group (CI strategy or the control group (ED strategy. The study population consists of the professionals included in each cluster and community-dwelling people with dementia and their caregivers. The primary outcome measures are the use of community OT, the adherence of OTs to the COTiD program, and the cost effectiveness of implementing the COTiD program in outpatient care. Secondary outcome measures are patient and caregiver outcomes and knowledge of managers, physicians and OTs about the COTiD program. Discussion Implementation research is fairly new in the field of occupational therapy, making this a unique study. This study does not only evaluate the effects of the CI-strategy on professionals, but also the effects of professionals' degree of implementation on client and caregiver outcomes. Clinical trials registration NCT01117285

  1. Comparing Two Story-Writing Mnemonic Strategies: A Randomized Control Trial Study

    Science.gov (United States)

    Dunn, Michael

    2013-01-01

    Educators often use mnemonic strategies as a prime method to help children who struggle with writing. This study analyzed 12 fourth-grade students' stories during their participation in one of three groups. The first group learned the Ask, Reflect, Text (ART) mnemonic strategy with art media in the pre-writing/planning phase. The second group used…

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

    Science.gov (United States)

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

    2016-01-01

    The endophytic filamentous fungus Harpophora oryzae is a beneficial endosymbiont isolated from the wild rice. H. oryzae could not only effectively improve growth rate and biomass yield of rice crops, but also induce systemic resistance against the rice blast fungus, Magnaporthe oryzae. In this study, Agrobacterium tumefaciens-mediated transformation (ATMT) was employed and optimized to modify the H. oryzae genes by either random DNA fragment integration or targeted gene replacement. Our results showed that co-cultivation of H. oryzae conidia with A. tumefaciens in the presence of acetosyringone for 48 h at 22 °C could lead to a relatively highest frequency of transformation, and 200 μM acetosyringone (AS) pre-cultivation of A. tumefaciens is also suggested. ATMT-mediated knockout mutagenesis was accomplished with the gene-deletion cassettes using a yeast homologous recombination method with a yeast-Escherichia-Agrobacterium shuttle vector pKOHo. Using the ATMT-mediated knockout mutagenesis, we successfully deleted three genes of H. oryzae (HoATG5, HoATG7, and HoATG8), and then got the null mutants ΔHoatg5, ΔHoatg7, and ΔHoatg8. These results suggest that ATMT is an efficient tool for gene modification including randomly insertional mutagenesis and gene deletion mutagenesis in H. oryzae. Copyright © 2015 Elsevier GmbH. All rights reserved.

  3. A randomized trial of an intervention to improve use and adherence to effective coronary heart disease prevention strategies

    Directory of Open Access Journals (Sweden)

    Sheridan Stacey L

    2011-12-01

    Full Text Available Abstract Background Efficacious strategies for the primary prevention of coronary heart disease (CHD are underused, and, when used, have low adherence. Existing efforts to improve use and adherence to these efficacious strategies have been so intensive that they are impractical for clinical practice. Methods We conducted a randomized trial of a CHD prevention intervention (including a computerized decision aid and automated tailored adherence messages at one university general internal medicine practice. After obtaining informed consent and collecting baseline data, we randomized patients (men and women age 40-79 with no prior history of cardiovascular disease to either the intervention or usual care. We then saw them for two additional study visits over 3 months. For intervention participants, we administered the decision aid at the primary study visit (1 week after baseline visit and then mailed 3 tailored adherence reminders at 2, 4, and 6 weeks. We assessed our outcomes (including the predicted likelihood of angina, myocardial infarction, and CHD death over 10 years (CHD risk and self-reported adherence between groups at 3 month follow-up. Data collection occurred from June 2007 through December 2009. All study procedures were IRB approved. Results We randomized 160 eligible patients (81 intervention; 79 control and followed 96% to study conclusion. Mean predicted CHD risk at baseline was 11.3%. The intervention increased self-reported adherence to chosen risk reducing strategies by 25 percentage points (95% CI 8% to 42%, with the biggest effect for aspirin. It also changed predicted CHD risk by -1.1% (95% CI -0.16% to -2%, with a larger effect in a pre-specified subgroup of high risk patients. Conclusion A computerized intervention that involves patients in CHD decision making and supports adherence to effective prevention strategies can improve adherence and reduce predicted CHD risk. Clinical trials registration number Clinical

  4. Genes Necessary for Bacterial Magnetite Biomineralization Identified by Transposon Mutagenesis

    Science.gov (United States)

    Nash, C. Z.; Komeili, A.; Newman, D. K.; Kirschvink, J. L.

    2004-12-01

    Magnetic bacteria synthesize nanoscale crystals of magnetite in intracellular, membrane-bounded organelles (magnetosomes). These crystals are preserved in the fossil record at least as far back as the late Neoproterozoic and have been tentatively identified in much older rocks (1). This fossil record may provide deep time calibration points for molecular evolution studies once the genes involved in biologically controlled magnetic mineralization (BCMM) are known. Further, a genetic and biochemical understanding of BCMM will give insight into the depositional environment and biogeochemical cycles in which magnetic bacteria play a role. The BCMM process is not well understood, though proteins have been identified from the magnetosome membrane and genetic manipulation and biochemical characterization of these proteins are underway. Most of the proteins currently thought to be involved are encoded within the mam cluster, a large cluster of genes whose products localize to the magnetosome membrane and are conserved among magnetic bacteria (2). In an effort to identify all of the genes necessary for bacterial BCMM, we undertook a transposon mutagenesis of Magnetospirillum magneticum AMB-1. Non-magnetic mutants (MNMs) were identified by growth in liquid culture followed by a magnetic assay. The insertion site of the transposon was identified two ways. First MNMs were screened with a PCR assay to determine if the transposon had inserted into the mam cluster. Second, the transposon was rescued from the mutant DNA and cloned for sequencing. The majority insertion sites are located within the mam cluster. Insertion sites also occur in operons which have not previously been suspected to be involved in magnetite biomineralization. None of the insertion sites have occurred within genes reported from previous transposon mutagenesis studies of AMB-1 (3, 4). Two of the non-mam cluster insertion sites occur in operons containing genes conserved particularly between MS-1 and MC-1. We

  5. Mechanisms of retroviral integration and mutagenesis.

    Science.gov (United States)

    Cavazza, Alessia; Moiani, Arianna; Mavilio, Fulvio

    2013-02-01

    Gene transfer vectors derived from oncoretroviruses or lentiviruses are the most robust and reliable tools to stably integrate therapeutic transgenes in human cells for clinical applications. Integration of these vectors in the genome may, however, have undesired effects caused by insertional deregulation of gene expression at the transcriptional or post-transcriptional level. The occurrence of severe adverse events in several clinical trials involving the transplantation of stem cells genetically corrected with retroviral vectors showed that insertional mutagenesis is not just a theoretical event, and that retroviral transgenesis is associated with a finite risk of genotoxicity. In addressing these issues, the gene therapy community offered a spectacular example of how scientific knowledge and technology can be put to work to understand the causes of unpredicted side effects, design new vectors, and develop tools and models to predict their safety and efficacy. As an added benefit, these efforts brought new basic knowledge on virus-host interactions and on the biology and dynamics of human somatic stem cells. This review summarizes the current knowledge on the interactions between retroviruses and the human genome and addresses the impact of target site selection on the safety of retroviral vector-mediated gene therapy.

  6. History of attempts to quantify environmental mutagenesis

    Energy Technology Data Exchange (ETDEWEB)

    Hollaender, A.

    1981-01-01

    It became obvious in the early 1960's that the ready recognition of mutations produced by chemicals could have a profound influence on the refinement of methods to detect environmental mutagens. The experience derived over the previous 30 years in characterizing the effects of ionizing and ultraviolet radiation on the genetic mechanism came to serve us in good stead. Although the effects of chemicals are considerably more complicated and often require the analysis of individual substances, nonetheless, the area has developed rapidly in recent decades. The establishment and historical background of the International Association of Environmental Mutagen Societies (IAEMS) will be discussed. An attempt at the quantitation of chemical effects has been developed in comparison with radiation mutagenesis. As a first step, a definition of the Mutagen Burden or unavoidable exposure to chemicals will be discussed. A mathematical approach (Haynes/Eckhardt) will be considered and finally an outline for the comprehensive investigation of detailed interscience study will be made of less than six chemicals.

  7. A targeted mutagenesis system for Actinobacillus pleuropneumoniae.

    Science.gov (United States)

    Mulks, M H; Buysse, J M

    1995-11-07

    We describe methods for the mutagenesis of cloned Actinobacillus pleuropneumoniae (Ap) genes and for the construction of Ap mutants by allelic exchange. We used these methods to construct isogenic mutants of Ap which no longer synthesized a 48-kDa outer membrane protein (AopA). The native aopA locus was replaced with a mutated locus that had been inactivated by insertion of a gene (KmR) encoding kanamycin resistance from Tn903. The inactivated aopA locus was cloned into a conjugative, R6K-derived, lambda pir-dependent suicide vector and introduced into Ap using a filtermating technique. Southern and Western blot analyses indicated that the wild-type locus was replaced by the mutated locus through either single- or double-crossover events, and that AopA was no longer produced by either type of mutant. These methods were used successfully to construct AopA- mutants in Ap serotypes 1 and 5. These methods should be generally useful in constructing mutant loci which can be used to analyze the roles of various Ap genes in the pathogenesis of contagious pleuropneumonia in swine.

  8. Genomic approaches to DNA repair and mutagenesis.

    Science.gov (United States)

    Wyrick, John J; Roberts, Steven A

    2015-12-01

    DNA damage is a constant threat to cells, causing cytotoxicity as well as inducing genetic alterations. The steady-state abundance of DNA lesions in a cell is minimized by a variety of DNA repair mechanisms, including DNA strand break repair, mismatch repair, nucleotide excision repair, base excision repair, and ribonucleotide excision repair. The efficiencies and mechanisms by which these pathways remove damage from chromosomes have been primarily characterized by investigating the processing of lesions at defined genomic loci, among bulk genomic DNA, on episomal DNA constructs, or using in vitro substrates. However, the structure of a chromosome is heterogeneous, consisting of heavily protein-bound heterochromatic regions, open regulatory regions, actively transcribed genes, and even areas of transient single stranded DNA. Consequently, DNA repair pathways function in a much more diverse set of chromosomal contexts than can be readily assessed using previous methods. Recent efforts to develop whole genome maps of DNA damage, repair processes, and even mutations promise to greatly expand our understanding of DNA repair and mutagenesis. Here we review the current efforts to utilize whole genome maps of DNA damage and mutation to understand how different chromosomal contexts affect DNA excision repair pathways. Copyright © 2015 Elsevier B.V. All rights reserved.

  9. 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)

  10. Insertional mutagenesis by a hybrid piggyBac and sleeping beauty transposon in the rat.

    Science.gov (United States)

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

    2012-12-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac transposase into zygotes. The levels of transgenic Tyr expression were influenced by chromosomal context, leading to transgenic rats with different pigmentation that enabled visual genotyping. Transgenic rats designed to ubiquitously express either piggyBac or Sleeping Beauty transposase were generated by standard zygote injection also on an albino background. Bigenic rats carrying single-copy transposons at known loci and transposase transgenes exhibited coat color mosaicism, indicating somatic transposition. PiggyBac or Sleeping Beauty transposase bigenic rats bred with wild-type albino rats yielded offspring with pigmentation distinct from the initial transposon insertions as a consequence of germline transposition to new loci. The germline transposition frequency for Sleeping Beauty and piggyBac was ∼10% or about one new insertion per litter. Approximately 50% of the insertions occurred in introns. Chimeric transcripts containing endogenous and gene trap sequences were identified in Gabrb1 mutant rats. This mutagenesis system based on simple crosses and visual genotyping can be used to generate a collection of single-gene mutations in the rat.

  11. CRISPR/Cas9-mediated mutagenesis of the RIN locus that regulates tomato fruit ripening.

    Science.gov (United States)

    Ito, Yasuhiro; Nishizawa-Yokoi, Ayako; Endo, Masaki; Mikami, Masafumi; Toki, Seiichi

    2015-11-06

    Site-directed mutagenesis using genetic approaches can provide a wealth of resources for crop breeding as well as for biological research. The clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated 9 endonuclease (CRISPR/Cas9) system is a novel strategy used to induce mutations in a specific genome region; the system functions in a variety of organisms, including plants. Here, we report application of the CRISPR/Cas9 system to efficient mutagenesis of the tomato genome. In this study, we targeted the tomato RIN gene, which encodes a MADS-box transcription factor regulating fruit ripening. Three regions within the gene were targeted and mutations consisting either of a single base insertion or deletion of more than three bases were found at the Cas9 cleavage sites in T0 regenerated plants. The RIN-protein-defective mutants produced incomplete-ripening fruits in which red color pigmentation was significantly lower than that of wild type, while heterologous mutants expressing the remaining wild-type gene reached full-ripening red color, confirming the important role of RIN in ripening. Several mutations that were generated at three independent target sites were inherited in the T1 progeny, confirming the applicability of this mutagenesis system in tomato. Copyright © 2015 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

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

    2012-01-01

    A hybrid piggyBac/Sleeping Beauty transposon-based insertional mutagenesis system that can be mobilized by simple breeding was established in the rat. These transposons were engineered to include gene trap sequences and a tyrosinase (Tyr) pigmentation reporter to rescue the albinism of the genetic background used in the mutagenesis strategy. Single-copy transposon insertions were transposed into the rat genome by co-injection of plasmids carrying the transposon and RNA encoding piggyBac transposase into zygotes. The levels of transgenic Tyr expression were influenced by chromosomal context, leading to transgenic rats with different pigmentation that enabled visual genotyping. Transgenic rats designed to ubiquitously express either piggyBac or Sleeping Beauty transposase were generated by standard zygote injection also on an albino background. Bigenic rats carrying single-copy transposons at known loci and transposase transgenes exhibited coat color mosaicism, indicating somatic transposition. PiggyBac or Sleeping Beauty transposase bigenic rats bred with wild-type albino rats yielded offspring with pigmentation distinct from the initial transposon insertions as a consequence of germline transposition to new loci. The germline transposition frequency for Sleeping Beauty and piggyBac was ∼10% or about one new insertion per litter. Approximately 50% of the insertions occurred in introns. Chimeric transcripts containing endogenous and gene trap sequences were identified in Gabrb1 mutant rats. This mutagenesis system based on simple crosses and visual genotyping can be used to generate a collection of single-gene mutations in the rat. PMID:23023007

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

    Directory of Open Access Journals (Sweden)

    Weir Jerry P

    2007-05-01

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

  14. A new strategy for complete identification of sea buckthorn cultivars by using random amplified polymorphic DNA markers.

    Science.gov (United States)

    Yang, G; Ding, J; Wu, L R; Duan, Y D; Li, A Y; Shan, J Y; Wu, Y X

    2015-03-13

    DNA fingerprinting is both a popular and important technique with several advantages in plant cultivar identification. However, this technique has not been used widely and efficiently in practical plant identification because the analysis and recording of data generated from fingerprinting and genotyping are tedious and difficult. We developed a novel approach known as a cultivar identification diagram (CID) strategy that uses DNA markers to separate plant individuals in a more efficient, practical, and referable manner. A CID was manually constructed and a polymorphic marker was generated from each polymerase chain reaction for sample separation. In this study, 67 important sea buckthorn cultivars cultivated in China were successfully separated with random amplified polymorphic DNA markers using the CID analysis strategy, with only seven 11-nucleotide primers employed. The utilization of the CID of these 67 sea buckthorn cultivars was verified by identifying 2 randomly chosen groups of cultivars among the 67 cultivars. The main advantages of this identification strategy include fewer primers used and separation of all cultivars using the corresponding primers. This sea buckthorn CID was able to separate any sea buckthorn cultivars among the 67 studied, which is useful for sea buckthorn cultivar identification, cultivar-right-protection, and for the sea buckthorn nursery industry in China.

  15. Assessment of strategies for switching patients from olanzapine to risperidone: A randomized, open-label, rater-blinded study

    Directory of Open Access Journals (Sweden)

    Berry Sally A

    2008-06-01

    Full Text Available Abstract Background In clinical practice, physicians often need to change the antipsychotic medications they give to patients because of an inadequate response or the presence of unacceptable or unsafe side effects. However, there is a lack of consensus in the field as to the optimal switching strategy for antipsychotics, especially with regards to the speed at which the dose of the previous antipsychotic should be reduced. This paper assesses the short-term results of strategies for the discontinuation of olanzapine when initiating risperidone. Methods In a 6-week, randomized, open-label, rater-blinded study, patients with schizophrenia or schizoaffective disorder, on a stable drug dose for more than 30 days at entry, who were intolerant of or exhibiting a suboptimal symptom response to more than 30 days of olanzapine treatment, were randomly assigned to the following switch strategies (common risperidone initiation scheme; varying olanzapine discontinuation: (i abrupt strategy, where olanzapine was discontinued at risperidone initiation; (ii gradual 1 strategy, where olanzapine was given at 50% entry dose for 1 week after risperidone initiation and then discontinued; or (iii gradual 2 strategy, where olanzapine was given at 100% entry dose for 1 week, then at 50% in the second week, and then discontinued. Results The study enrolled 123 patients on stable doses of olanzapine. Their mean age was 40.3 years and mean (± standard deviation (SD baseline Positive and Negative Syndrome Scale (PANSS total score of 75.6 ± 11.5. All-cause treatment discontinuation was lowest (12% in the group with the slowest olanzapine dose reduction (gradual 2 and occurred at half the discontinuation rate in the other two groups (25% in abrupt and 28% in gradual 1. The relative risk of early discontinuation was 0.77 (confidence interval 0.61–0.99 for the slowest dose reduction compared with the other two strategies. After the medication was changed, improvements at

  16. 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.

  17. 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.

    2015-01-01

    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. PMID:25775519

  18. A cognitive strategy instruction to improve math calculation for children with ADHD and LD: a randomized controlled study.

    Science.gov (United States)

    Iseman, Jackie S; Naglieri, Jack A

    2011-01-01

    The authors examined the effectiveness of cognitive strategy instruction based on PASS (Planning, Attention, Simultaneous, Successive) given by special education teachers to students with ADHD randomly assigned by classroom. Students in the experimental group were exposed to a brief cognitive strategy instruction for 10 days, which was designed to encourage development and application of effective planning for mathematical computation, whereas the comparison group received-standard math instruction. Standardized tests of cognitive processes and math achievement were given at pretest. All students completed math worksheets throughout the experimental phase. Standardized achievement tests (Woodcock-Johnson Tests of Achievement, Third Edition, Math Fluency and Wechsler Individualized Achievement Test, Second Edition, Numerical Operations) were administered pre- and postintervention, and Math Fluency was also administered at 1 year follow-up. Large pre-post effect sizes were found for students in the experimental group but not the comparison group on math worksheets (0.85 and 0.26), Math Fluency (1.17 and 0.09), and Numerical Operations (0.40 and -0.14, respectively). At 1 year follow-up, the experimental group continued to outperform the comparison group. These findings suggest that students with ADHD evidenced greater improvement in math worksheets, far transfer to standardized tests of math (which measured the skill of generalizing learned strategies to other similar tasks), and continued advantage 1 year later when provided the PASS-based cognitive strategy instruction.

  19. Postoperative blood transfusion strategy in frail, anemic elderly patients with hip fracture: the TRIFE randomized controlled trial.

    Science.gov (United States)

    Gregersen, Merete; Borris, Lars C; Damsgaard, Else Marie

    2015-06-01

    Hip fracture (HF) in frail elderly patients is associated with poor physical recovery and death. There is often postoperative blood loss and the hemoglobin (Hb) threshold for red blood cell (RBC) transfusions in these patients is unknown. We investigated whether RBC transfusion strategies were associated with the degree of physical recovery or with reduced mortality after HF surgery. We enrolled 284 consecutive post-surgical HF patients (aged ≥ 65 years) with Hb levels nursing homes or sheltered housing. Allocation was stratified by residence. The patients were randomly assigned to either restrictive (Hb nursing home residents in the restrictive transfusion group (36%) than for those in the liberal group (20%) (HR = 2.0, 95% CI: 1.1-3.6; p = 0.01). According to our Hb thresholds, recovery from physical disabilities in frail elderly hip fracture patients was similar after a restrictive RBC transfusion strategy and after a liberal strategy. Implementation of a liberal RBC transfusion strategy in nursing home residents has the potential to increase survival.

  20. Pioneering Strategies for Relieving Dental Anxiety in Hearing Impaired Children: a Randomized Controlled Clinical Study

    OpenAIRE

    Shalini Chandrasekhar; Ghanashyam Prasad Madu; Naga Radhakrishna Ambati; Pavani Reddy Suravarapu; Kalyani Uppu; Deepthi Bolla

    2017-01-01

    Statement of the Problem: Hearing impaired children have a problem in understanding and comprehending with dental treatments. Visual language is the sensible answer of how to improve communication with them. Purpose: To evaluate the applicability of dental sign language in Hearing impaired children in relieving anxiety during stressful dental treatment by improving their means of communication. Materials and Method: This randomized clinical trial was carried out in the Department of Ped...

  1. Recruitment of lactating women into a randomized dietary intervention: successful strategies and factors promoting enrollment and retention.

    Science.gov (United States)

    Stendell-Hollis, Nicole R; Laudermilk, Monica J; West, Julie L; Thompson, Patricia A; Thomson, Cynthia A

    2011-07-01

    Recruitment and retention of lactating women require unique strategies to prevent high attrition. The purpose of this report is to identify successful recruitment strategies and evaluate demographic and lifestyle characteristics associated with study completion. A randomized, controlled trial was initiated to test the hypothesis that lactating women adhering to a Mediterranean diet will show a significant reduction in anthropometric measurements as compared to lactating women randomized to the USDA's MyPyramid diet for Pregnancy and Breastfeeding (control diet). Measurements were collected at baseline, 2 months, and 4 months. Recruitment methods and baseline characteristics of completers and non-completers are described. The largest percentage of women, 24.8%, were recruited from a local parenting magazine, 20.9% from Craig's List, 20.2% from local hospitals, and 34.1% from various other sources. At baseline, women (n = 129) were mostly Non-Hispanic (75.2%), average age 29.7 years, BMI averaged 27.2 kg/m(2), waist:hip ratio 0.84 cm (SD: 0.07), and body fat averaged 30.8%. Approximately 72% were exclusively breastfeeding, a mean 17.5 weeks postpartum, and 69.0% had a college degree. Non-completers were more likely to have supplemented with formula at baseline as compared to completers (Pwomen may consider "exclusive breastfeeding" as a study inclusion criterion to prevent high attrition rates or include additional breastfeeding support to study participants. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Implementing school nursing strategies to reduce LGBTQ adolescent suicide: a randomized cluster trial study protocol

    OpenAIRE

    Willging, Cathleen E; Green, Amy E; Ramos, Mary M.

    2016-01-01

    Background Reducing youth suicide in the United States (U.S.) is a national public health priority, and lesbian, gay, bisexual, transgender, and queer or questioning (LGBTQ) youth are at elevated risk. The Centers for Disease Control and Prevention (CDC) endorses six evidence-based (EB) strategies that center on meeting the needs of LGBTQ youth in schools; however, fewer than 6?% of U.S. schools implement all of them. The proposed intervention model, ?RLAS? (Implementing School Nursing Strate...

  3. Pioneering Strategies for Relieving Dental Anxiety in Hearing Impaired Children: a Randomized Controlled Clinical Study.

    Science.gov (United States)

    Chandrasekhar, Shalini; Madu, Ghanashyam Prasad; Ambati, Naga Radhakrishna; Suravarapu, Pavani Reddy; Uppu, Kalyani; Bolla, Deepthi

    2017-06-01

    Hearing impaired children have a problem in understanding and comprehending with dental treatments. Visual language is the sensible answer of how to improve communication with them. To evaluate the applicability of dental sign language in Hearing impaired children in relieving anxiety during stressful dental treatment by improving their means of communication. This randomized clinical trial was carried out in the Department of Pedodontics and Preventive Dentistry which included 40 Hearing Impaired children meeting inclusion criteria. The selected children were randomly divided into the study and control group comprising of 20 each. In the control group, initial oral examination and dental treatment (oral prophylaxis and class I restoration) were performed without the use of dental sign language. In the study group, the dental sign language specific to dental treatment was educated and during their subsequent visit to the dental clinic after dental sign language reinforcement, oral prophylaxis and class I restoration were done. Subjective and objective measurements of anxiety were recorded for both groups using facial image scale (FIS), pulse oximeter and electronic blood pressure apparatus to compare for correlation. The obtained data were subjected to statistical analysis using unpaired t-test. There was a statistically significant reduction in the anxiety levels (panxiety in children who are hard of hearing. Dental sign language was able to improve behavior positively during dental treatment and may also aid in developing a positive dental attitude among children who are hard of hearing.

  4. Effect of a novel movement strategy in decreasing ACL risk factors in female adolescent soccer players: a randomized controlled trial.

    Science.gov (United States)

    Celebrini, Richard G; Eng, Janice J; Miller, William C; Ekegren, Christina L; Johnston, James D; Depew, Thomas A; Macintyre, Donna L

    2014-03-01

    To determine the effect of a novel movement strategy incorporated within a soccer warm-up on biomechanical risk factors for anterior cruciate ligament injury during 3 sport-specific movement tasks. Single-blind, randomized controlled clinical trial. Laboratory setting. Twenty top-tier female teenage soccer players. Subjects were randomized to the Core Position and Control movement strategy (Core-PAC) warm-up or standard warm-up, which took place before their regular soccer practice over a 6-week period. The Core-PAC focuses on getting the centre of mass closer to the plant foot or base of support. Peak knee flexion angle and abduction moments during a side-hop (SH), side-cut, and unanticipated side-cut task after the 6 weeks with (intervention group only) and without a reminder to use the Core-PAC strategy. The Core-PAC group increased peak flexion angles during the SH task [mean difference = 6.2 degrees; 95% confidence interval (CI), 1.9-10.5 degrees; effect size = 1.01; P = 0.034] after the 6-week warm-up program without a reminder. In addition, the Core-PAC group demonstrated increased knee flexion angles for the side-cut (mean difference = 8.5 degrees; 95% CI, 4.8-12.2 degrees; ES = 2.02; P = 0.001) and SH (mean difference = 10.0 degrees; 95% CI, 5.7-14.3 degrees; ES = 1.66; P = 0.001) task after a reminder. No changes in abduction moments were found. The results of this study suggest that the Core-PAC may be one method of modifying high-risk soccer-specific movements and can be implemented within a practical, team-based soccer warm-up. The results should be interpreted with caution because of the small sample size.

  5. Targeted Mutagenesis of Guinea Pig Cytomegalovirus Using CRISPR/Cas9-Mediated Gene Editing.

    Science.gov (United States)

    Bierle, Craig J; Anderholm, Kaitlyn M; Wang, Jian Ben; McVoy, Michael A; Schleiss, Mark R

    2016-08-01

    The cytomegaloviruses (CMVs) are among the most genetically complex mammalian viruses, with viral genomes that often exceed 230 kbp. Manipulation of cytomegalovirus genomes is largely performed using infectious bacterial artificial chromosomes (BACs), which necessitates the maintenance of the viral genome in Escherichia coli and successful reconstitution of virus from permissive cells after transfection of the BAC. Here we describe an alternative strategy for the mutagenesis of guinea pig cytomegalovirus that utilizes clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9)-mediated genome editing to introduce targeted mutations to the viral genome. Transient transfection and drug selection were used to restrict lytic replication of guinea pig cytomegalovirus to cells that express Cas9 and virus-specific guide RNA. The result was highly efficient editing of the viral genome that introduced targeted insertion or deletion mutations to nonessential viral genes. Cotransfection of multiple virus-specific guide RNAs or a homology repair template was used for targeted, markerless deletions of viral sequence or to introduce exogenous sequence by homology-driven repair. As CRISPR/Cas9 mutagenesis occurs directly in infected cells, this methodology avoids selective pressures that may occur during propagation of the viral genome in bacteria and may facilitate genetic manipulation of low-passage or clinical CMV isolates. The cytomegalovirus genome is complex, and viral adaptations to cell culture have complicated the study of infection in vivo Recombineering of viral bacterial artificial chromosomes enabled the study of recombinant cytomegaloviruses. Here we report the development of an alternative approach using CRISPR/Cas9-based mutagenesis in guinea pig cytomegalovirus, a small-animal model of congenital cytomegalovirus disease. CRISPR/Cas9 mutagenesis can introduce the same types of mutations to the viral genome as bacterial

  6. Implementing targeted expectant management in fertility care using prognostic modelling: a cluster randomized trial with a multifaceted strategy.

    Science.gov (United States)

    Kersten, F A M; Nelen, W L D M; van den Boogaard, N M; van Rumste, M M; Koks, C A; IntHout, J; Verhoeve, H R; Pelinck, M J; Boks, D E S; Gianotten, J; Broekmans, F J M; Goddijn, M; Braat, D D M; Mol, B W J; Hermens, R P G M

    2017-08-01

    What is the effectiveness of a multifaceted implementation strategy compared to usual care on improving the adherence to guideline recommendations on expectant management for couples with unexplained infertility? The multifaceted implementation strategy did not significantly increase adherence to guideline recommendations on expectant management compared to care as usual. Intrauterine insemination (IUI) with or without ovarian hyperstimulation has no beneficial effect compared to no treatment for 6 months after the fertility work-up for couples with unexplained infertility and a good prognosis of natural conception. Therefore, various professionals and policy makers have advocated the use of prognostic profiles and expectant management in guideline recommendations. A cluster randomized controlled trial in 25 clinics in the Netherlands was conducted between March 2013 and May 2014. Clinics were randomized between the implementation strategy (intervention, n = 13) and care as usual (control, n = 12). The effect of the implementation strategy was evaluated by comparing baseline and effect measurement data. Data collection was retrospective and obtained from medical record research and a patient questionnaire. A total of 544 couples were included at baseline and 485 at the effect measurement (247 intervention group/238 control group). Guideline adherence increased from 49 to 69% (OR 2.66; 95% CI 1.45-4.89) in the intervention group, and from 49 to 61% (OR 2.03; 95% CI 1.38-3.00) in the control group. Multilevel analysis with case-mix adjustment showed that the difference of 8% was not statistically significant (OR 1.31; 95% CI 0.67-2.59). The ongoing pregnancy rate within six months after fertility work-up did not significantly differ between intervention and control group (25% versus 27%: OR 0.72; 95% CI 0.40-1.27). There is a possible selection bias, couples included in the study had a higher socio-economic status than non-responders. How this affects guideline

  7. Teaching basic life support: a prospective randomized study on low-cost training strategies in secondary schools.

    Science.gov (United States)

    Van Raemdonck, Veerle; Monsieurs, Koenraad G; Aerenhouts, Dirk; De Martelaer, Kristine

    2014-08-01

    Cardiopulmonary resuscitation (CPR) training at school is recommended. Limited school resources prevent implementation. The learning efficacy of low-cost training strategies is unknown. To evaluate the efficacy of different CPR learning strategies using low-cost didactic tools. Children (n=593, 15-16 years) were randomized to four training conditions: (1) manikin+teacher instruction (control group), (2) manikin+video instruction, (3) foam dice+plastic bag+peer training+teacher instruction, and (4) foam dice+plastic bag+peer training+video instruction. After a 50 min training, a 3 min CPR test on a manikin was performed using SkillReporting Software (Laerdal, Norway), and repeated after 6 months. The data of children without previous CPR training were analysed. Analysis of variance and the χ-test assessed differences between groups. Complete data sets were available for 165 pupils. Initially, group 3 scored lower on the mean ventilation volume (PTraining efficacy with low-cost equipment was not different from training with a manikin. The outcome for all training strategies was suboptimal. The basics of CPR can be taught with alternative equipment if manikins are not available.

  8. Worksite Tobacco Prevention: A Randomized, Controlled Trial of Adoption, Dissemination Strategies, and Aggregated Health-Related Outcomes across Companies

    Directory of Open Access Journals (Sweden)

    Verena Friedrich

    2015-01-01

    Full Text Available Evidence based public health requires knowledge about successful dissemination of public health measures. This study analyses (a the changes in worksite tobacco prevention (TP in the Canton of Zurich, Switzerland, between 2007 and 2009; (b1 the results of a multistep versus a “brochure only” dissemination strategy; (b2 the results of a monothematic versus a comprehensive dissemination strategy that aim to get companies to adopt TP measures; and (c whether worksite TP is associated with health-related outcomes. A longitudinal design with randomized control groups was applied. Data on worksite TP and health-related outcomes were gathered by a written questionnaire (baseline n=1627; follow-up n=1452 and analysed using descriptive statistics, nonparametric procedures, and ordinal regression models. TP measures at worksites improved slightly between 2007 and 2009. The multistep dissemination was superior to the “brochure only” condition. No significant differences between the monothematic and the comprehensive dissemination strategies were observed. However, improvements in TP measures at worksites were associated with improvements in health-related outcomes. Although dissemination was approached at a mass scale, little change in the advocated adoption of TP measures was observed, suggesting the need for even more aggressive outreach or an acceptance that these channels do not seem to be sufficiently effective.

  9. A randomized controlled trial of an inference generation strategy intervention for adults with high-functioning autism spectrum disorder.

    Science.gov (United States)

    Murza, Kimberly A; Nye, Chad; Schwartz, Jamie B; Ehren, Barbara J; Hahs-Vaughn, Debbie L

    2014-08-01

    The present intervention study investigated the efficacy of the ACT & Check Strategy intervention to improve inference generation when reading, metacognitive ability, general reading comprehension, and social inference ability in adults with high-functioning autism spectrum disorder (HF-ASD). Twenty-five adults with HF-ASD were randomly assigned to either a treatment or a control group. Treatment sessions were conducted in 1-hr sessions, twice a week, for a total of 6 weeks. Treatment focused on explicit instruction of components of inference generation, categories of inferences, and increasingly independent strategy use. The treatment group demonstrated significantly superior performance on 1 of 2 measures of inference generation in reading and 1 measure of metacognitive ability compared with the control group. Significant differences between groups were not found on measures of reading comprehension or social inference ability. These findings suggest that the ACT & Check Strategy was effective in improving participants' ability to generate inferences in reading and certain metacognitive abilities, but the skills do not appear to generalize to other social communication contexts, such as social inference generation. This research provides a measure of support for explicitly teaching inference generation to address a reading inference deficit in adults with HF-ASD.

  10. A new interdisciplinary treatment strategy versus usual medical care for the treatment of subacromial impingement syndrome: a randomized controlled trial

    Directory of Open Access Journals (Sweden)

    van der Meer Klaas

    2007-02-01

    Full Text Available Abstract Background Subacromial impingement syndrome (SIS is the most frequently recorded shoulder disorder. When conservative treatment of SIS fails, a subacromial decompression is warranted. However, the best moment of referral for surgery is not well defined. Both early and late referrals have disadvantages – unnecessary operations and smaller improvements in shoulder function, respectively. This paper describes the design of a new interdisciplinary treatment strategy for SIS (TRANSIT, which comprises rules to treat SIS in primary care and a well-defined moment of referral for surgery. Methods/Design The effectiveness of an arthroscopic subacromial decompression versus usual medical care will be evaluated in a randomized controlled trial (RCT. Patients are eligible for inclusion when experiencing a recurrence of SIS within one year after a first episode of SIS which was successfully treated with a subacromial corticosteroid injection. After inclusion they will receive injection treatment again by their general practitioner. When, after this treatment, there is a second recurrence within a year post-injection, the participants will be randomized to either an arthroscopic subacromial decompression (intervention group or continuation of usual medical care (control group. The latter will be performed by a general practitioner according to the Dutch National Guidelines for Shoulder Problems. At inclusion, at randomization and three, six and 12 months post-randomization an outcome assessment will take place. The primary outcome measure is the patient-reported Shoulder Disability Questionnaire. The secondary outcome measures include both disease-specific and generic measures, and an economic evaluation. Treatment effects will be compared for all measurement points by using a GLM repeated measures analyses. Discussion The rationale and design of an RCT comparing arthroscopic subacromial decompression with usual medical care for subacromial

  11. A randomized comparison of different ventilator strategies during thoracotomy for pulmonary resection.

    Science.gov (United States)

    Maslow, Andrew D; Stafford, Todd S; Davignon, Kristopher R; Ng, Thomas

    2013-07-01

    Protective lung ventilation is reported to benefit patients with acute respiratory distress syndrome. It is not known whether protective lung ventilation is also beneficial to patients undergoing single-lung ventilation for elective pulmonary resection. In an institutional review board-approved prospective randomized trial, 34 patients undergoing elective pulmonary resection requiring single-lung ventilation were enrolled. Informed consent was obtained. Patients were randomized to 1 of 2 groups: (1) high tidal volume (Hi-TV) of 10 mL/kg, rate of 7 breaths/min, and zero positive end-expiratory pressure or (2) low tidal volume (Lo-TV) of 5 mL/kg, rate of 14 breaths/min, and 5 cmH2O positive end-expiratory pressure. Ventilator settings were continued during both double- and single-lung ventilation. Pulmonary functions, hemodynamics, and postoperative outcomes were recorded. Patient demographics, operative characteristics, intraoperative hemodynamics, and postoperative pain and sedation scores were similar between the 2 groups. During most time periods, airway pressures (peak and plateau) were significantly higher in the Hi-TV group; however, plateau pressures remained less than 30 cmH2O at all times for all patients. The Hi-TV group had significantly lower arterial carbon dioxide tension, less arterial carbon dioxide tension-end-tidal carbon dioxide gradient, lower alveolar dead space ratio, and higher dynamic pulmonary compliance. There were no differences in postoperative morbidity and hospital days between the 2 groups, but atelectasis scores on postoperative days 1 and 2 were lower in the Hi-TV group. The use of Hi-TV during single-lung ventilation for pulmonary resection resulted in no increase in morbidity and was associated with less hypercarbia, less dead space ventilation, better dynamic compliance, and less postoperative atelectasis. Copyright © 2013 The American Association for Thoracic Surgery. Published by Mosby, Inc. All rights reserved.

  12. Comparison of minimalist footwear strategies for simulating barefoot running: a randomized crossover study.

    Directory of Open Access Journals (Sweden)

    Karsten Hollander

    Full Text Available Possible benefits of barefoot running have been widely discussed in recent years. Uncertainty exists about which footwear strategy adequately simulates barefoot running kinematics. The objective of this study was to investigate the effects of athletic footwear with different minimalist strategies on running kinematics. Thirty-five distance runners (22 males, 13 females, 27.9 ± 6.2 years, 179.2 ± 8.4 cm, 73.4 ± 12.1 kg, 24.9 ± 10.9 km x week(-1 performed a treadmill protocol at three running velocities (2.22, 2.78 and 3.33 m x s(-1 using four footwear conditions: barefoot, uncushioned minimalist shoes, cushioned minimalist shoes, and standard running shoes. 3D kinematic analysis was performed to determine ankle and knee angles at initial foot-ground contact, rate of rear-foot strikes, stride frequency and step length. Ankle angle at foot strike, step length and stride frequency were significantly influenced by footwear conditions (p<0.001 at all running velocities. Posthoc pairwise comparisons showed significant differences (p<0.001 between running barefoot and all shod situations as well as between the uncushioned minimalistic shoe and both cushioned shoe conditions. The rate of rear-foot strikes was lowest during barefoot running (58.6% at 3.33 m x s(-1, followed by running with uncushioned minimalist shoes (62.9%, cushioned minimalist (88.6% and standard shoes (94.3%. Aside from showing the influence of shod conditions on running kinematics, this study helps to elucidate differences between footwear marked as minimalist shoes and their ability to mimic barefoot running adequately. These findings have implications on the use of footwear applied in future research debating the topic of barefoot or minimalist shoe running.

  13. Comparison of minimalist footwear strategies for simulating barefoot running: a randomized crossover study.

    Science.gov (United States)

    Hollander, Karsten; Argubi-Wollesen, Andreas; Reer, Rüdiger; Zech, Astrid

    2015-01-01

    Possible benefits of barefoot running have been widely discussed in recent years. Uncertainty exists about which footwear strategy adequately simulates barefoot running kinematics. The objective of this study was to investigate the effects of athletic footwear with different minimalist strategies on running kinematics. Thirty-five distance runners (22 males, 13 females, 27.9 ± 6.2 years, 179.2 ± 8.4 cm, 73.4 ± 12.1 kg, 24.9 ± 10.9 km x week(-1)) performed a treadmill protocol at three running velocities (2.22, 2.78 and 3.33 m x s(-1)) using four footwear conditions: barefoot, uncushioned minimalist shoes, cushioned minimalist shoes, and standard running shoes. 3D kinematic analysis was performed to determine ankle and knee angles at initial foot-ground contact, rate of rear-foot strikes, stride frequency and step length. Ankle angle at foot strike, step length and stride frequency were significantly influenced by footwear conditions (p<0.001) at all running velocities. Posthoc pairwise comparisons showed significant differences (p<0.001) between running barefoot and all shod situations as well as between the uncushioned minimalistic shoe and both cushioned shoe conditions. The rate of rear-foot strikes was lowest during barefoot running (58.6% at 3.33 m x s(-1)), followed by running with uncushioned minimalist shoes (62.9%), cushioned minimalist (88.6%) and standard shoes (94.3%). Aside from showing the influence of shod conditions on running kinematics, this study helps to elucidate differences between footwear marked as minimalist shoes and their ability to mimic barefoot running adequately. These findings have implications on the use of footwear applied in future research debating the topic of barefoot or minimalist shoe running.

  14. Efficacy of different strategies to treat anemia in children: a randomized clinical trial

    Directory of Open Access Journals (Sweden)

    García Olga P

    2010-09-01

    Full Text Available Abstract Background Anemia continues to be a major public health problem among children in many regions of the world, and it is still not clear which strategy to treat it is most effective. Objective To evaluate the efficacy and children's acceptance of several recognized strategies to treat anemia. Methods Non-breastfed children (n = 577, 6 to 43 mo of age, were screened for the trial; 267 were anemic (hemoglobin Results All treatments significantly increased Hb and total iron concentration; ferritin did not change significantly. Groups MMS, IS and IFS increased Hb (g/dL [1.50 (95%CI: 1.17, 1.83, 1.48 [(1.18, 1.78 and 1.57 (1.26, 1.88, respectively] and total iron ((μg/dL [0.15 (0.01, 0.29, 0.19 (0.06, 0.31 and 0.12(-0.01, 0.25, respectively] significantly more than FCF [0.92 (0.64, 1.20] but not to FW group [0.14 (0.04, 0.24]. The prevalence of anemia was reduced to a greater extent in the MMS and IFS groups (72% and 69%, respectively than in the FCF group (45% (p Conclusion The three supplements IS, ISF and MMS increased Hb more than the FCF; the supplements that contained micronutrients (IFS and MMS were more effective for reducing the prevalence of anemia. In general, fortified foods were better accepted by the study participants than supplements. ClinicalTrial.gov Identifier NCT00822380

  15. A behavioral strategy to minimize air pollution exposure in pregnant women: a randomized controlled trial.

    Science.gov (United States)

    Araban, Marzieh; Tavafian, Sedigheh Sadat; Zarandi, Saeed Motesaddi; Hidarnia, Ali Reza; Burri, Andrea; Montazeri, Ali

    2017-04-04

    Pregnant women and their fetus belong to a sensitive group in response to air pollution hazards. The aim of this study was to evaluate the effectiveness of a theory-based educational program to change pollution exposure behavior in pregnant women. In this randomized controlled trial, pregnant women attending a prenatal clinic in Tehran, Iran were selected and randomized into the experimental and control groups. The inclusion criteria were age between 18 and 35 years, having a history of pregnancies without adverse outcomes and not suffering from chronic diseases. Data collected at baseline and 2-month follow-up. At baseline face-to-face interviews were conducted using a valid and reliable questionnaire including items on demographic characteristics, stages of change, self-efficacy, decisional balance and practice regarding air pollution preventive behaviors. The intervention composed of three parts: motivational interviewing, a booklet and daily small message service (SMS). The control group received no intervention except receiving usual care. Follow-up data were collected after the intervention. Data were analyzed performing t-test, Mann-Whitney U test, and chi-squared. In all the data for 104 pregnant women (53 in the intervention and 51 in the control group) were analyzed. The mean age of participants was 27.2 (SD = 4.11) years and it was 22.89 (SD = 8.75) weeks for gestational age. At baseline there were no significant statistical differences between intervention and control groups on the study measures while we found significant group differences in terms of stages of change, self-efficacy, perceived benefits and practice regarding air pollution preventive behaviors at follow-up assessment (P pollution preventive behaviors among pregnant women. This study provided a framework to modify some psychosocial determinants of air pollution preventive behavior other than knowledge using constructs of Transtheoretical model of behavior change, additionally

  16. Eye Movement Training and Suggested Gaze Strategies in Tunnel Vision - A Randomized and Controlled Pilot Study.

    Directory of Open Access Journals (Sweden)

    Iliya V Ivanov

    Full Text Available Degenerative retinal diseases, especially retinitis pigmentosa (RP, lead to severe peripheral visual field loss (tunnel vision, which impairs mobility. The lack of peripheral information leads to fewer horizontal eye movements and, thus, diminished scanning in RP patients in a natural environment walking task. This randomized controlled study aimed to improve mobility and the dynamic visual field by applying a compensatory Exploratory Saccadic Training (EST.Oculomotor responses during walking and avoiding obstacles in a controlled environment were studied before and after saccade or reading training in 25 RP patients. Eye movements were recorded using a mobile infrared eye tracker (Tobii glasses that measured a range of spatial and temporal variables. Patients were randomly assigned to two training conditions: Saccade (experimental and reading (control training. All subjects who first performed reading training underwent experimental training later (waiting list control group. To assess the effect of training on subjects, we measured performance in the training task and the following outcome variables related to daily life: Response Time (RT during exploratory saccade training, Percent Preferred Walking Speed (PPWS, the number of collisions with obstacles, eye position variability, fixation duration, and the total number of fixations including the ones in the subjects' blind area of the visual field.In the saccade training group, RTs on average decreased, while the PPWS significantly increased. The improvement persisted, as tested 6 weeks after the end of the training. On average, the eye movement range of RP patients before and after training was similar to that of healthy observers. In both, the experimental and reading training groups, we found many fixations outside the subjects' seeing visual field before and after training. The average fixation duration was significantly shorter after the training, but only in the experimental training

  17. Eye Movement Training and Suggested Gaze Strategies in Tunnel Vision - A Randomized and Controlled Pilot Study

    Science.gov (United States)

    Ivanov, Iliya V.; Mackeben, Manfred; Vollmer, Annika; Martus, Peter; Nguyen, Nhung X.; Trauzettel-Klosinski, Susanne

    2016-01-01

    Purpose Degenerative retinal diseases, especially retinitis pigmentosa (RP), lead to severe peripheral visual field loss (tunnel vision), which impairs mobility. The lack of peripheral information leads to fewer horizontal eye movements and, thus, diminished scanning in RP patients in a natural environment walking task. This randomized controlled study aimed to improve mobility and the dynamic visual field by applying a compensatory Exploratory Saccadic Training (EST). Methods Oculomotor responses during walking and avoiding obstacles in a controlled environment were studied before and after saccade or reading training in 25 RP patients. Eye movements were recorded using a mobile infrared eye tracker (Tobii glasses) that measured a range of spatial and temporal variables. Patients were randomly assigned to two training conditions: Saccade (experimental) and reading (control) training. All subjects who first performed reading training underwent experimental training later (waiting list control group). To assess the effect of training on subjects, we measured performance in the training task and the following outcome variables related to daily life: Response Time (RT) during exploratory saccade training, Percent Preferred Walking Speed (PPWS), the number of collisions with obstacles, eye position variability, fixation duration, and the total number of fixations including the ones in the subjects' blind area of the visual field. Results In the saccade training group, RTs on average decreased, while the PPWS significantly increased. The improvement persisted, as tested 6 weeks after the end of the training. On average, the eye movement range of RP patients before and after training was similar to that of healthy observers. In both, the experimental and reading training groups, we found many fixations outside the subjects' seeing visual field before and after training. The average fixation duration was significantly shorter after the training, but only in the

  18. 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.

  19. 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.

  20. Implementation of kangaroo mother care: a randomized trial of two outreach strategies.

    Science.gov (United States)

    Pattinson, Robert C; Arsalo, Irmeli; Bergh, Anne-Marie; Malan, Atties F; Patrick, Mark; Phillips, Noel

    2005-07-01

    To test whether a well-designed educational package on the implementation of kangaroo mother care (KMC) used on its own can be as effective in implementing KMC in a healthcare facility as the combination of a visiting facilitator used in conjunction with the package. Thirty-four hospitals in KwaZulu-Natal Province, South Africa. The hospitals were paired with respect to their geographical location and annual number of births at the facility. One hospital in each pair was randomly allocated to receive either the implementation package alone (group A) or the implementation package and visits from a facilitator (group B). Hospitals in group B received three facilitation visits. All hospitals were evaluated by a site visit 8 mo after launching the process and were scored by means of a progress-monitoring tool. Successful implementation was regarded as demonstrating evidence of practice (score>10) during the site visit. Group B scored significantly better than group A (ppackage was clearly superior to using a package alone. Some sites do not need facilitation for successful implementation.

  1. Effectiveness of home visit falls prevention strategy for Taiwanese community-dwelling elders: randomized trial.

    Science.gov (United States)

    Huang, Tzu-Ting; Acton, Gayle J

    2004-01-01

    The purpose of this research was to examine the effect of a multifactorial intervention to prevent falls by increasing self-efficacy to prevent falls, improving the knowledge of medication safety, and decreasing the number of environmental risks in older persons dwelling in the community. A sample of 120 cognitively intact residents of this community who were 65 years of age and older were recruited into a two-group pretest-post-test experimental design and randomly assigned to an experimental group and a comparison group (60 in each group). The intervention was delivered, and data were collected during three home visits in a 4-month period. (1) Experimental subjects improved their fall self-efficacy, environmental safety, and knowledge of medication safety significantly (p falls was reduced at post-test in both groups compared to pretest scores, and the falling was more serious in the comparison group at post-test compared to that in the experimental group. The results can help community health professionals to individualize their interventions to the specific needs of the elderly, thus helping to prevent falls among community-dwelling elders.

  2. The utility of the random controlled trial for evaluating sexual offender treatment: the gold standard or an inappropriate strategy?

    Science.gov (United States)

    Marshall, W L; Marshall, L E

    2007-06-01

    This paper examines the scientific, practical, and ethical issues surrounding the employment of the Random Controlled Trial (RCT) in the evaluation of sexual offender treatment. Consideration of these issues leads us to conclude that the RCT design is not suitable for determining the effectiveness of sexual offender treatment. We also examine the RCT study by Marques et al. (Sexual Abuse: A Journal of Research and Treatment and Evaluation 17:79-107, 2005) that is often held up as the model for the evaluation of sexual offender treatment. We found several problems with this study that, in our opinion, reduce its relevance for deciding whether treatment is effective with these clients. Finally, we examine two alternative strategies for evaluating treatment that may allow treatment providers to more readily examine, and report, the results of their programs.

  3. Efficacy of different strategies to treat anemia in children: a randomized clinical trial

    Science.gov (United States)

    2010-01-01

    Background Anemia continues to be a major public health problem among children in many regions of the world, and it is still not clear which strategy to treat it is most effective. Objective To evaluate the efficacy and children's acceptance of several recognized strategies to treat anemia. Methods Non-breastfed children (n = 577), 6 to 43 mo of age, were screened for the trial; 267 were anemic (hemoglobin acid supplement (IFS), a multiple micronutrient supplement (MMS), a micronutrient-fortified complementary food as porridge powder (FCF), or zinc+iron+ascorbic acid fortified water (FW). The iron content of each daily dose was 20, 12.5, 10, 10 and 6.7 mg respectively. Hemoglobin (Hb), ferritin, total iron, weight and height were measured at baseline and after 4 months of treatment. Morbidity, treatment acceptability and adherence were recorded during the intervention. Results All treatments significantly increased Hb and total iron concentration; ferritin did not change significantly. Groups MMS, IS and IFS increased Hb (g/dL) [1.50 (95%CI: 1.17, 1.83), 1.48 [(1.18, 1.78) and 1.57 (1.26, 1.88), respectively] and total iron ((μg/dL) [0.15 (0.01, 0.29), 0.19 (0.06, 0.31) and 0.12(-0.01, 0.25), respectively] significantly more than FCF [0.92 (0.64, 1.20)] but not to FW group [0.14 (0.04, 0.24)]. The prevalence of anemia was reduced to a greater extent in the MMS and IFS groups (72% and 69%, respectively) than in the FCF group (45%) (p children, than IFS, FCF and FW. Conclusion The three supplements IS, ISF and MMS increased Hb more than the FCF; the supplements that contained micronutrients (IFS and MMS) were more effective for reducing the prevalence of anemia. In general, fortified foods were better accepted by the study participants than supplements. ClinicalTrial.gov Identifier NCT00822380 PMID:20863398

  4. Use of online recruitment strategies in a randomized trial of cancer survivors.

    Science.gov (United States)

    Juraschek, Stephen P; Plante, Timothy B; Charleston, Jeanne; Miller, Edgar R; Yeh, Hsin-Chieh; Appel, Lawrence J; Jerome, Gerald J; Gayles, Debra; Durkin, Nowella; White, Karen; Dalcin, Arlene; Hermosilla, Manuel

    2017-12-01

    Despite widespread Internet adoption, online advertising remains an underutilized tool to recruit participants into clinical trials. Whether online advertising is a cost-effective method to enroll participants compared to other traditional forms of recruitment is not known. Recruitment for the Survivorship Promotion In Reducing IGF-1 Trial, a community-based study of cancer survivors, was conducted from June 2015 through December 2016 via in-person community fairs, advertisements in periodicals, and direct postal mailings. In addition, "Right Column" banner ads were purchased from Facebook to direct participants to the Survivorship Promotion In Reducing IGF-1 Trial website. Response rates, costs of traditional and online advertisements, and demographic data were determined and compared across different online and traditional recruitment strategies. Micro-trials optimizing features of online advertisements were also explored. Of the 406 respondents to our overall outreach efforts, 6% (24 of 406) were referred from online advertising. Facebook advertisements were shown over 3 million times (impressions) to 124,476 people, which resulted in 4401 clicks on our advertisement. Of these, 24 people ultimately contacted study staff, 6 underwent prescreening, and 4 enrolled in the study. The cost of online advertising per enrollee was $794 when targeting a general population versus $1426 when accounting for strategies that specifically targeted African Americans or men. By contrast, community fairs, direct mail, or periodicals cost $917, $799, or $436 per enrollee, respectively. Utilization of micro-trials to assess online ads identified subtleties (e.g. use of an advertisement title) that substantially impacted viewer interest in our trial. Online advertisements effectively directed a relevant population to our website, which resulted in new enrollees in the Survivorship Promotion In Reducing IGF-1 Trial at a cost comparable to traditional methods. Costs were

  5. Effectiveness of a clinical practice guideline implementation strategy for patients with anxiety disorders in primary care: cluster randomized trial

    Directory of Open Access Journals (Sweden)

    Tello-Bernabé Eugenia

    2011-12-01

    Full Text Available Abstract Background Anxiety is a common mental health problem seen in primary care. However, its management in clinical practice varies greatly. Clinical practice guidelines (CPGs have the potential to reduce variations and improve the care received by patients by promoting interventions of proven benefit. However, uptake and adherence to their recommendations can be low. Method/design This study involves a community based on cluster randomized trial in primary healthcare centres in the Madrid Region (Spain. The project aims to determine whether the use of implementation strategy (including training session, information, opinion leader, reminders, audit, and feed-back of CPG for patients with anxiety disorders in primary care is more effective than usual diffusion. The number of patients required is 296 (148 in each arm, all older than 18 years and diagnosed with generalized anxiety disorder, panic disorder, and panic attacks by the Diagnostic and Statistical Manual of Mental Disorders-IV (DSM-IV. They are chosen by consecutive sampling. The main outcome variable is the change in two or more points into Goldberg anxiety scale at six and twelve months. Secondary outcome variables include quality of life (EuroQol 5D, and degree of compliance with the CPG recommendations on treatment, information, and referrals to mental health services. Main effectiveness will be analyzed by comparing the patients percentage improvement on the Goldberg scale between the intervention group and the control group. Logistic regression with random effects will be used to adjust for prognostic factors. Confounding factors or factors that might alter the effect recorded will be taken into account in this analysis. Discussion There is a need to identify effective implementation strategies for CPG for the management of anxiety disorders present in primary care. Ensuring the appropriate uptake of guideline recommendations can reduce clinical variation and improve the care

  6. [Randomized clinical trial of a fall-prevention strategy for institutionalized elderly based on the Mini Falls Assessment Instrument].

    Science.gov (United States)

    Salvà, Antoni; Rojano, Xavier; Coll-Planas, Laura; Domènech, Sara; Roqué I Figuls, Marta

    2016-01-01

    The Mini Falls Assessment Instrument (MFAI) identifies risk factors for falls in an individual and links them to specific interventions. This study evaluates the effectiveness of MFAI as the basis for a falls prevention strategy in institutionalized elderly. A cluster randomized clinical trial (identifier NCT00888953) was conducted in 16 nursing homes randomized to apply MFAI (intervention) or a modified version not linked to actions (control). The primary endpoint was the occurrence of falls during follow-up (12 months). Secondary variables were total number of falls, physical function, quality of life, functional status, and adverse effects. Data from 330 participants (197 intervention, 137 control) were analyzed. Both groups had a similar number of risk factors: 7 in the intervention group (range 1-12) and 8 (1-13) in the control group. In the intervention group there were more fallers (49% vs. 38%), and higher number of falls (315 vs. 109), and fall rate per 100 person-years (192.5 vs. 179.8) than the control group. In the multivariate analysis, there were no significant differences in fall risk (odds ratio=1.45; 95% confidence interval [CI]: .67 to 3.14; P=.350), but the incidence rate is significantly higher in the intervention group (Incidence rate ratio=2.23; 95% CI: 1.43 to 3.48; P<.001). The results on the efficacy of the MFAI as a fall prevention strategy are inconclusive. Additional studies are needed in order to provide good quality evidence. Copyright © 2014 SEGG. Published by Elsevier Espana. All rights reserved.

  7. Randomized Trial of Hypnosis as a Pain and Symptom Management Strategy in Adults with Sickle Cell Disease

    Science.gov (United States)

    Wallen, Gwenyth R; Middleton, Kimberly R; Ames, Nancy; Brooks, Alyssa T; Handel, Daniel

    2014-01-01

    Sickle cell disease (SCD) is the most common genetic disease in African-Americans, characterized by recurrent painful vaso-occlusive crises. Medical therapies for controlling or preventing crises are limited because of efficacy and/or toxicity. This is a randomized, controlled, single-crossover protocol of hypnosis for managing pain in SCD patients. Participants receive hypnosis from a trained hypnosis therapist followed by six weeks of self-hypnosis using digital media. Those in the control arm receive SCD education followed by a six-week waiting period before crossing over to the hypnosis arm of the study. Outcome measures include assessments of pain (frequency, intensity and quality), anxiety, coping strategies, sleep, depression, and health care utilization. To date, there are no published randomized, controlled trials evaluating the efficacy of hypnosis on SCD pain modulation in adults. Self-hypnosis for pain management may be helpful in modulating chronic pain, improving sleep quality, and decreasing use of narcotics in patients with SCD. TRIAL REGISTRATION ClinicalTrials.gov: NCT00393250 PMID:25520557

  8. Randomized Trial of Hypnosis as a Pain and Symptom Management Strategy in Adults with Sickle Cell Disease

    Directory of Open Access Journals (Sweden)

    Gwenyth R. Wallen

    2014-01-01

    Full Text Available Sickle cell disease (SCD is the most common genetic disease in African-Americans, characterized by recurrent painful vaso-occlusive crises. Medical therapies for controlling or preventing crises are limited because of efficacy and/or toxicity. This is a randomized, controlled, single-crossover protocol of hypnosis for managing pain in SCD patients. Participants receive hypnosis from a trained hypnosis therapist followed by six weeks of self-hypnosis using digital media. Those in the control arm receive SCD education followed by a six-week waiting period before crossing over to the hypnosis arm of the study. Outcome measures include assessments of pain (frequency, intensity and quality, anxiety, coping strategies, sleep, depression, and health care utilization. To date, there are no published randomized, controlled trials evaluating the efficacy of hypnosis on SCD pain modulation in adults. Self-hypnosis for pain management may be helpful in modulating chronic pain, improving sleep quality, and decreasing use of narcotics in patients with SCD. TRIAL REGISTRATION: ClinicalTrials.gov: NCT00393250

  9. Financial Incentives for Adherence to Hepatitis C Virus Clinical Care and Treatment: A Randomized Trial of Two Strategies

    Science.gov (United States)

    Allmon, Andrew G.; Evon, Donna; Hurt, Christopher; Reifeis, Sarah Ailleen; Thirumurthy, Harsha; Straub, Becky; Edwards, Angela; Mollan, Katie R.

    2017-01-01

    Abstract Background. Although rates of sustained virologic response (SVR) after hepatitis C virus (HCV) treatment with direct-acting antivirals (DAAs) surpass 90% in trials and some more “real world” settings, some patients, such as those with substance use disorders, will be challenged to adhere to HCV care. Methods. To assess the feasibility of 2 strategies for financially incentivizing adherence to HCV care, patients with a substance use history prescribed 12 weeks of a sofosbuvir-containing regimen were randomized to either fixed or lottery-based monetary incentives for attending clinic appointments, pill count adherence >90%, and SVR achievement. Electronic medication monitoring provided an objective measure of DAA adherence. Results. Fifty-nine participants were randomized to the lottery (n = 31) or fixed-incentive (n = 28) arms. All 31 (100%) in the lottery arm and 24 of 28 (86%) in the fixed arm completed 12 weeks of therapy. By intent-to-treat, 93% in the lottery arm and 92% in the fixed arm achieved SVR (estimated difference: 0.5%; 95% confidence interval, −17.5 to 18.8). Overall, 92% of scheduled visits were attended without significant differences between arms. The mean adherence ratio (days with ≥1 bottle opening:monitored days) was 0.91 for lottery and 0.92 for fixed arms. Conclusions. In this pilot, fixed- and lottery-based financial incentives were successfully implemented and accepted by patients with a substance use history. High levels of HCV therapy and care adherence, as well as rates of SVR, were observed. Financial incentives may be useful to support treatment adherence in patients with substance use disorders and should be tested in a larger, randomized, controlled trial. PMID:28695144

  10. Caries management strategies for primary molars: 1-yr randomized control trial results.

    Science.gov (United States)

    Santamaria, R M; Innes, N P T; Machiulskiene, V; Evans, D J P; Splieth, C H

    2014-11-01

    Minimal invasive approaches to managing caries, such as partial caries removal techniques, are showing increasing evidence of improved outcomes over the conventional complete caries removal. There is also increasing interest in techniques where no caries is removed. We present the 1-yr results of clinical efficacy for 3 caries management options for occlusoproximal cavitated lesions in primary molars: conventional restorations (CR; complete caries removal and compomer restoration), Hall technique (HT; no caries removal, sealing in with stainless steel crowns), and nonrestorative caries treatment (NRCT; no caries removal, opening up the cavity, teaching brushing and fluoride application). In sum, 169 children (3-8 yr old; mean, 5.56 ± 1.45 yr) were enrolled in this secondary care-based, 3-arm, parallel-group, randomized clinical trial. Treatments were carried out by specialist pediatric dentists or postgraduate trainees. One lesion per child received CR, HT, or NRCT. Outcome measures were clinical failure rates, grouped as minor failure (restoration loss/need for replacement, reversible pulpitis, caries progression, etc.) and major failure (irreversible pulpitis, abscess, etc.). There were 148 children (87.6%) with a minimum follow-up of 11 mo (mean, 12.23 ± 0.98 mo). Twenty teeth were recorded as having at least 1 minor failure: NRCT, n = 8 (5%); CR, n = 11 (7%); HT, n = 1 (1%) (p = .002, 95% CI = 0.001 to 0.003). Only the comparison between NRCT and CR showed no significant difference (p = .79, 95% CI = 0.78 to 0.80). Nine (6%) experienced at least 1 major failure: NRCT, n = 4 (2%); CR, n = 5 (3%); HT, n = 0 (0%) (p = .002, 95% CI = 0.001 to 0.003). Individual comparison of NRCT and CR showed no statistically significant difference in major failures (p = .75, 95% CI = 0.73 to 0.76). Success and failure rates were not significantly affected by pediatric dentists' level of experience (p = .13, 95% CI = 0.12 to 0.14). The HT was significantly more successful

  11. Bacterial Artificial Chromosome Mutagenesis Using Recombineering

    Directory of Open Access Journals (Sweden)

    Kumaran Narayanan

    2011-01-01

    Full Text Available Gene expression from bacterial artificial chromosome (BAC clones has been demonstrated to facilitate physiologically relevant levels compared to viral and nonviral cDNA vectors. BACs are large enough to transfer intact genes in their native chromosomal setting together with flanking regulatory elements to provide all the signals for correct spatiotemporal gene expression. Until recently, the use of BACs for functional studies has been limited because their large size has inherently presented a major obstacle for introducing modifications using conventional genetic engineering strategies. The development of in vivo homologous recombination strategies based on recombineering in E. coli has helped resolve this problem by enabling facile engineering of high molecular weight BAC DNA without dependence on suitably placed restriction enzymes or cloning steps. These techniques have considerably expanded the possibilities for studying functional genetics using BACs in vitro and in vivo.

  12. New approach for fish breeding by chemical mutagenesis: establishment of TILLING method in fugu (Takifugu rubripes) with ENU mutagenesis

    OpenAIRE

    Kuroyanagi, Miwa; Katayama, Takashi; Imai, Tadashi; Yamamoto, Yoshihisa; Chisada, Shin-ichi; Yoshiura, Yasutoshi; Ushijima, Tomokazu; Matsushita, Tomonao; Fujita, Masashi; Nozawa, Aoi; Suzuki, Yuzuru; Kikuchi, Kiyoshi; Okamoto, Hiroyuki

    2013-01-01

    Background In fish breeding, it is essential to discover and generate fish exhibiting an effective phenotype for the aquaculture industry, but screening for natural mutants by only depending on natural spontaneous mutations is limited. Presently, reverse genetics has become an important tool to generate mutants, which exhibit the phenotype caused by inactivation of a gene. TILLING (Targeting Induced Local Lesions IN Genomes) is a reverse genetics strategy that combines random chemical mutagen...

  13. 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.

  14. Stationary-state mutagenesis in Escherichia coli: a model

    Indian Academy of Sciences (India)

    Stationary-phase mutagenesis in nondividing E. coli cells exposed to a nonlethal stress was, a few years ago, claimed to be a likely case of a Lamarckian mechanism capable of producing exclusively useful mutations in a directed manner. After a heated debate over the last decade it now appears to involve a Darwinian ...

  15. 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

  16. 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...

  17. Effect of Colchicine Induced Mutagenesis on Growth and Yield of ...

    African Journals Online (AJOL)

    Chemical mutagenesis through the use of colchicine on the seeds of two varieties of sesame (Sesamum indicum L. Var. Ex-Sudan and E-8) with the aim of inducing variability that could be exploited in the genetic improvement of its growth and yield was carried out. The sesame seeds were treated with colchicines at four ...

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

    DEFF Research Database (Denmark)

    Nilsson, Martin; Christiansen, Natalia; Høiby, Niels

    2014-01-01

    ATs-pWV01, a selectable kanamycin resistance gene, a Himar1 transposase gene regulated by a xylose-inducible promoter, and an erythromycin resistance gene flanked by himar inverted repeats. The pMN100 plasmid was transformed into Streptococcus mutans UA159 and transposon mutagenesis was performed via...

  19. Rationale and study design for an individualized perioperative open lung ventilatory strategy (iPROVE): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Ferrando, Carlos; Soro, Marina; Canet, Jaume; Unzueta, Ma Carmen; Suárez, Fernando; Librero, Julián; Peiró, Salvador; Llombart, Alicia; Delgado, Carlos; León, Irene; Rovira, Lucas; Ramasco, Fernando; Granell, Manuel; Aldecoa, César; Diaz, Oscar; Balust, Jaume; Garutti, Ignacio; de la Matta, Manuel; Pensado, Alberto; Gonzalez, Rafael; Durán, M Eugenia; Gallego, Lucia; Del Valle, Santiago García; Redondo, Francisco J; Diaz, Pedro; Pestaña, David; Rodríguez, Aurelio; Aguirre, Javier; García, Jose M; García, Javier; Espinosa, Elena; Charco, Pedro; Navarro, Jose; Rodríguez, Clara; Tusman, Gerardo; Belda, Francisco Javier

    2015-04-27

    Postoperative pulmonary and non-pulmonary complications are common problems that increase morbidity and mortality in surgical patients, even though the incidence has decreased with the increased use of protective lung ventilation strategies. Previous trials have focused on standard strategies in the intraoperative or postoperative period, but without personalizing these strategies to suit the needs of each individual patient and without considering both these periods as a global perioperative lung-protective approach. The trial presented here aims at comparing postoperative complications when using an individualized ventilatory management strategy in the intraoperative and immediate postoperative periods with those when using a standard protective ventilation strategy in patients scheduled for major abdominal surgery. This is a comparative, prospective, multicenter, randomized, and controlled, four-arm trial that will include 1012 patients with an intermediate or high risk for postoperative pulmonary complications. The patients will be divided into four groups: (1) individualized perioperative group: intra- and postoperative individualized strategy; (2) intraoperative individualized strategy + postoperative continuous positive airway pressure (CPAP); (3) intraoperative standard ventilation + postoperative CPAP; (4) intra- and postoperative standard strategy (conventional strategy). The primary outcome is a composite analysis of postoperative complications. The Individualized Perioperative Open-lung Ventilatory Strategy (iPROVE) is the first multicenter, randomized, and controlled trial to investigate whether an individualized perioperative approach prevents postoperative pulmonary complications. Registered on 5 June 2014 with identification no. NCT02158923 .

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

    LENUS (Irish Health Repository)

    Biniecka, Monika

    2012-02-01

    OBJECTIVE: To assess the levels and spectrum of mitochondrial DNA (mtDNA) point mutations in synovial tissue from patients with inflammatory arthritis in relation to in vivo hypoxia and oxidative stress levels. METHODS: Random Mutation Capture assay was used to quantitatively evaluate alterations of the synovial mitochondrial genome. In vivo tissue oxygen levels (tPO(2)) were measured at arthroscopy using a Licox probe. Synovial expression of lipid peroxidation (4-hydroxynonenal [4-HNE]) and mitochondrial cytochrome c oxidase subunit II (CytcO II) deficiency were assessed by immunohistochemistry. In vitro levels of mtDNA point mutations, reactive oxygen species (ROS), mitochondrial membrane potential, and markers of oxidative DNA damage (8-oxo-7,8-dihydro-2\\'-deoxyguanine [8-oxodG]) and lipid peroxidation (4-HNE) were determined in human synoviocytes under normoxia and hypoxia (1%) in the presence or absence of superoxide dismutase (SOD) or N-acetylcysteine (NAC) or a hydroxylase inhibitor (dimethyloxalylglycine [DMOG]). Patients were categorized according to their in vivo tPO(2) level (<20 mm Hg or >20 mm Hg), and mtDNA point mutations, immunochemistry features, and stress markers were compared between groups. RESULTS: The median tPO(2) level in synovial tissue indicated significant hypoxia (25.47 mm Hg). Higher frequency of mtDNA mutations was associated with reduced in vivo oxygen tension (P = 0.05) and with higher synovial 4-HNE cytoplasmic expression (P = 0.04). Synovial expression of CytcO II correlated with in vivo tPO(2) levels (P = 0.03), and levels were lower in patients with tPO(2) <20 mm Hg (P < 0.05). In vitro levels of mtDNA mutations, ROS, mitochondrial membrane potential, 8-oxo-dG, and 4-HNE were higher in synoviocytes exposed to 1% hypoxia (P < 0.05); all of these increased levels were rescued by SOD and DMOG and, with the exception of ROS, by NAC. CONCLUSION: These findings demonstrate that hypoxia-induced mitochondrial dysfunction drives

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

    NARCIS (Netherlands)

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

    2015-01-01

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

  2. An Improved Ensemble of Random Vector Functional Link Networks Based on Particle Swarm Optimization with Double Optimization Strategy.

    Science.gov (United States)

    Ling, Qing-Hua; Song, Yu-Qing; Han, Fei; Yang, Dan; Huang, De-Shuang

    2016-01-01

    For ensemble learning, how to select and combine the candidate classifiers are two key issues which influence the performance of the ensemble system dramatically. Random vector functional link networks (RVFL) without direct input-to-output links is one of suitable base-classifiers for ensemble systems because of its fast learning speed, simple structure and good generalization performance. In this paper, to obtain a more compact ensemble system with improved convergence performance, an improved ensemble of RVFL based on attractive and repulsive particle swarm optimization (ARPSO) with double optimization strategy is proposed. In the proposed method, ARPSO is applied to select and combine the candidate RVFL. As for using ARPSO to select the optimal base RVFL, ARPSO considers both the convergence accuracy on the validation data and the diversity of the candidate ensemble system to build the RVFL ensembles. In the process of combining RVFL, the ensemble weights corresponding to the base RVFL are initialized by the minimum norm least-square method and then further optimized by ARPSO. Finally, a few redundant RVFL is pruned, and thus the more compact ensemble of RVFL is obtained. Moreover, in this paper, theoretical analysis and justification on how to prune the base classifiers on classification problem is presented, and a simple and practically feasible strategy for pruning redundant base classifiers on both classification and regression problems is proposed. Since the double optimization is performed on the basis of the single optimization, the ensemble of RVFL built by the proposed method outperforms that built by some single optimization methods. Experiment results on function approximation and classification problems verify that the proposed method could improve its convergence accuracy as well as reduce the complexity of the ensemble system.

  3. Recruiting and retaining low-income, multi-ethnic women into randomized controlled trials: successful strategies and staffing.

    Science.gov (United States)

    Barnett, Josephine; Aguilar, Stephanie; Brittner, Mindy; Bonuck, Karen

    2012-09-01

    Developing effective recruitment and retention strategies in populations with traditionally high attrition rates is critical to the success of Randomized Controlled Trials (RCTs). Data on successful participation of women from low-income, minority populations in RCTs of behavioral interventions are limited. This is problematic given the multiplicity of Healthy People 2020 goals that target health disparities in these populations. This paper reports successful recruitment and retention methods from two separately funded NIH clinical trials of primary care-based prenatal interventions to increase breastfeeding among ethnically diverse, low-income women in urban medical centers in the Bronx, NY. It also presents the required staff effort necessary to conduct such a successful RCT, in terms of full-time equivalents (FTEs). Results include timely recruitment of 941 participants over 29 months, with 98.1% completing >¯¯1 follow-up interview. A recruitment and retention plan that maximized study staff access and availability to the participant, as well as strong study staff rapport with participants, addressed previously reported barriers in this population, optimizing follow-up rates. A qualitative assessment of the participants' study experience suggesting that high retention was due to strong rapport with participants, short interviews requiring little time commitment, and participants' perception of the study as informative, provides further evidence of our approach's effectiveness. Logistical protocol procedures and staff management strategies relating to successful recruitment/retention are provided to propose a practical, cost-effective and translational recruitment-retention plan for other researchers to adopt. Copyright © 2012 Elsevier Inc. All rights reserved.

  4. Comparative Effectiveness of Post-Discharge Strategies for Hospitalized Smokers: study protocol for the Helping HAND 2 randomized controlled trial.

    Science.gov (United States)

    Reid, Zachary Z; Regan, Susan; Kelley, Jennifer H K; Streck, Joanna M; Ylioja, Thomas; Tindle, Hilary A; Chang, Yuchiao; Levy, Douglas E; Park, Elyse R; Singer, Daniel E; Carpenter, Kelly M; Reyen, Michele; Rigotti, Nancy A

    2015-02-07

    Smoking cessation interventions for hospitalized smokers are effective in promoting smoking cessation, but only if the tobacco dependence treatment continues after the patient leaves the hospital. Sustaining tobacco dependence treatment after hospital discharge is a challenge for health care systems. Our previous single-site randomized controlled trial demonstrated the effectiveness of an intervention that facilitated the delivery of comprehensive tobacco cessation treatment, including both medication and counseling, after hospital discharge. We subsequently streamlined the intervention model to increase its potential for dissemination. This new model is being tested in a larger multi-site trial with broader eligibility criteria in order to enroll a more representative sample of hospitalized smokers. This paper describes the trial design and contrasts it with the earlier study. A 2-arm, 3-site randomized controlled trial is testing the hypothesis that a multi-component Sustained Care intervention is more effective than Standard Care in helping hospitalized cigarette smokers stop smoking after hospital discharge. The trial enrolls adult daily cigarette smokers who are admitted to 1 of 3 participating hospitals in Massachusetts or Pennsylvania. Participants receive the same smoking cessation intervention in the hospital. They are randomly assigned to receive either Standard Care or Sustained Care after hospital discharge. Participants in the Sustained Care arm receive a free 3-month supply of FDA-approved smoking cessation medication and 5 interactive voice response calls that provide tailored motivational messages, medication refills, and access to a live tobacco treatment counselor. Participants in the Standard Care arm receive a smoking cessation medication recommendation and information about community resources. Outcomes are assessed at 1, 3, and 6 months after discharge. The primary outcome is biochemically-validated tobacco abstinence for the past 7 days at 6

  5. Cost-effectiveness of a mild compared with a standard strategy for IVF: a randomized comparison using cumulative term live birth as the primary endpoint.

    Science.gov (United States)

    Polinder, S; Heijnen, E M E W; Macklon, N S; Habbema, J D F; Fauser, B J C M; Eijkemans, M J C

    2008-02-01

    BACKGROUND Conventional ovarian stimulation and the transfer of two embryos in IVF exhibits an inherent high probability of multiple pregnancies, resulting in high costs. We evaluated the cost-effectiveness of a mild compared with a conventional strategy for IVF. METHODS Four hundred and four patients were randomly assigned to undergo either mild ovarian stimulation/GnRH antagonist co-treatment combined with single embryo transfer, or standard stimulation/GnRH agonist long protocol and the transfer of two embryos. The main outcome measures are total costs of treatment within a 12 months period after randomization, and the relationship between total costs and proportion of cumulative pregnancies resulting in term live birth within 1 year of randomization. RESULTS Despite a significantly increased average number of IVF cycles (2.3 versus 1.7; P strategy. This was mainly due to higher costs of the obstetric and post-natal period for the standard strategy, related to multiple pregnancies. The costs per pregnancy leading to term live birth were euro19 156 in the mild strategy and euro24 038 in the standard. The incremental cost-effectiveness ratio of the standard strategy compared with the mild strategy was euro185 000 per extra pregnancy leading to term live birth. CONCLUSIONS Despite an increased mean number of IVF cycles within 1 year, from an economic perspective, the mild treatment strategy is more advantageous per term live birth. It is unlikely, over a wide range of society's willingness-to-pay, that the standard treatment strategy is cost-effective, compared with the mild strategy.

  6. The optimal strategy of percutaneous coronary intervention for ST-elevation myocardial infarction patients with multivessel disease: an updated meta-analysis of 9 randomized controlled trials.

    Science.gov (United States)

    Fan, Zhong G; Gao, Xiao F; Li, Xiao B; Mao, Wen X; Chen, Li W; Tian, Nai L

    2017-04-01

    The optimal strategy of percutaneous coronary intervention (PCI) for patients with ST-elevation myocardial infarction (STEMI) and multivessel disease (MVD) still remains controversial. This study sought to explore the optimal PCI strategy for those patients. Medline, EMBASE and the Cochrane Controlled Trials Registry were searched for relevant studies. We analyzed the comparison of major adverse cardiac events (MACEs) as the primary end point between the preventive PCI strategy and the culprit only PCI strategy (CV-PCI). The further analysis of two subgroups described as the complete multivessel PCI strategy during primary procedure (CMV-PCI) and the staged PCI strategy (S-PCI) was also performed. Nine randomized trials were identified. The risk of MACEs was reduced significantly regarding to preventive PCI strategy (OR=0.41, 95% CI: 0.31-0.53, Pstrategy. There were lower risks of long-term mortality, reinfarction and repeat revascularization in the preventive PCI group compared to the CV-PCI group (OR=0.41, 95% CI: 0.27-0.62, Pstrategy reduced the incidence of long-term mortality versus CMV-PCI strategy. The preventive PCI is associated with the lower risk of MACEs in STEMI patients with MVD compared to the CV-PCI strategy, and the S-PCI strategy seems to be an optimal choice for these patients rather than the CMV-PCI.

  7. Cost-effectiveness of antibiotic treatment strategies for community-acquired pneumonia : results from a cluster randomized cross-over trial

    NARCIS (Netherlands)

    van Werkhoven, Cornelis H; Postma, Douwe F; Mangen, Marie-Josee J; Oosterheert, Jan Jelrik; Bonten, Marc J M

    2017-01-01

    BACKGROUND: To determine the cost-effectiveness of strategies of preferred antibiotic treatment with beta-lactam/macrolide combination or fluoroquinolone monotherapy compared to beta-lactam monotherapy. METHODS: Costs and effects were estimated using data from a cluster-randomized cross-over trial

  8. Efficacy of Self-Regulated Strategy Development Instruction for Developing Writers with and without Disabilities in Rural Schools: A Randomized Controlled Trial

    Science.gov (United States)

    Mason, Linda H.; Cramer, Anne Mong; Garwood, Justin D.; Varghese, Cheryl; Hamm, Jill; Murray, Allen

    2017-01-01

    A workshop with virtual consultation practice-based professional development model for self-regulated strategy development persuasive writing instruction was evaluated in a randomized controlled trial. Nineteen general education teachers and 564 Grade 5 and 6 students in 16 low-wealth rural schools participated. Following training, teachers…

  9. Examining Contextual Influences on Classroom-Based Implementation of Positive Behavior Support Strategies: Findings from a Randomized Controlled Effectiveness Trial.

    Science.gov (United States)

    Pas, Elise T; Waasdorp, Tracy E; Bradshaw, Catherine P

    2015-11-01

    Although it is widely recognized that variation in implementation fidelity influences the impact of preventive interventions, little is known about how specific contextual factors may affect the implementation of social and behavioral interventions in classrooms. Theoretical research highlights the importance of multiple contextual influences on implementation, including factors at the classroom and school level (Domitrovich et al., Advances in School Mental Health Promotion, 1, 6-28, 2008). The current study used multi-level modeling to empirically examine the influence of teacher, classroom, and school characteristics on the implementation of classroom-based positive behavior support strategies over the course of 4 years. Data were collected in the context of a 37-school randomized controlled trial examining the effectiveness of school-wide Positive Behavioral Interventions and Supports. Multi-level results identified several school-level contextual factors (e.g., school size, behavioral disruptions) and teacher-level factors (perceptions of school organizational health and grade level taught) associated with variability in the implementation of classroom-based positive behavior supports. Implications for prevention research and practice are discussed.

  10. 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.

  11. 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.

  12. UV-Induced DNA Damage and Mutagenesis in Chromatin.

    Science.gov (United States)

    Mao, Peng; Wyrick, John J; Roberts, Steven A; Smerdon, Michael J

    2017-01-01

    UV radiation induces photolesions that distort the DNA double helix and, if not repaired, can cause severe biological consequences, including mutagenesis or cell death. In eukaryotes, both the formation and repair of UV damage occur in the context of chromatin, in which genomic DNA is packaged with histones into nucleosomes and higher order chromatin structures. Here, we review how chromatin impacts the formation of UV photoproducts in eukaryotic cells. We describe the initial discovery that nucleosomes and other DNA binding proteins induce characteristic "photofootprints" during the formation of UV photoproducts. We also describe recent progress in genomewide methods for mapping UV damage, which echoes early biochemical studies, and highlights the role of nucleosomes and transcription factors in UV damage formation and repair at unprecedented resolution. Finally, we discuss our current understanding of how the distribution and repair of UV-induced DNA damage influence mutagenesis in human skin cancers. © 2016 The American Society of Photobiology.

  13. A cluster randomized controlled trial of strategies to increase adolescents' physical activity and motivation in physical education: results of the Motivating Active Learning in Physical Education (MALP) trial.

    Science.gov (United States)

    Lonsdale, Chris; Rosenkranz, Richard R; Sanders, Taren; Peralta, Louisa R; Bennie, Andrew; Jackson, Ben; Taylor, Ian M; Lubans, David R

    2013-11-01

    Physical education (PE) programs aim to promote physical activity (PA) and reach most school-aged youth. However, PA levels within PE lessons are often low. In this cluster-randomized controlled trial, we examined the effects of three self-determination theory-based motivational strategies on PA and sedentary behavior, as well as their hypothesized antecedents during PE lessons. Data were collected in Sydney, Australia (October-December 2011). After baseline testing, teachers (n=16) and their classes (n=288 students; M=13.6 years, 50.4% male) were randomly assigned to one of four teaching strategy conditions: (1) explaining relevance; (2) providing choice; (3) complete free choice; or (4) usual practice. Teachers then delivered the assigned strategy. Primary outcomes were accelerometer-assessed PA and student motivation during lessons. Secondary outcomes included sedentary behavior, perceptions of teachers' support and psychological needs satisfaction. The 'free choice' intervention increased PA (pPE lessons. © 2013.

  14. Oligonucleotide?directed mutagenesis for precision gene editing

    OpenAIRE

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

    2015-01-01

    Summary Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide?directed mutagenesis (ODM), one of the many tools of Cibus? Rapid Trait Development System ( RTDS ?) technology, offers a rapid, precise and non?transgenic breeding a...

  15. Environmental mutagenesis and radiation biology: The legacy of William Morgan.

    Science.gov (United States)

    Schwartz, Jeffrey L

    2017-12-01

    A symposium entitled Environmental Mutagenesis and Radiation Biology was held on September 27, 2016 to honor the memory of Dr. William F. Morgan who passed away unexpectedly on November 13, 2015. The speakers presented the latest reviews on homologous recombination repair, induced genetic instability, bystander effects, and risk estimate development. Their presentations are presented following the introduction. Copyright © 2017 Elsevier B.V. All rights reserved.

  16. Systematic identification of genetic loci required for polymyxin resistance in Campylobacter jejuni using an efficient in vivo transposon mutagenesis system.

    Science.gov (United States)

    Lin, Jun; Wang, Ying; Hoang, Ky Van

    2009-03-01

    The aim of this study was to identify genetic loci required for polymyxin (PM) resistance in Campylobacter jejuni using an efficient in vivo random mutagenesis system. PM has been widely used as a model peptide to examine mechanisms of bacterial resistance to antimicrobial peptides (AMPs), the major effectors of host innate immunity and also candidates for a new generation of antibiotics. In this study, a commercially available transposon mutagenesis approach (EZ-Tn5 Transposome; Epicentre, Madison, WI) was evaluated and used to systematically identify Campylobacter mutants with increased susceptibility to PM. This simple, yet efficient, transposon mutagenesis approach identified 12 mutants representing seven different genes of C. jejuni 81-176 involved in acquired PM resistance. Backcrossing of the transposon mutations into the parent strain confirmed that the PM-sensitive phenotype in each mutant was linked to the gene with a specific transposon insertion. The genes are identified as being involved in the synthesis of cell-surface carbohydrates, modification of intracellular targets, signal transduction, and modulation of transmembrane potential. The mutant with the highest susceptibility to PM contains a transposon insertion in a putative galU gene that is essential for production of uridine diphosphate glucose (UDP)-glucose, a precursor required for lipooligosaccharide (LOS) synthesis. LOS analysis by tricine SDSPAGE showed significant truncation of the LOS core structure in the galU mutant. Susceptibility assays also indicated that GalU contributed C. jejuni resistance to some natural AMPs. Complementation of the galU mutant in trans fully restored LOS synthesis and resistance to the levels of the parent strain. Together, these results define seven C. jejuni genetic loci that will be useful for characterizing the molecular basis of Campylobacter resistance to PM and natural AMPs, and also highlight the usefulness of the in vivo mutagenesis approach for

  17. GATMD: γ-Aminobutyric Acid Transporter Mutagenesis Database

    Science.gov (United States)

    Anderson, Cynthia M.; Kidd, Patrick D.; Eskandari, Sepehr

    2010-01-01

    Since the cloning of the first γ-aminobutyric acid (GABA) transporter (GAT1; SLC6A1) from rat brain in 1990, more than 50 published studies have provided structure–function information on investigator-designed rat and mouse GAT1 mutants. To date, more than 200 of 599 GAT1 residues have been subjected to mutagenesis experiments by substitution with different amino acids, and the resulting transporter functional properties have significantly advanced our understanding of the mechanism of Na+- and Cl–-coupled GABA transport by this important member of the neurotransmitter:sodium symporter family. Moreover, many studies have addressed the functional consequences of amino acid deletion or insertion at various positions along the primary sequence. The enormity of this growing body of structure–function information has prompted us to develop GABA Transporter Mutagenesis Database (GATMD), a web-accessible, relational database of manually annotated biochemical, functional and pharmacological data reported on GAT1—the most intensely studied GABA transporter isoform. As of the last update of GATMD, 52 GAT1 mutagenesis papers have yielded 3360 experimental records, which collectively contain a total of ∼100 000 annotated parameters. Database URL: http://physiology.sci.csupomona.edu/GATMD/ PMID:21131297

  18. Effect of a lung protective strategy for organ donors on eligibility and availability of lungs for transplantation: a randomized controlled trial.

    Science.gov (United States)

    Mascia, Luciana; Pasero, Daniela; Slutsky, Arthur S; Arguis, M Jose; Berardino, Maurizio; Grasso, Salvatore; Munari, Marina; Boifava, Silvia; Cornara, Giuseppe; Della Corte, Francesco; Vivaldi, Nicoletta; Malacarne, Paolo; Del Gaudio, Paolo; Livigni, Sergio; Zavala, Elisabeth; Filippini, Claudia; Martin, Erica L; Donadio, Pier Paolo; Mastromauro, Ilaria; Ranieri, V Marco

    2010-12-15

    Many potential donor lungs deteriorate between the time of brain death and evaluation for transplantation suitability, possibly because of the ventilatory strategy used after brain death. To test whether a lung protective strategy increases the number of lungs available for transplantation. Multicenter randomized controlled trial of patients with beating hearts who were potential organ donors conducted at 12 European intensive care units from September 2004 to May 2009 in the Protective Ventilatory Strategy in Potential Lung Donors Study. Interventions Potential donors were randomized to the conventional ventilatory strategy (with tidal volumes of 10-12 mL/kg of predicted body weight, positive end-expiratory pressure [PEEP] of 3-5 cm H(2)O, apnea tests performed by disconnecting the ventilator, and open circuit for airway suction) or the protective ventilatory strategy (with tidal volumes of 6-8 mL/kg of predicted body weight, PEEP of 8-10 cm H(2)O, apnea tests performed by using continuous positive airway pressure, and closed circuit for airway suction). The number of organ donors meeting eligibility criteria for harvesting, number of lungs harvested, and 6-month survival of lung transplant recipients. The trial was stopped after enrolling 118 patients (59 in the conventional ventilatory strategy and 59 in the protective ventilatory strategy) because of termination of funding. The number of patients who met lung donor eligibility criteria after the 6-hour observation period was 32 (54%) in the conventional strategy vs 56 (95%) in the protective strategy (difference of 41% [95% confidence interval {CI}, 26.5% to 54.8%]; P <.001). The number of patients in whom lungs were harvested was 16 (27%) in the conventional strategy vs 32 (54%) in the protective strategy (difference of 27% [95% CI, 10.0% to 44.5%]; P = .004). Six-month survival rates did not differ between recipients who received lungs from donors ventilated with the conventional strategy compared with the

  19. Comparison of mailed invitation strategies to improve fecal occult blood test participation in men: protocol for a randomized controlled trial.

    Science.gov (United States)

    Duncan, Amy; Zajac, Ian; Flight, Ingrid; Stewart, Benjamin J R; Wilson, Carlene; Turnbull, Deborah

    2013-07-31

    Men have a significantly increased risk of being diagnosed with, and dying from, colorectal cancer (CRC) than women. Men also participate in fecal occult blood test (FOBT) screening at a lower rate than women. This study will determine whether strategies that target men's attitudes toward screening, and matched to stage of readiness to screen, increase men's FOBT participation compared to a standard approach. Eligible trial participants will be a national sample of 9,200 men aged 50 to 74 years, living in urban Australia and randomly selected from the Australian electoral roll. Trial participants will be mailed an advance notification letter, followed 2 weeks later by an invitation letter and a free fecal immunochemical test (FIT) kit. The intervention is a factorial design, randomized controlled trial (RCT) with four trial arms, including a control. The content of the advance notification and invitation letters will differ by trial arm as follows: 1) standard advance notification and standard invitation (control arm); 2) targeted advance notification and standard invitation; 3) standard advance notification and targeted invitation; and 4) targeted advance notification and targeted invitation. The standard letters will replicate as closely as possible the letters included in the Australian National Bowel Cancer Screening Program (NBCSP). Modified advance notification and invitation letters will incorporate additional messages to target men in the precontemplation (advance notification) and contemplation stages (invitation). The primary outcome is return of the completed FIT within 12 weeks of invitation. Analysts will be blinded to trial assignment and participants will be blinded to the use of varying invitational materials. Subsamples from each trial arm will complete baseline and endpoint surveys to measure the psychological impact of the intervention, and qualitative interviews will be conducted to evaluate attitudes toward the intervention. The outcomes of

  20. 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

  1. Recruitment strategies should not be randomly selected: empirically improving recruitment success and diversity in developmental psychology research

    Science.gov (United States)

    Sugden, Nicole A.; Moulson, Margaret C.

    2015-01-01

    Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: (1) recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy), (2) recruiters of particular races were more successful than recruiters of other races, and (3) differences in success were related to what the recruiter said to engage the potential participant (i.e., the script). The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: (1) some scripts were more successful than others and (2) we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families. PMID:25972829

  2. Strategies to Maximize Data Collection Response Rates in a Randomized Control Trial Focused on Children with Medical Complexity.

    Science.gov (United States)

    Finkelstein, Stanley M; Celebrezze, Margaret; Cady, Rhonda; Lunos, Scott; Looman, Wendy S

    2016-04-01

    Obtaining complete and timely subject data is key to the success of clinical trials, particularly for studies requiring data collected from subjects at home or other remote sites. A multifaceted strategy for data collection in a randomized controlled trial (RCT) focused on care coordination for children with medical complexity is described. The influences of data collection mode, incentives, and study group membership on subject response patterns are analyzed. Data collection included monthly healthcare service utilization (HCSU) calendars and annual surveys focused on care coordination outcomes. One hundred sixty-three families were enrolled in the 30-month TeleFamilies RCT. Subjects were 2-15 years of age at enrollment. HCSU data were collected by parent/guardian self-report using mail, e-mail, telephone, or texting. Surveys were collected by mail. Incentives were provided for completed surveys after 8 months to improve collection returns. Outcome measures were the number of HCSU calendars and surveys returned, the return interval, data collection mode, and incentive impact. Return rates of 90% for HCSU calendars and 82% for annual surveys were achieved. Mean return intervals were 72 and 65 days for HCSU and surveys, respectively. Survey response increased from 55% to 95% after introduction of a gift card and added research staff. High return rates for HCSU calendars and health-related surveys are attainable but required a flexible and personnel-intensive approach to collection methods. Family preference for data collection approach should be obtained at enrollment, should be modified as needed, and requires flexible options, training, intensive staff/family interaction, and patience.

  3. Recruitment strategies should not be randomly selected: empirically improving recruitment success and diversity in developmental psychology research.

    Science.gov (United States)

    Sugden, Nicole A; Moulson, Margaret C

    2015-01-01

    Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: (1) recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy), (2) recruiters of particular races were more successful than recruiters of other races, and (3) differences in success were related to what the recruiter said to engage the potential participant (i.e., the script). The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: (1) some scripts were more successful than others and (2) we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families.

  4. Recruitment strategies shouldn’t be randomly selected: Empirically improving recruitment success and diversity in developmental psychology research

    Directory of Open Access Journals (Sweden)

    Nicole Andrea Sugden

    2015-04-01

    Full Text Available Psychological and developmental research have been critiqued for the lack of diversity of research samples. Because differences in culture, race, and ethnicity can influence participant behavior, limited diversity limits the generalizability of the findings. These differences may also impact how participants behave in response to recruitment attempts, which suggests that recruitment itself may be leveraged to increase sample diversity. The goal of the current study was to determine what factors, within a recruitment interaction, could be leveraged to increase success and diversity when recruiting families with children for developmental research. Study 1 found three factors influenced success: 1 recruitment was more successful when other potential participants were also interested (i.e., recruiters were busy, 2 recruiters of particular races were more successful than recruiters of other races, and 3 differences in success were related to what the recruiter said to engage the potential participant (i.e., the script. The latter two factors interacted, suggesting some recruiters were using less optimal scripts. To improve success rates, study 2 randomly assigned scripts to recruiters and encouraged them to recruit more vigorously during busy periods. Study 2 found that two factors influenced success: 1 some scripts were more successful than others and 2 we were more successful at recruiting non-White potential participants than White participants. These two interacted, with some scripts being more successful with White and other scripts being more successful with non-White families. This intervention significantly increased recruitment success rate by 8.1% and the overall number of families recruited by 15.3%. These findings reveal that empirically evaluating and tailoring recruitment efforts based on the most successful strategies is effective in boosting diversity through increased participation of children from non-White families.

  5. Comparison of two strategies for initiating renal replacement therapy in the intensive care unit: study protocol for a randomized controlled trial (AKIKI).

    Science.gov (United States)

    Gaudry, Stéphane; Hajage, David; Schortgen, Fréderique; Martin-Lefevre, Laurent; Tubach, Florence; Pons, Bertrand; Boulet, Eric; Boyer, Alexandre; Lerolle, Nicolas; Chevrel, Guillaume; Carpentier, Dorothée; Lautrette, Alexandre; Bretagnol, Anne; Mayaux, Julien; Thirion, Marina; Markowicz, Philippe; Thomas, Guillemette; Dellamonica, Jean; Richecoeur, Jack; Darmon, Michael; de Prost, Nicolas; Yonis, Hodane; Megarbane, Bruno; Loubières, Yann; Blayau, Clarisse; Maizel, Julien; Zuber, Benjamin; Nseir, Saad; Bigé, Naïke; Hoffmann, Isabelle; Ricard, Jean-Damien; Dreyfuss, Didier

    2015-04-17

    There is currently no validated strategy for the timing of renal replacement therapy (RRT) for acute kidney injury (AKI) in the intensive care unit (ICU) when short-term life-threatening metabolic abnormalities are absent. No adequately powered prospective randomized study has addressed this issue to date. As a result, significant practice heterogeneity exists and may expose patients to either unnecessary hazardous procedures or undue delay in RRT. This is a multicenter, prospective, randomized, open-label parallel-group clinical trial that compares the effect of two RRT initiation strategies on overall survival of critically ill patients receiving intravenous catecholamines or invasive mechanical ventilation and presenting with AKI classification stage 3 (KDIGO 2012). In the 'early' strategy, RRT is initiated immediately. In the 'delayed' strategy, clinical and metabolic conditions are closely monitored and RRT is initiated only when one or more events (severity criteria) occur, including: oliguria or anuria for more than 72 hours after randomization, serum urea concentration >40 mmol/l, serum potassium concentration >6 mmol/l, serum potassium concentration >5.5 mmol/l persisting despite medical treatment, arterial blood pH 5 l/min to maintain SpO2 > 95% or FiO2 > 50% under invasive or noninvasive mechanical ventilation. The primary outcome measure is overall survival, measured from randomization (D0) until death, regardless of the cause. The minimum follow-up duration for each patient will be 60 days. Two interim analyses are planned, blinded to group allocation. It is expected that there will be 620 subjects in all. The AKIKI study will be one of the very few large randomized controlled trials evaluating mortality according to the timing of RRT in critically ill patients with AKI classification stage 3 (KDIGO 2012). Results should help clinicians decide when to initiate RRT. ClinicalTrials.gov NCT01932190.

  6. Electronic search strategies to identify reports of cluster randomized trials in MEDLINE: low precision will improve with adherence to reporting standards

    Directory of Open Access Journals (Sweden)

    Grimshaw Jeremy M

    2010-02-01

    Full Text Available Abstract Background Cluster randomized trials (CRTs present unique methodological and ethical challenges. Researchers conducting systematic reviews of CRTs (e.g., addressing methodological or ethical issues require efficient electronic search strategies (filters or hedges to identify trials in electronic databases such as MEDLINE. According to the CONSORT statement extension to CRTs, the clustered design should be clearly identified in titles or abstracts; however, variability in terminology may make electronic identification challenging. Our objectives were to (a evaluate sensitivity ("recall" and precision of a well-known electronic search strategy ("randomized controlled trial" as publication type with respect to identifying CRTs, (b evaluate the feasibility of new search strategies targeted specifically at CRTs, and (c determine whether CRTs are appropriately identified in titles or abstracts of reports and whether there has been improvement over time. Methods We manually examined a wide range of health journals to identify a gold standard set of CRTs. Search strategies were evaluated against the gold standard set, as well as an independent set of CRTs included in previous systematic reviews. Results The existing strategy (randomized controlled trial.pt is sensitive (93.8% for identifying CRTs, but has relatively low precision (9%, number needed to read 11; the number needed to read can be halved to 5 (precision 18.4% by combining with cluster design-related terms using the Boolean operator AND; combining with the Boolean operator OR maximizes sensitivity (99.4% but would require 28.6 citations read to identify one CRT. Only about 50% of CRTs are clearly identified as cluster randomized in titles or abstracts; approximately 25% can be identified based on the reported units of randomization but are not amenable to electronic searching; the remaining 25% cannot be identified except through manual inspection of the full-text article. The

  7. Electronic search strategies to identify reports of cluster randomized trials in MEDLINE: low precision will improve with adherence to reporting standards.

    Science.gov (United States)

    Taljaard, Monica; McGowan, Jessie; Grimshaw, Jeremy M; Brehaut, Jamie C; McRae, Andrew; Eccles, Martin P; Donner, Allan

    2010-02-16

    Cluster randomized trials (CRTs) present unique methodological and ethical challenges. Researchers conducting systematic reviews of CRTs (e.g., addressing methodological or ethical issues) require efficient electronic search strategies (filters or hedges) to identify trials in electronic databases such as MEDLINE. According to the CONSORT statement extension to CRTs, the clustered design should be clearly identified in titles or abstracts; however, variability in terminology may make electronic identification challenging. Our objectives were to (a) evaluate sensitivity ("recall") and precision of a well-known electronic search strategy ("randomized controlled trial" as publication type) with respect to identifying CRTs, (b) evaluate the feasibility of new search strategies targeted specifically at CRTs, and (c) determine whether CRTs are appropriately identified in titles or abstracts of reports and whether there has been improvement over time. We manually examined a wide range of health journals to identify a gold standard set of CRTs. Search strategies were evaluated against the gold standard set, as well as an independent set of CRTs included in previous systematic reviews. The existing strategy (randomized controlled trial.pt) is sensitive (93.8%) for identifying CRTs, but has relatively low precision (9%, number needed to read 11); the number needed to read can be halved to 5 (precision 18.4%) by combining with cluster design-related terms using the Boolean operator AND; combining with the Boolean operator OR maximizes sensitivity (99.4%) but would require 28.6 citations read to identify one CRT. Only about 50% of CRTs are clearly identified as cluster randomized in titles or abstracts; approximately 25% can be identified based on the reported units of randomization but are not amenable to electronic searching; the remaining 25% cannot be identified except through manual inspection of the full-text article. The proportion of trials clearly identified has

  8. 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...... technique that involved replacing this portion of the v-rasH effector domain with a linker carrying two BspMI sites in opposite orientations. Since BspMI cleaves outside its recognition sequence, BspMI digestion of the plasmid completely removed the linker, creating a double-stranded gap whose missing ras...

  9. A protocol for chemical mutagenesis in Strongyloides ratti.

    Science.gov (United States)

    Guo, Li; Chang, Zisong; Dieterich, Christoph; Streit, Adrian

    2015-11-01

    Genetic analysis using experimentally induced mutations has been a most valuable tool in the analysis of various organisms. However, genetic analysis of endoparasitic organisms tends to be difficult because of the limited accessibility of the sexually reproducing adults, which are normally located within the host. Nematodes of the genera Strogyloides and Parastrongyloides represent an exception to this because they can form facultative free-living sexually reproducing generations in between parasitic generations. Here we present a protocol for the chemical mutagenesis of Strongyloides ratti. Further we evaluate the feasibility of identifying the induced mutations by whole genome re-sequencing. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Environmental stress and mutagenesis in enteric and non-enteric bacteria

    OpenAIRE

    Babudri, Nora; Lancioni, Hovirag; Achilli, Alessandro

    2012-01-01

    Mutations are fundamental for evolution. For many years it has been thought that mutagenesis occurs only in dividing cells. Now it is clear that mutations arise in non-dividing or slowly dividing microorganisms. Natural populations spend most of the time in stressful environments where their growth rate is highly reduced. Thus, the existence of a mutagenesis process, independent of multiplication (stress-induced mutagenesis, SIM), might have a profound evolutionary role. In the presented pape...

  11. 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 ...... insertions per cell. MO-MAGE enables cost-effective large-scale targeted genome engineering that should be useful for a variety of applications in synthetic biology and metabolic engineering.......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...

  12. The effect of an intraoperative, lung-protective ventilation strategy in neurosurgical patients undergoing craniotomy: study protocol for a randomized controlled trial.

    Science.gov (United States)

    Zhang, Liyong; Xiong, Wei; Peng, Yuming; Zhang, Wei; Han, Ruquan

    2018-02-02

    Ventilator-induced lung injury is a major cause of postoperative pulmonary complications (PPCs) in patients undergoing neurosurgery after general anesthesia. However, there is no study on the effect of a lung-protective ventilation strategy in patients undergoing neurosurgery. This is a single-center, randomized, parallel-group controlled trial which will be carried out at Beijing Tiantan Hospital, Capital Medical University. Three hundred and thirty-four patients undergoing intracranial tumor surgery will be randomly allocated to the control group and the protective-ventilation strategy group. In the control group, tidal volume (VT) will be set at 10-12 ml/kg of predicted body weight but PEEP and recruitment maneuvers will not be used. In the protective group, VT will be set at 6-8 ml/kg of predicted body weight, PEEP at 6-8 cmH 2 O, and a recruitment maneuver will be used intermittently. The primary outcome is pulmonary complications within 7 days postoperatively. Secondary outcomes include intraoperative brain relaxation, the postoperative complications within 30 days and the cost analysis. This study aims to determine if the protective, pulmonary-ventilation strategy decreases the incidence of PPCs in patients undergoing neurosurgical anesthesia. If our results are positive, the study will indicate whether the protective, pulmonary-ventilation strategy is efficiently and safely used in neurosurgical patients undergoing the craniotomy. ClinicalTrials.gov, ID: NCT02386683 . Registered on 18 October 2014.

  13. National evaluation of strategies to reduce safety violations for working from heights in construction companies: results from a randomized controlled trial.

    Science.gov (United States)

    van der Molen, Henk F; den Herder, Aalt; Warning, Jan; Frings-Dresen, Monique H W

    2016-01-09

    The objective of this study is to evaluate the effectiveness of a face-to-face strategy and a direct mail strategy on safety violations while working from heights among construction companies compared to a control condition. Construction companies with workers at risk for fall injuries were eligible for this three-armed randomized controlled trial. In total, 27 cities were randomly assigned to intervention groups-where eligible companies were given either a face-to-face guidance strategy or a direct mailing strategy with access to internet facilities-or to a control group. The primary outcomes were the number and type of safety violations recorded by labor inspectors after three months. A process evaluation for both strategies was performed to determine reach, program implementation, satisfaction, knowledge and perceived safety behavior. A cost analysis was performed to establish the financial costs for each intervention strategy. Analyses were done by intention to treat. In total, 41% (n = 88) of the companies eligible for the face-to-face intervention participated and 73% (n = 69) for direct mail. Intervention materials were delivered to 69 % (face-to-face group) and 100 % (direct mail group); completion of intervention activities within companies was low. Satisfaction, increase in knowledge, and safety behavior did not differ between the intervention groups. Costs for personal advice were 28% higher than for direct mail. Ultimately, nine intervention companies were captured in the 288 worksite measurements performed by the labor inspectorate. No statistical differences in mean number of safety violations (1.8-2.4) or penalties (72%-100%) were found between the intervention and control groups based on all worksite inspections. No conclusions about the effect of face-to-face and direct mail strategies on safety violations could be drawn due to the limited number of intervention companies captured in the primary outcome measurements. The costs for a face

  14. Effective Strategies to Recruit Young Adults Into the TXT2BFiT mHealth Randomized Controlled Trial for Weight Gain Prevention

    Science.gov (United States)

    Balestracci, Kate; Wong, Annette TY; Hebden, Lana; McGeechan, Kevin; Denney-Wilson, Elizabeth; Harris, Mark F; Phongsavan, Philayrath; Bauman, Adrian; Allman-Farinelli, Margaret

    2015-01-01

    Background Younger adults are difficult to engage in preventive health, yet in Australia they are gaining more weight and increasing in waist circumference faster than middle-to-older adults. A further challenge to engaging 18- to 35-year-olds in interventions is the limited reporting of outcomes of recruitment strategies. Objective This paper describes the outcomes of strategies used to recruit young adults to a randomized controlled trial (RCT), healthy lifestyle mHealth program, TXT2BFiT, for prevention of weight gain. The progression from enquiry through eligibility check to randomization into the trial and the costs of recruitment strategies are reported. Factors associated with nonparticipation are explored. Methods Participants were recruited either via letters of invitation from general practitioners (GPs) or via electronic or print advertisements, including Facebook and Google—social media and advertising—university electronic newsletters, printed posters, mailbox drops, and newspapers. Participants recruited from GP invitation letters had an appointment booked with their GP for eligibility screening. Those recruited from other methods were sent an information pack to seek approval to participate from their own GP. The total number and source of enquiries were categorized according to eligibility and subsequent completion of steps to enrolment. Cost data and details of recruitment strategies were recorded. Results From 1181 enquiries in total from all strategies, 250 (21.17%) participants were randomized. A total of 5311 invitation letters were sent from 12 GP practices—16 participating GPs. A total of 131 patients enquired with 68 participants randomized (68/74 of those eligible, 92%). The other recruitment methods yielded the remaining 182 randomized participants. Enrolment from print media was 26% of enquiries, from electronic media was 20%, and from other methods was 3%. Across all strategies the average cost of recruitment was Australian Dollar

  15. Effective Strategies to Recruit Young Adults Into the TXT2BFiT mHealth Randomized Controlled Trial for Weight Gain Prevention.

    Science.gov (United States)

    Partridge, Stephanie R; Balestracci, Kate; Wong, Annette Ty; Hebden, Lana; McGeechan, Kevin; Denney-Wilson, Elizabeth; Harris, Mark F; Phongsavan, Philayrath; Bauman, Adrian; Allman-Farinelli, Margaret

    2015-06-05

    Younger adults are difficult to engage in preventive health, yet in Australia they are gaining more weight and increasing in waist circumference faster than middle-to-older adults. A further challenge to engaging 18- to 35-year-olds in interventions is the limited reporting of outcomes of recruitment strategies. This paper describes the outcomes of strategies used to recruit young adults to a randomized controlled trial (RCT), healthy lifestyle mHealth program, TXT2BFiT, for prevention of weight gain. The progression from enquiry through eligibility check to randomization into the trial and the costs of recruitment strategies are reported. Factors associated with nonparticipation are explored. Participants were recruited either via letters of invitation from general practitioners (GPs) or via electronic or print advertisements, including Facebook and Google-social media and advertising-university electronic newsletters, printed posters, mailbox drops, and newspapers. Participants recruited from GP invitation letters had an appointment booked with their GP for eligibility screening. Those recruited from other methods were sent an information pack to seek approval to participate from their own GP. The total number and source of enquiries were categorized according to eligibility and subsequent completion of steps to enrolment. Cost data and details of recruitment strategies were recorded. From 1181 enquiries in total from all strategies, 250 (21.17%) participants were randomized. A total of 5311 invitation letters were sent from 12 GP practices-16 participating GPs. A total of 131 patients enquired with 68 participants randomized (68/74 of those eligible, 92%). The other recruitment methods yielded the remaining 182 randomized participants. Enrolment from print media was 26% of enquiries, from electronic media was 20%, and from other methods was 3%. Across all strategies the average cost of recruitment was Australian Dollar (AUD) $139 per person. The least expensive

  16. Cell-mediated mutagenesis and cell transformation by chemical carcinogens

    Energy Technology Data Exchange (ETDEWEB)

    Huberman, E.; Langenbach, R.

    1977-01-01

    Results are reported from studies that showed that mutagenesis of mammalian cells can be achieved by carcinogenic polycyclic hydrocarbons, nitrosamines, and aflatoxins when tested in the presence of fibroblasts and hepatocytes which are able to metabolize these carcinogens. Further, we have found that there is a relationship between the degree of mutant induction and the degree of carcinogenicity of the different chemicals tested. By simultaneously measuring the frequency of cell transformation and the frequency of mutation at one locus (ouabain resistance) in the same cell system, it was possible to estimate the genetic target site for cell transformation. The results indicated that the target site for transformation is approximately 20 times larger than that determined for ouabain resistance. The results suggest that cell transformation may be due to a mutational event and the mutation can occur in one out of a small number of the same or different genes, and that the cell-mediated mutagenesis approach may be a valuable means of detecting tissue-specific carcinogens.

  17. Lethal Mutagenesis of Hepatitis C Virus Induced by Favipiravir.

    Directory of Open Access Journals (Sweden)

    Ana I de Ávila

    Full Text Available Lethal mutagenesis is an antiviral approach that consists in extinguishing a virus by an excess of mutations acquired during replication in the presence of a mutagen. Here we show that favipiravir (T-705 is a potent mutagenic agent for hepatitis C virus (HCV during its replication in human hepatoma cells. T-705 leads to an excess of G → A and C → U transitions in the mutant spectrum of preextinction HCV populations. Infectivity decreased significantly in the presence of concentrations of T-705 which are 2- to 8-fold lower than its cytotoxic concentration 50 (CC50. Passaging the virus five times in the presence of 400 μM T-705 resulted in virus extinction. Since T-705 has undergone advanced clinical trials for approval for human use, the results open a new approach based on lethal mutagenesis to treat hepatitis C virus infections. If proven effective for HCV in vivo, this new anti-HCV agent may be useful in patient groups that fail current therapeutic regimens.

  18. Comparison of on-demand vs planned relaparotomy strategy in patients with severe peritonitis: a randomized trial

    NARCIS (Netherlands)

    van Ruler, Oddeke; Mahler, Cecilia W.; Boer, Kimberly R.; Reuland, E. Ascelijn; Gooszen, Hein G.; Opmeer, Brent C.; de Graaf, Peter W.; Lamme, Bas; Gerhards, Michael F.; Steller, E. Philip; van Till, J. W. Olivier; de Borgie, Corianne J. A. M.; Gouma, Dirk J.; Reitsma, Johannes B.; Boermeester, Marja A.

    2007-01-01

    CONTEXT: In patients with severe secondary peritonitis, there are 2 surgical treatment strategies following an initial emergency laparotomy: planned relaparotomy and relaparotomy only when the patient's condition demands it ("on-demand"). The on-demand strategy may reduce mortality, morbidity,

  19. A Cluster-Randomized Trial of Two Strategies to Improve Antibiotic Use for Patients with a Complicated Urinary Tract Infection

    NARCIS (Netherlands)

    Spoorenberg, V.; Hulscher, M.E.J.L.; Geskus, R.B.; Reijke, T.M. de; Opmeer, B.C.; Prins, J.M.; Geerlings, S.E.

    2015-01-01

    BACKGROUND: Up to 50% of hospital antibiotic use is inappropriate and therefore improvement strategies are urgently needed. We compared the effectiveness of two strategies to improve the quality of antibiotic use in patients with a complicated urinary tract infection (UTI). METHODS: In a

  20. Patients' and providers' perspectives of a polypill strategy to improve cardiovascular prevention in Australian primary health care: a qualitative study set within a pragmatic randomized, controlled trial.

    Science.gov (United States)

    Liu, Hueiming; Massi, Luciana; Laba, Tracey-Lea; Peiris, David; Usherwood, Tim; Patel, Anushka; Cass, Alan; Eades, Anne-Marie; Redfern, Julie; Hayman, Noel; Howard, Kirsten; Brien, Jo-anne; Jan, Stephen

    2015-05-01

    This study explores health provider and patient attitudes toward the use of a cardiovascular polypill as a health service strategy to improve cardiovascular prevention. In-depth, semistructured interviews (n=94) were conducted with health providers and patients from Australian general practice, Aboriginal community-controlled and government-run Indigenous Health Services participating in a pragmatic randomized controlled trial evaluating a polypill-based strategy for high-risk primary and secondary cardiovascular disease prevention. Interview topics included polypill strategy acceptability, factors affecting adherence, and trial implementation. Transcribed interview data were analyzed thematically and interpretively. Polypill patients commented frequently on cost-savings, ease, and convenience of a daily-dosing pill. Most providers considered a polypill strategy to facilitate improved patient medication use. Indigenous Health Services providers and indigenous patients thought the strategy acceptable and beneficial for indigenous patients given the high disease burden. Providers noted the inflexibility of the fixed dose regimen, with dosages sometimes inappropriate for patients with complex management considerations. Future polypill formulations with varied strengths and classes of medications may overcome this barrier. Many providers suggested the polypill strategy, in its current formulations, might be more suited to high-risk primary prevention patients. The polypill strategy was generally acceptable to patients and providers in cardiovascular prevention. Limitations to provider acceptability of this particular polypill were revealed, as was a perception it might be more suitable for high-risk primary prevention patients, though future combinations could facilitate its use in secondary prevention. Participants suggested a polypill-based strategy as particularly appropriate for lowering the high cardiovascular burden in indigenous populations. URL: http

  1. Best practice guidance for the use of strategies to improve retention in randomized trials developed from two consensus workshops.

    Science.gov (United States)

    Brueton, Valerie; Stenning, Sally P; Stevenson, Fiona; Tierney, Jayne; Rait, Greta

    2017-08-01

    To develop best practice guidance for the use of retention strategies in randomized clinical trials (RCTs). Consensus development workshops conducted at two UK Clinical Trials Units. Sixty-six statisticians, clinicians, RCT coordinators, research scientists, research assistants, and data managers associated with RCTs participated. The consensus development workshops were based on the consensus development conference method used to develop best practice for treatment of medical conditions. Workshops commenced with a presentation of the evidence for incentives, communication, questionnaire format, behavioral, case management, and methodological retention strategies identified by a Cochrane review and associated qualitative study. Three simultaneous group discussions followed focused on (1) how convinced the workshop participants were by the evidence for retention strategies, (2) barriers to the use of effective retention strategies, (3) types of RCT follow-up that retention strategies could be used for, and (4) strategies for future research. Summaries of each group discussion were fed back to the workshop. Coded content for both workshops was compared for agreement and disagreement. Agreed consensus on best practice guidance for retention was identified. Workshop participants agreed best practice guidance for the use of small financial incentives to improve response to postal questionnaires in RCTs. Use of second-class post was thought to be adequate for postal communication with RCT participants. The most relevant validated questionnaire was considered best practice for collecting RCT data. Barriers identified for the use of effective retention strategies were: the small improvements seen in questionnaire response for the addition of monetary incentives, and perceptions among trialists that some communication strategies are outdated. Furthermore, there was resistance to change existing retention practices thought to be effective. Face-to-face and electronic follow

  2. RANDOMIZED STUDY OF IMPLANTABLE DEFIBRILLATOR AS FIRST-CHOICE THERAPY VERSUS CONVENTIONAL STRATEGY IN POSTINFARCT SUDDEN-DEATH SURVIVORS

    NARCIS (Netherlands)

    WEVER, EFD; HAUER, RNW; VANCAPELLE, FJL; TIJSSEN, JGP; CRIJNS, HJGM; ALGRA, A; WIESFELD, ACP; BAKKER, PFA; DEMEDINA, EOR

    1995-01-01

    Background In retrospective studies of sudden cardiac death survivors, the implantable cardioverter-defibrillator (ICD) compares favorably with medical and surgical therapy. Thus, use of the conventional strategy of starting treatment with antiarrhythmic drugs (AD), at least in certain patient

  3. A description of a knowledge broker role implemented as part of a randomized controlled trial evaluating three knowledge translation strategies

    National Research Council Canada - National Science Library

    Dobbins, Maureen; Robeson, Paula; Ciliska, Donna; Hanna, Steve; Cameron, Roy; O'Mara, Linda; DeCorby, Kara; Mercer, Shawna

    2009-01-01

    A knowledge broker (KB) is a popular knowledge translation and exchange (KTE) strategy emerging in Canada to promote interaction between researchers and end users, as well as to develop capacity for evidence-informed decision making...

  4. Best strategies to implement clinical pathways in an emergency department setting: study protocol for a cluster randomized controlled trial

    National Research Council Canada - National Science Library

    Jabbour, Mona; Curran, Janet; Scott, Shannon D; Guttman, Astrid; Rotter, Thomas; Ducharme, Francine M; Lougheed, M Diane; McNaughton-Filion, M Louise; Newton, Amanda; Shafir, Mark; Paprica, Alison; Klassen, Terry; Taljaard, Monica; Grimshaw, Jeremy; Johnson, David W

    2013-01-01

    ... teams in hospital settings. While high-quality, expert-developed clinical pathways have many potential benefits, their impact has been limited by variable implementation strategies and suboptimal research designs...

  5. Engaging foster parents in treatment: a randomized trial of supplementing trauma-focused cognitive behavioral therapy with evidence-based engagement strategies.

    Science.gov (United States)

    Dorsey, Shannon; Pullmann, Michael D; Berliner, Lucy; Koschmann, Elizabeth; McKay, Mary; Deblinger, Esther

    2014-09-01

    The goal of this study was to examine the impact of supplementing Trauma-focused Cognitive Behavioral Therapy (TF-CBT; Cohen et al., 2006) with evidence-based engagement strategies on foster parent and foster youth engagement in treatment, given challenges engaging foster parents in treatment. A randomized controlled trial of TF-CBT standard delivery compared to TF-CBT plus evidence-based engagement strategies was conducted with 47 children and adolescents in foster care and one of their foster parents. Attendance, engagement, and clinical outcomes were assessed 1 month into treatment, end of treatment, and 3 months post-treatment. Youth and foster parents who received TF-CBT plus evidence-based engagement strategies were more likely to be retained in treatment through four sessions and were less likely to drop out of treatment prematurely. The engagement strategies did not appear to have an effect on the number of canceled or no-show sessions or on treatment satisfaction. Clinical outcomes did not differ by study condition, but exploratory analyses suggest that youth had significant improvements with treatment. Strategies that specifically target engagement may hold promise for increasing access to evidence-based treatments and for increasing likelihood of treatment completion. Copyright © 2014 Elsevier Ltd. All rights reserved.

  6. Construction of a high-efficiency multi-site-directed mutagenesis ...

    African Journals Online (AJOL)

    Although site-directed mutagenesis has been used in many fields, it still has low rate of success and high cost because of low-yield target products. A modified method for multi-site-directed mutagenesis was developed with shifted primer design and cold-start polymerase chain reaction (PCR). The developed method was ...

  7. A cluster-randomized controlled trial of strategies to increase adolescents' physical activity and motivation during physical education lessons: the Motivating Active Learning in Physical Education (MALP) trial.

    Science.gov (United States)

    Rosenkranz, Richard R; Lubans, David R; Peralta, Louisa R; Bennie, Andrew; Sanders, Taren; Lonsdale, Chris

    2012-10-01

    The physical activity (PA) levels of many children and adolescents in Australia are currently insufficient to promote health benefits. Physical education (PE) programs aim to promote PA and reach nearly all school-aged children, but PA levels within PE lessons are often low. PE teachers may influence children's motivation to be physically active in PE lessons, but little is known about teacher strategies that effectively motivate children to participate in PA, and few intervention studies have examined motivational strategies in PE. The purpose of this study was to compare the effect of three motivational strategies, each based on Self-Determination Theory (SDT), on PA levels, and their hypothesized antecedents, during year 8 PE lessons. This study employed a cluster-randomized controlled trial design. Following a familiarization session, PA levels and hypothesized PA antecedents were measured during a baseline lesson and a post-intervention or control lesson. Teachers (n = 16) and their classes from five secondary schools in Sydney, Australia were randomly assigned into four blocks and instructed to provide one of four 20-min lesson teaching strategy conditions: (1) explaining the relevance of activities; (2) providing choice from PA options selected by the teacher; (3) providing equipment and free choice of activities; or (4) usual practice. The primary outcomes were lesson time spent in moderate-to-vigorous PA, and motivation towards the lesson. Secondary outcomes were perceptions of teacher behavior, psychological needs satisfaction, and lesson time spent in sedentary behavior. PA and sedentary behavior were measured during baseline and post-intervention lessons with waist-mounted Actigraph GT3X accelerometers. Teacher behavior, psychological needs satisfaction, and motivation were assessed via questionnaires at the end of each lesson. Linear mixed-model analyses will be run on all outcomes, with students nested within teachers as a random effect. Study

  8. A cluster-randomized controlled trial of strategies to increase adolescents’ physical activity and motivation during physical education lessons: the Motivating Active Learning in Physical Education (MALP trial

    Directory of Open Access Journals (Sweden)

    Rosenkranz Richard R

    2012-10-01

    Full Text Available Abstract Background The physical activity (PA levels of many children and adolescents in Australia are currently insufficient to promote health benefits. Physical education (PE programs aim to promote PA and reach nearly all school-aged children, but PA levels within PE lessons are often low. PE teachers may influence children’s motivation to be physically active in PE lessons, but little is known about teacher strategies that effectively motivate children to participate in PA, and few intervention studies have examined motivational strategies in PE. The purpose of this study was to compare the effect of three motivational strategies, each based on Self-Determination Theory (SDT, on PA levels, and their hypothesized antecedents, during year 8 PE lessons. Methods/design This study employed a cluster-randomized controlled trial design. Following a familiarization session, PA levels and hypothesized PA antecedents were measured during a baseline lesson and a post-intervention or control lesson. Teachers (n = 16 and their classes from five secondary schools in Sydney, Australia were randomly assigned into four blocks and instructed to provide one of four 20-min lesson teaching strategy conditions: (1 explaining the relevance of activities; (2 providing choice from PA options selected by the teacher; (3 providing equipment and free choice of activities; or (4 usual practice. The primary outcomes were lesson time spent in moderate-to-vigorous PA, and motivation towards the lesson. Secondary outcomes were perceptions of teacher behavior, psychological needs satisfaction, and lesson time spent in sedentary behavior. PA and sedentary behavior were measured during baseline and post-intervention lessons with waist-mounted Actigraph GT3X accelerometers. Teacher behavior, psychological needs satisfaction, and motivation were assessed via questionnaires at the end of each lesson. Linear mixed-model analyses will be run on all outcomes, with students nested

  9. Placement and promotion strategies to increase sales of healthier products in supermarkets in low-income, ethnically diverse neighborhoods: a randomized controlled trial.

    Science.gov (United States)

    Foster, Gary D; Karpyn, Allison; Wojtanowski, Alexis C; Davis, Erica; Weiss, Stephanie; Brensinger, Colleen; Tierney, Ann; Guo, Wensheng; Brown, Jeffery; Spross, Carly; Leuchten, Donna; Burns, Patrick J; Glanz, Karen

    2014-06-01

    The greater presence of supermarkets in low-income, high-minority neighborhoods has the potential to positively affect diet quality among those at greatest risk of obesity. In-store marketing strategies that draw attention to healthier products may be effective, sustainable, and scalable for improving diet quality and health. Few controlled studies of in-store marketing strategies to promote sales of healthier items in low-income, high-minority neighborhoods have been conducted. The objective of this study was to evaluate the effects of in-store marketing strategies to promote the purchase of specific healthier items in 5 product categories: milk, ready-to-eat cereal, frozen meals, in-aisle beverages, and checkout cooler beverages. The design was a cluster-randomized controlled trial conducted from 2011 to 2012. Eight urban supermarkets in low-income, high-minority neighborhoods were the unit of randomization, intervention, and analysis. Stores were matched on the percentage of sales from government food-assistance programs and store size and randomly assigned to an intervention or control group. The 4 intervention stores received a 6-mo, in-store marketing intervention that promoted the sales of healthier products through placement, signage, and product availability strategies. The 4 control stores received no intervention and were assessment-only controls. The main outcome measure was weekly sales of the targeted products, which was assessed on the basis of the stores' sales data. Intervention stores showed significantly greater sales of skim and 1% milk, water (in aisle and at checkout), and 2 of 3 types of frozen meals compared with control store sales during the same time period. No differences were found between the stores in sales of cereal, whole or 2% milk, beverages, or diet beverages. These data indicate that straightforward placement strategies can significantly enhance the sales of healthier items in several food and beverage categories. Such

  10. A Proposed Multisite Double-Blind Randomized Clinical Trial of Neurofeedback for ADHD: Need, Rationale, and Strategy

    Science.gov (United States)

    Kerson, Cynthia

    2013-01-01

    Objective: Additional treatments with persisting benefit are needed for ADHD. Because ADHD often shows excessive theta electroencephalogram (EEG) power, low beta, and excessive theta-beta ratio (TBR), a promising treatment is neurofeedback (NF) downtraining TBR. Although several nonblind randomized clinical trials (RCTs) show a medium-large…

  11. Quantitative studies of the mutagenesis of Toxoplasma gondii

    Energy Technology Data Exchange (ETDEWEB)

    Pfefferkorn, E.R.; Pfefferkorn, L.C.

    1979-06-01

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

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

    Directory of Open Access Journals (Sweden)

    Devita Surjana

    2010-01-01

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

  13. Precision Targeted Mutagenesis via Cas9 Paired Nickases in Rice.

    Science.gov (United States)

    Mikami, Masafumi; Toki, Seiichi; Endo, Masaki

    2016-05-01

    Recent reports of CRISPR- (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) mediated heritable mutagenesis in plants highlight the need for accuracy of the mutagenesis directed by this system. Off-target mutations are an important issue when considering functional gene analysis, as well as the molecular breeding of crop plants with large genome size, i.e. with many duplicated genes, and where the whole-genome sequence is still lacking. In mammals, off-target mutations can be suppressed by using Cas9 paired nickases together with paired guide RNAs (gRNAs). However, the performance of Cas9 paired nickases has not yet been fully assessed in plants. Here, we analyzed on- and off-target mutation frequency in rice calli and regenerated plants using Cas9 nuclease or Cas9 nickase with paired gRNAs. When Cas9 paired nickases were used, off-target mutations were fully suppressed in rice calli and regenerated plants. However, on-target mutation frequency also decreased compared with that induced by the Cas9 paired nucleases system. Since the gRNA sequence determines specific binding of Cas9 protein-gRNA ribonucleoproteins at the targeted sequence, the on-target mutation frequency of Cas9 paired nickases depends on the design of paired gRNAs. Our results suggest that a combination of gRNAs that can induce mutations at high efficiency with Cas9 nuclease should be used together with Cas9 nickase. Furthermore, we confirmed that a combination of gRNAs containing a one nucleotide (1 nt) mismatch toward the target sequence could not induce mutations when expressed with Cas9 nickase. Our results clearly show the effectiveness of Cas9 paired nickases in delivering on-target specific mutations. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

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

    Directory of Open Access Journals (Sweden)

    Alexandro Rodríguez-Rojas

    2015-10-01

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

  15. A randomized matched-pairs study of feasibility, acceptability, and effectiveness of systems consultation: a novel implementation strategy for adopting clinical guidelines for Opioid prescribing in primary care.

    Science.gov (United States)

    Quanbeck, Andrew; Brown, Randall T; Zgierska, Aleksandra E; Jacobson, Nora; Robinson, James M; Johnson, Roberta A; Deyo, Brienna M; Madden, Lynn; Tuan, Wen-Jan; Alagoz, Esra

    2018-01-25

    This paper reports on the feasibility, acceptability, and effectiveness of an innovative implementation strategy named "systems consultation" aimed at improving adherence to clinical guidelines for opioid prescribing in primary care. While clinical guidelines for opioid prescribing have been developed, they have not been widely implemented, even as opioid abuse reaches epidemic levels. We tested a blended implementation strategy consisting of several discrete implementation strategies, including audit and feedback, academic detailing, and external facilitation. The study compares four intervention clinics to four control clinics in a randomized matched-pairs design. Each systems consultant aided clinics on implementing the guidelines during a 6-month intervention consisting of monthly site visits and teleconferences/videoconferences. The mixed-methods evaluation employs the RE-AIM (Reach, Effectiveness, Adoption, Implementation, Maintenance) framework. Quantitative outcomes are compared using time series analysis. Qualitative methods included focus groups, structured interviews, and ethnographic field techniques. Seven clinics were randomly approached to recruit four intervention clinics. Each clinic designated a project team consisting of six to eight staff members, each with at least one prescriber. Attendance at intervention meetings was 83%. More than 80% of staff respondents agreed or strongly agreed with the statements: "I am more familiar with guidelines for safe opioid prescribing" and "My clinic's workflow for opioid prescribing is easier." At 6 months, statistically significant improvements were noted in intervention clinics in the percentage of patients with mental health screens, treatment agreements, urine drug tests, and opioid-benzodiazepine co-prescribing. At 12 months, morphine-equivalent daily dose was significantly reduced in intervention clinics compared to controls. The cost to deliver the strategy was $7345 per clinic. Adaptations were

  16. Drinker prototype alteration and cue reminders as strategies in a tailored web-based intervention reducing adults' alcohol consumption: randomized controlled trial.

    Science.gov (United States)

    van Lettow, Britt; de Vries, Hein; Burdorf, Alex; Boon, Brigitte; van Empelen, Pepijn

    2015-02-04

    Excessive alcohol use is a prevalent and worldwide problem. Excessive drinking causes a significant burden of disease and is associated with both morbidity and excess mortality. Prototype alteration and provision of a cue reminder could be useful strategies to enhance the effectiveness of online tailored interventions for excessive drinking. Through a Web-based randomized controlled trial, 2 strategies (ie, prototype alteration and cue reminders) within an existing online personalized feedback intervention (Drinktest) aimed to reduce adults' excessive drinking. It was expected that both strategies would add to Drinktest and would result in reductions in alcohol consumption by intrinsic motivation and the seizure of opportunities to act. Participants were recruited online and through printed materials. Excessive drinking adults (N=2634) were randomly assigned to 4 conditions: original Drinktest, Drinktest plus prototype alteration, Drinktest plus cue reminder, and Drinktest plus prototype alteration and cue reminder. Evaluation took place at 1-month posttest and 6-month follow-up. Differences in drinking behavior, intentions, and behavioral willingness (ie, primary outcomes) were assessed by means of longitudinal multilevel analyses using a last observation carried forward method. Measures were based on self-reports. All conditions showed reductions in drinking behavior and willingness to drink, and increased intentions to reduce drinking. Prototype alteration (B=-0.15, Pprototypes. Thus, prototype alteration and cue reminder usage may be feasible and simple intervention strategies to promote reductions in alcohol consumption among adults, with an effect up to 6 months. Nederlands Trial Register (NTR): 4169; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4169 (Archived by WebCite at http://www.webcitation.org/6VD2jnxmB).

  17. Drinker Prototype Alteration and Cue Reminders as Strategies in a Tailored Web-Based Intervention Reducing Adults’ Alcohol Consumption: Randomized Controlled Trial

    Science.gov (United States)

    2015-01-01

    Background Excessive alcohol use is a prevalent and worldwide problem. Excessive drinking causes a significant burden of disease and is associated with both morbidity and excess mortality. Prototype alteration and provision of a cue reminder could be useful strategies to enhance the effectiveness of online tailored interventions for excessive drinking. Objective Through a Web-based randomized controlled trial, 2 strategies (ie, prototype alteration and cue reminders) within an existing online personalized feedback intervention (Drinktest) aimed to reduce adults’ excessive drinking. It was expected that both strategies would add to Drinktest and would result in reductions in alcohol consumption by intrinsic motivation and the seizure of opportunities to act. Methods Participants were recruited online and through printed materials. Excessive drinking adults (N=2634) were randomly assigned to 4 conditions: original Drinktest, Drinktest plus prototype alteration, Drinktest plus cue reminder, and Drinktest plus prototype alteration and cue reminder. Evaluation took place at 1-month posttest and 6-month follow-up. Differences in drinking behavior, intentions, and behavioral willingness (ie, primary outcomes) were assessed by means of longitudinal multilevel analyses using a last observation carried forward method. Measures were based on self-reports. Results All conditions showed reductions in drinking behavior and willingness to drink, and increased intentions to reduce drinking. Prototype alteration (B=–0.15, Pprototypes. Thus, prototype alteration and cue reminder usage may be feasible and simple intervention strategies to promote reductions in alcohol consumption among adults, with an effect up to 6 months. Trial Registration Nederlands Trial Register (NTR): 4169; http://www.trialregister.nl/trialreg/admin/rctview.asp?TC=4169 (Archived by WebCite at http://www.webcitation.org/6VD2jnxmB). PMID:25653199

  18. Feasibility and acceptability of two incentive-based implementation strategies for mental health therapists implementing cognitive-behavioral therapy: a pilot study to inform a randomized controlled trial.

    Science.gov (United States)

    Beidas, Rinad S; Becker-Haimes, Emily M; Adams, Danielle R; Skriner, Laura; Stewart, Rebecca E; Wolk, Courtney Benjamin; Buttenheim, Alison M; Williams, Nathaniel J; Inacker, Patricia; Richey, Elizabeth; Marcus, Steven C

    2017-12-15

    Informed by our prior work indicating that therapists do not feel recognized or rewarded for implementation of evidence-based practices, we tested the feasibility and acceptability of two incentive-based implementation strategies that seek to improve therapist adherence to cognitive-behavioral therapy for youth, an evidence-based practice. This study was conducted over 6 weeks in two community mental health agencies with therapists (n = 11) and leaders (n = 4). Therapists were randomized to receive either a financial or social incentive if they achieved a predetermined criterion on adherence to cognitive-behavioral therapy. In the first intervention period (block 1; 2 weeks), therapists received the reward they were initially randomized to if they achieved criterion. In the second intervention period (block 2; 2 weeks), therapists received both rewards if they achieved criterion. Therapists recorded 41 sessions across 15 unique clients over the project period. Primary outcomes included feasibility and acceptability. Feasibility was assessed quantitatively. Fifteen semi-structured interviews were conducted with therapists and leaders to assess acceptability. Difference in therapist adherence by condition was examined as an exploratory outcome. Adherence ratings were ascertained using an established and validated observational coding system of cognitive-behavioral therapy. Both implementation strategies were feasible and acceptable-however, modifications to study design for the larger trial will be necessary based on participant feedback. With respect to our exploratory analysis, we found a trend suggesting the financial reward may have had a more robust effect on therapist adherence than the social reward. Incentive-based implementation strategies can be feasibly administered in community mental health agencies with good acceptability, although iterative pilot work is essential. Larger, fully powered trials are needed to compare the effectiveness of

  19. The EBC TWO Study (European Bifurcation Coronary TWO): A Randomized Comparison of Provisional T-Stenting Versus a Systematic 2 Stent Culotte Strategy in Large Caliber True Bifurcations.

    Science.gov (United States)

    Hildick-Smith, David; Behan, Miles W; Lassen, Jens F; Chieffo, Alaide; Lefèvre, Thierry; Stankovic, Goran; Burzotta, Francesco; Pan, Manuel; Ferenc, Miroslaw; Bennett, Lorraine; Hovasse, Thomas; Spence, Mark J; Oldroyd, Keith; Brunel, Philippe; Carrie, Didier; Baumbach, Andreas; Maeng, Michael; Skipper, Nicola; Louvard, Yves

    2016-09-01

    For the treatment of coronary bifurcation lesions, a provisional strategy is superior to systematic 2-stent techniques for the most bifurcation lesions. However, complex anatomies with large side branches (SBs) with significant ostial disease length are considered by expert consensus to warrant a 2-stent technique upfront. This consensus view has not been scientifically assessed. Symptomatic patients with large caliber true bifurcation lesions (SB diameter ≥2.5 mm) and significant ostial disease length (≥5 mm) were randomized to either a provisional T-stent strategy or a dual stent culotte technique. Two hundred patients aged 64±10 years, 82% male, were randomized in 20 European centers. The clinical presentations were stable coronary disease (69%) and acute coronary syndromes (31%). SB stent diameter (2.67±0.27 mm) and length (20.30±5.89 mm) confirmed the extent of SB disease. Procedural success (provisional 97%, culotte 94%) and kissing balloon inflation (provisional 95%, culotte 98%) were high. Sixteen percent of patients in the provisional group underwent T-stenting. The primary end point (a composite of death, myocardial infarction, and target vessel revascularization at 12 months) occurred in 7.7% of the provisional T-stent group versus 10.3% of the culotte group (hazard ratio, 1.02; 95% confidence interval, 0.78-1.34; P=0.53). Procedure time, x-ray dose, and cost all favored the simpler procedure. When treating complex coronary bifurcation lesions with large stenosed SBs, there is no difference between a provisional T-stent strategy and a systematic 2-stent culotte strategy in a composite end point of death, myocardial infarction, and target vessel revascularization at 12 months. URL: http://www.clinicaltrials.gov. Unique identifier: NCT 01560455. © 2016 American Heart Association, Inc.

  20. Mnemonic strategy training improves memory for object location associations in both healthy elderly and patients with amnestic mild cognitive impairment: a randomized, single-blind study.

    Science.gov (United States)

    Hampstead, Benjamin M; Sathian, Krish; Phillips, Pamela A; Amaraneni, Akshay; Delaune, William R; Stringer, Anthony Y

    2012-05-01

    To evaluate the efficacy of mnemonic strategy training versus a matched-exposure control condition and to examine the relationship between training-related gains, neuropsychological abilities, and medial temporal lobe volumetrics in patients with amnestic mild cognitive impairment (aMCI) and age-matched healthy controls. Twenty-three of 45 screened healthy controls and 29 of 42 screened patients with aMCI were randomized to mnemonic strategy or matched-exposure groups. Groups were run in parallel, with participants blind to the other intervention. All participants completed five sessions within 2 weeks. Memory testing for object-location associations (OLAs) was performed during sessions one and five and at a 1-month follow-up. During Sessions 2-4, participants received either mnemonic strategy training or a matched number of exposures with corrective feedback for a total of 45 OLAs. Structural magnetic resonance imaging was performed in most participants, and medial temporal lobe volumetrics were acquired. Twenty-one healthy controls and 28 patients with aMCI were included in data analysis. Mnemonic strategy training was significantly more beneficial than matched exposure immediately after training, p = .006, partial η2 = .16, and at 1 month, p Mnemonic strategy-related improvement was correlated positively with baseline memory and executive functioning and negatively with inferior lateral ventricle volume in patients with aMCI; no significant relationships were evident in matched-exposure patients. Mnemonic strategies effectively improve memory for specific content for at least 1 month in patients with aMCI.

  1. Investigating bang for your training buck: a randomized controlled trial comparing three methods of training clinicians in two core strategies of dialectical behavior therapy.

    Science.gov (United States)

    Dimeff, Linda A; Harned, Melanie S; Woodcock, Eric A; Skutch, Julie M; Koerner, Kelly; Linehan, Marsha M

    2015-05-01

    The present study examined the efficacy of online training (OLT), instructor-led training (ILT), and a treatment manual (TM) in training mental health clinicians in two core strategies of Dialectical Behavior Therapy (DBT): chain analysis and validation. A randomized controlled trial compared OLT, ILT, and TM among clinicians naïve to DBT (N=172) who were assessed at baseline, post-training, and 30, 60, and 90 days following training. Primary outcomes included satisfaction, self-efficacy, motivation, knowledge, clinical proficiency, and clinical use. Overall, ILT outperformed OLT and TM in satisfaction, self-efficacy, and motivation, whereas OLT was the most effective method for increasing knowledge. The conditions did not differ in observer-rated clinical proficiency or self-reported clinical use, which both increased to moderate levels after training. In addition, ILT was particularly effective at improving motivation to use chain analysis, whereas OLT was particularly effective at increasing knowledge of validation strategies. These findings suggest that these types of brief, didactic trainings may be effective methods of increasing knowledge of new treatment strategies, but may not be sufficient to enable clinicians to achieve a high level of clinical use or proficiency. Additional research examining the possible advantages of matching training methods to types of treatment strategies may help to determine a tailored, more effective approach to training clinicians in empirically supported treatments. Copyright © 2015. Published by Elsevier Ltd.

  2. Random sampling or geostatistical modelling? Choosing between design-based and model-based sampling strategies for soil (with discussion)

    NARCIS (Netherlands)

    Brus, D.J.; Gruijter, de J.J.

    1997-01-01

    Classical sampling theory has been repeatedly identified with classical statistics which assumes that data are identically and independently distributed. This explains the switch of many soil scientists from design-based sampling strategies, based on classical sampling theory, to the model-based

  3. Effect of Individualized vs Standard Blood Pressure Management Strategies on Postoperative Organ Dysfunction Among High-Risk Patients Undergoing Major Surgery: A Randomized Clinical Trial.

    Science.gov (United States)

    Futier, Emmanuel; Lefrant, Jean-Yves; Guinot, Pierre-Gregoire; Godet, Thomas; Lorne, Emmanuel; Cuvillon, Philippe; Bertran, Sebastien; Leone, Marc; Pastene, Bruno; Piriou, Vincent; Molliex, Serge; Albanese, Jacques; Julia, Jean-Michel; Tavernier, Benoit; Imhoff, Etienne; Bazin, Jean-Etienne; Constantin, Jean-Michel; Pereira, Bruno; Jaber, Samir

    2017-10-10

    Perioperative hypotension is associated with an increase in postoperative morbidity and mortality, but the appropriate management strategy remains uncertain. To evaluate whether an individualized blood pressure management strategy tailored to individual patient physiology could reduce postoperative organ dysfunction. The Intraoperative Norepinephrine to Control Arterial Pressure (INPRESS) study was a multicenter, randomized, parallel-group clinical trial conducted in 9 French university and nonuniversity hospitals. Adult patients (n = 298) at increased risk of postoperative complications with a preoperative acute kidney injury risk index of class III or higher (indicating moderate to high risk of postoperative kidney injury) undergoing major surgery lasting 2 hours or longer under general anesthesia were enrolled from December 4, 2012, through August 28, 2016 (last follow-up, September 28, 2016). Individualized management strategy aimed at achieving a systolic blood pressure (SBP) within 10% of the reference value (ie, patient's resting SBP) or standard management strategy of treating SBP less than 80 mm Hg or lower than 40% from the reference value during and for 4 hours following surgery. The primary outcome was a composite of systemic inflammatory response syndrome and dysfunction of at least 1 organ system of the renal, respiratory, cardiovascular, coagulation, and neurologic systems by day 7 after surgery. Secondary outcomes included the individual components of the primary outcome, durations of ICU and hospital stay, adverse events, and all-cause mortality at 30 days after surgery. Among 298 patients who were randomized, 292 patients completed the trial (mean [SD] age, 70 [7] years; 44 [15.1%] women) and were included in the modified intention-to-treat analysis. The primary outcome event occurred in 56 of 147 patients (38.1%) assigned to the individualized treatment strategy vs 75 of 145 patients (51.7%) assigned to the standard treatment strategy

  4. A comparison of 3 ventilation strategies in children younger than 1 year using a Proseal laryngeal mask airway: a randomized controlled trial.

    Science.gov (United States)

    Templeton, T Wesley; Hoke, Lauren K; Templeton, Leah B; Ririe, Douglas G; Rose, Danielle M; Bryan, Yvon F

    2016-12-01

    To determine quantitative differences in several routinely measured ventilation parameters using a standardized anesthetic technique and 3 different ventilation modalities in patients younger than 1 year with a ProSeal laryngeal mask airway (PLMA). Randomized prospective study. Tertiary care pediatric hospital. Thirty-nine American Society Anesthesiologists classifications 1 to 2, pediatric patients younger than 1 year. Three different ventilation strategies (spontaneous ventilation [SV], pressure support ventilation [PSV], and pressure-controlled ventilation [PCV]) were randomly applied to patients who underwent a standardized mask induction with sevoflurane/oxygen and propofol 2 mg/kg and fentanyl 2 μg/kg administered intravenously followed by PLMA insertion. Patients were maintained on sevoflurane and N 2 O. We measured the differences in end-tidal CO 2 (etco 2 ), tidal volume (TV), and respiratory rate (RR) over time between SV, PSV, and PCV. These data were recorded at 5-minute intervals. etco 2 (mm Hg) was not significantly higher in the SV vs PSV (P=2.11) and SV vs PCV (P=.24). TV (mL/kg) was significantly lower in SV vs PSV (Pchildren younger than 1 year. Although we did not observe a statistically significant increase in etco 2 , differences in TV and RR, and the small but significant incidence of apnea may make PSV or PCV more optimal ventilation strategies in children younger than 1 year when using a PLMA. Copyright © 2016 Elsevier Inc. All rights reserved.

  5. Experimental blunt chest trauma--cardiorespiratory effects of different mechanical ventilation strategies with high positive end-expiratory pressure: a randomized controlled study.

    Science.gov (United States)

    Schreiter, Dierk; Carvalho, Nadja C; Katscher, Sebastian; Mende, Ludger; Reske, Alexander P; Spieth, Peter M; Carvalho, Alysson R; Beda, Alessandro; Lachmann, Burkhard; Amato, Marcelo B P; Wrigge, Hermann; Reske, Andreas W

    2016-01-12

    Uncertainty persists regarding the optimal ventilatory strategy in trauma patients developing acute respiratory distress syndrome (ARDS). This work aims to assess the effects of two mechanical ventilation strategies with high positive end-expiratory pressure (PEEP) in experimental ARDS following blunt chest trauma. Twenty-six juvenile pigs were anesthetized, tracheotomized and mechanically ventilated. A contusion was applied to the right chest using a bolt-shot device. Ninety minutes after contusion, animals were randomized to two different ventilation modes, applied for 24 h: Twelve pigs received conventional pressure-controlled ventilation with moderately low tidal volumes (VT, 8 ml/kg) and empirically chosen high external PEEP (16 cmH2O) and are referred to as the HP-CMV-group. The other group (n = 14) underwent high-frequency inverse-ratio pressure-controlled ventilation (HFPPV) involving respiratory rate of 65 breaths · min(-1), inspiratory-to-expiratory-ratio 2:1, development of intrinsic PEEP and recruitment maneuvers, compatible with the rationale of the Open Lung Concept. Hemodynamics, gas exchange and respiratory mechanics were monitored during 24 h. Computed tomography and histology were analyzed in subgroups. Comparing changes which occurred from randomization (90 min after chest trauma) over the 24-h treatment period, groups differed statistically significantly (all P values for group effect ventilation improved respiratory function and fulfilled relevant ventilation endpoints for trauma patients, i.e. restoration of oxygenation and lung aeration while avoiding hypercapnia and respiratory acidosis.

  6. 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

  7. The yeast environmental stress response regulates mutagenesis induced by proteotoxic stress.

    Directory of Open Access Journals (Sweden)

    Erika Shor

    Full Text Available 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.

  8. Hemodialysis without systemic anticoagulation: a prospective randomized trial to evaluate 3 strategies in patients at risk of bleeding.

    Directory of Open Access Journals (Sweden)

    Bruno Guéry

    Full Text Available In this clinical trial, we aimed to compare three means of performing chronic hemodialysis in patients with contra-indication to systemic heparinization.This open-label monocentric randomized « n-of-one » trial, conducted in a single tertiary care center, recruited chronic hemodialysis patients with a contra-indication to systemic heparinization for at least 3 consecutive sessions. All patients underwent hemodialysis with an AN69ST dialyzer, and were administered three alternative dialysis procedures in a random sequence: intermittent saline flushes, constant saline infusion, or pre-dialysis heparin coating of the membrane. The primary outcome was the need to interrupt the dialysis session because of clotting events due to either (i a complete coagulation of the circuit; (ii a partial coagulation of the circuit; (iii a>50% rise over baseline in the venous pressure.At the end of the inclusion period (May, 2007 to December, 2008, the number of patients to include (n=75 was not reached: only 46 patients were included and underwent randomization. The study was terminated, and statistical analysis took into account 224 hemodialysis sessions performed in 44 patients with analyzable data. Heparin adsorption was associated with a significant reduction of the need to interrupt the dialysis session because of clotting events: odds ratio 0.3 (CI 95% 0.2 to 0.6; p3 h dialysis sessions and for having complete blood restitution. There were no significant effects of the dialysis procedure on weight loss, online ionic dialysance, and adverse events.Heparin-coated AN69ST dialysis membrane is a safe and effective method to avoid or delay per-dialytic clotting events in patients with contra-indication to systemic anticoagulation. However, results are not generalizable safely to patients with active bleeding, since weak heparinemia, not assessed in this study, may occur.ClinicalTrials.gov NCT00473109.

  9. Random Assignment of Schools to Groups in the Drug Resistance Strategies Rural Project: Some New Methodological Twists

    Science.gov (United States)

    Pettigrew, Jonathan; Miller-Day, Michelle; Krieger, Janice L.; Zhou, Jiangxiu; Hecht, Michael L.

    2014-01-01

    Random assignment to groups is the foundation for scientifically rigorous clinical trials. But assignment is challenging in group randomized trials when only a few units (schools) are assigned to each condition. In the DRSR project, we assigned 39 rural Pennsylvania and Ohio schools to three conditions (rural, classic, control). But even with 13 schools per condition, achieving pretest equivalence on important variables is not guaranteed. We collected data on six important school-level variables: rurality, number of grades in the school, enrollment per grade, percent white, percent receiving free/assisted lunch, and test scores. Key to our procedure was the inclusion of school-level drug use data, available for a subset of the schools. Also, key was that we handled the partial data with modern missing data techniques. We chose to create one composite stratifying variable based on the seven school-level variables available. Principal components analysis with the seven variables yielded two factors, which were averaged to form the composite inflate-suppress (CIS) score which was the basis of stratification. The CIS score was broken into three strata within each state; schools were assigned at random to the three program conditions from within each stratum, within each state. Results showed that program group membership was unrelated to the CIS score, the two factors making up the CIS score, and the seven items making up the factors. Program group membership was not significantly related to pretest measures of drug use (alcohol, cigarettes, marijuana, chewing tobacco; smallest p>.15), thus verifying that pretest equivalence was achieved. PMID:23722619

  10. Agrobacterium-mediated insertional mutagenesis in the mycorrhizal fungus Laccaria bicolor.

    Science.gov (United States)

    Stephan, B I; Alvarez Crespo, M C; Kemppainen, M J; Pardo, A G

    2017-05-01

    Agrobacterium-mediated gene transfer (AMT) is extensively employed as a tool in fungal functional genomics and accordingly, in previous studies we used AMT on a dikaryotic strain of the ectomycorrhizal basidiomycete Laccaria bicolor. The interest in this fungus derives from its capacity to establish a symbiosis with tree roots, thereby playing a major role in nutrient cycling of forest ecosystems. The ectomycorrhizal symbiosis is a highly complex interaction involving many genes from both partners. To advance in the functional characterization of fungal genes, AMT was used on a monokaryotic L. bicolor. A collection of over 1200 transgenic strains was produced, of which 200 randomly selected strains were analyzed for their genomic T-DNA insertion patterns. By means of insertional mutagenesis, a number of transgenic strains were obtained displaying differential growth features. Moreover, mating with a compatible strain resulted in dikaryons that retained altered phenotypic features of the transgenic monokaryon. The analysis of the T-DNA integration pattern revealed mostly similar results to those reported in earlier studies, confirming the usefulness of AMT on different genetic backgrounds of L. bicolor. Taken together, our studies display the great versatility and potentiality of AMT as a tool for the genetic characterization of L. bicolor.

  11. A pragmatic randomized trial of a polypill-based strategy to improve use of indicated preventive treatments in people at high cardiovascular disease risk.

    Science.gov (United States)

    Patel, Anushka; Cass, Alan; Peiris, David; Usherwood, Tim; Brown, Alex; Jan, Stephen; Neal, Bruce; Hillis, Graham S; Rafter, Natasha; Tonkin, Andrew; Webster, Ruth; Billot, Laurent; Bompoint, Severine; Burch, Carol; Burke, Hugh; Hayman, Noel; Molanus, Barbara; Reid, Christopher M; Shiel, Louise; Togni, Samantha; Rodgers, Anthony

    2015-07-01

    Most individuals at high cardiovascular disease (CVD) risk worldwide do not receive any or optimal preventive drugs. We aimed to determine whether fixed dose combinations of generic drugs ('polypills') would promote use of such medications. We conducted a randomized, open-label trial involving 623 participants from Australian general practices. Participants had established CVD or an estimated five-year CVD risk of ≥15%, with indications for antiplatelet, statin and ≥2 blood pressure lowering drugs ('combination treatment'). Participants randomized to the 'polypill-based strategy' received a polypill containing aspirin 75 mg, simvastatin 40 mg, lisinopril 10 mg and either atenolol 50 mg or hydrochlorothiazide 12.5 mg. Participants randomized to 'usual care' continued with separate medications and doses as prescribed by their doctor. Primary outcomes were self-reported combination treatment use, systolic blood pressure and total cholesterol. After a median of 18 months, the polypill-based strategy was associated with greater use of combination treatment (70% vs. 47%; relative risk 1.49, (95% confidence interval (CI) 1.30 to 1.72) p study end, 17% and 67% of participants in polypill and usual care groups, respectively, were taking atorvastatin or rosuvastatin. Provision of a polypill improved self-reported use of indicated preventive treatments. The lack of differences in blood pressure and cholesterol may reflect limited study power, although for cholesterol, improved statin use in the polypill group counter-balanced use of more potent statins with usual care. © The European Society of Cardiology 2014 Reprints and permissions: sagepub.co.uk/journalsPermissions.nav.

  12. Improving the solubility of anti-LINGO-1 monoclonal antibody Li33 by isotype switching and targeted mutagenesis.

    Science.gov (United States)

    Pepinsky, R Blake; Silvian, Laura; Berkowitz, Steven A; Farrington, Graham; Lugovskoy, Alexey; Walus, Lee; Eldredge, John; Capili, Allan; Mi, Sha; Graff, Christilyn; Garber, Ellen

    2010-05-01

    Monoclonal antibodies (Mabs) are a favorite drug platform of the biopharmaceutical industry. Currently, over 20 Mabs have been approved and several hundred others are in clinical trials. The anti-LINGO-1 Mab Li33 was selected from a large panel of antibodies by Fab phage display technology based on its extraordinary biological activity in promoting oligodendrocyte differentiation and myelination in vitro and in animal models of remyelination. However, the Li33 Fab had poor solubility when converted into a full antibody in an immunoglobulin G1 framework. A detailed analysis of the biochemical and structural features of the antibody revealed several possible reasons for its propensity to aggregate. Here, we successfully applied three molecular approaches (isotype switching, targeted mutagenesis of complementarity determining region residues, and glycosylation site insertion mutagenesis) to address the solubility problem. Through these efforts we were able to improve the solubility of the Li33 Mab from 0.3 mg/mL to >50 mg/mL and reduce aggregation to an acceptable level. These strategies can be readily applied to other proteins with solubility issues.

  13. The effect of feedback regarding coping strategies and illness behavior on hand surgery patient satisfaction and communication: a randomized controlled trial.

    Science.gov (United States)

    Mellema, Jos J; O'Connor, Casey M; Overbeek, Celeste L; Hageman, Michiel G; Ring, David

    2015-09-01

    Patients and surgeons can feel uncomfortable discussing coping strategies, psychological distress, and stressful circumstances. It has been suggested that patient-reported outcome measures (PROMs) facilitate the discussion of factors associated with increased symptoms and disability. This study assessed the effect of providing feedback to patients regarding their coping strategy and illness behavior on patient satisfaction and patient-physician communication in orthopedic surgery. In a prospective study, 136 orthopedic patients were randomly assigned to either receive feedback about the Patient-Reported Outcomes Measurement Information System (PROMIS) Pain Interference computer-adaptive test (CAT) prior to the visit with the hand surgeon or not. The primary outcome was patient satisfaction with the consultation and secondary outcomes involved patient-physician communication. Bivariate and multivariable analyses were performed to determine the influence of the feedback on patient satisfaction and communication. There was no significant difference in patient satisfaction between patients who received feedback and patients who did not (P = 0.70). Feedback was associated with more frequent discussion of coping strategies (P = 0.045) in bivariate analysis but was not independently associated: in multivariable analysis, only PROMIS Pain Interference CAT and age were identified as independent predictors (odds ratio (OR) 1.1; 95 % confidence interval (CI) 1.0-1.1, P = 0.013, and OR 0.97, 95 % CI 0.94-0.99, P = 0.032, respectively). No factors were associated with discussion of stressors. Discussion of circumstances was independently associated with increased PROMIS Pain Interference CAT, marital status, and work status. We found that feedback regarding coping strategies and illness behavior using the PROMIS Pain Interference CAT did not affect patient satisfaction. Although feedback was associated with increased discussion of illness behavior in bivariate

  14. Effectiveness of a multi-strategy intervention in increasing the implementation of vegetable and fruit breaks by Australian primary schools: a non-randomized controlled trial

    Science.gov (United States)

    2012-01-01

    Background Limited evidence exists describing the effectiveness of strategies in facilitating the implementation of vegetable and fruit programs by schools on a population wide basis. The aim of this study was to examine the effectiveness of a multi-strategy intervention in increasing the population-wide implementation of vegetable and fruit breaks by primary schools and to determine if intervention effectiveness varied by school characteristics. Methods A quasi-experimental study was conducted in primary schools in the state of New South Wales, Australia. All primary schools in one region of the state (n = 422) received a multi-strategy intervention. A random sample of schools (n = 406) in the remainder of the state served as comparison schools. The multi-strategy intervention to increase vegetable and fruit breaks involved the development and provision of: program consensus and leadership; staff training; program materials; incentives; follow-up support; and implementation feedback. Comparison schools had access to routine information-based Government support. Data to assess the prevalence of vegetable and fruit breaks were collected by telephone from Principals of the intervention and comparison schools at baseline (2006–2007) and 11 to 15 months following the commencement of the intervention (2009–2010). GEE analysis was used to examine the change in the prevalence of vegetable and fruit breaks in intervention schools compared to comparison schools. Results At follow-up, prevalence of vegetable and fruit breaks increased significantly in both intervention (50.3 % to 82.0 %, p schools. The increase in prevalence in intervention schools was significantly larger than among comparison schools (OR 2.36; 95 % CI 1.60-3.49, p effect size was similar between schools regardless of the rurality or socioeconomic status of school location, school size or government or non-government school type. Conclusion The findings suggest that a multi-strategy intervention can

  15. Effectiveness of an (18)F-FDG-PET based strategy to optimize the diagnostic trajectory of suspected recurrent laryngeal carcinoma after radiotherapy: The RELAPS multicenter randomized trial.

    Science.gov (United States)

    de Bree, Remco; van der Putten, Lisa; van Tinteren, Harm; Wedman, Jan; Oyen, Wim J G; Janssen, Luuk M; van den Brekel, Michiel W M; Comans, Emile F I; Pruim, Jan; Takes, Robert P; Hobbelink, Monique G G; Valdés Olmos, Renato; van der Laan, Bernard F A M; Boers, Maarten; Hoekstra, Otto S; Leemans, C René

    2016-02-01

    The purpose of this study is to evaluate the efficacy of (18)F-FDG-PET as first-line diagnostic investigation, prior to performing a direct laryngoscopy with biopsy under general anesthesia, in patients suspected of recurrent laryngeal carcinoma after radiotherapy. 150 patients suspected of recurrent T2-4 laryngeal carcinoma at least two months after prior (chemo)radiotherapy with curative intent for resectable disease were randomized to direct laryngoscopy (CWU: conventional workup strategy) or to (18)F-FDG-PET only followed by direct laryngoscopy if PET was assessed 'positive' or 'equivocal' (PWU: PET based workup strategy), to compare the effectiveness of these strategies. Primary endpoint was the number of indications for direct laryngoscopies classified as unnecessary based on absence of recurrence, both on direct laryngoscopy and on six month follow up. Safety endpoints comprised resectability of recurrent lesions and completeness of surgical margins following salvage laryngectomy. Intention-to-treat analyses were performed on all randomized patients (CWU: n=74, PWU: n=76). Tumor recurrence was similar in both groups: 45 patients (30%; 21 CWU, 24 PWU) within six months. In 53 patients in the CWU arm (72%, 95% CI: 60-81) unnecessary direct laryngoscopies were performed compared to 22 in the PWU arm (29%, 95% CI: 19-40) (p<0·0001). The percentage of salvage laryngectomies (resectability) and positive surgical margins were similar between CWU and PWU (81%, 63% respectively, p=0·17, and 29%, 7%, respectively, p=0.20). The prevalence of the combination of local unresectability and positive margins is in the CWU group 24% and in the PWU group 8%. No difference (p=0.32) in disease specific survival between both groups was found. In patients with suspected laryngeal carcinoma after radiotherapy, PET as the first diagnostic procedure can reduce the need for direct laryngoscopy by more than 50% without jeopardizing quality of treatment. Copyright © 2015 Elsevier

  16. Effectiveness of a two-step population-based osteoporosis screening program using FRAX: the randomized Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study.

    Science.gov (United States)

    Rubin, K H; Rothmann, M J; Holmberg, T; Høiberg, M; Möller, S; Barkmann, R; Glüer, C C; Hermann, A P; Bech, M; Gram, J; Brixen, K

    2017-12-07

    The Risk-stratified Osteoporosis Strategy Evaluation (ROSE) study investigated the effectiveness of a two-step screening program for osteoporosis in women. We found no overall reduction in fractures from systematic screening compared to the current case-finding strategy. The group of moderate- to high-risk women, who accepted the invitation to DXA, seemed to benefit from the program. The purpose of the ROSE study was to investigate the effectiveness of a two-step population-based osteoporosis screening program using the Fracture Risk Assessment Tool (FRAX) derived from a self-administered questionnaire to select women for DXA scan. After the scanning, standard osteoporosis management according to Danish national guidelines was followed. Participants were randomized to either screening or control group, and randomization was stratified according to age and area of residence. Inclusion took place from February 2010 to November 2011. Participants received a self-administered questionnaire, and women in the screening group with a FRAX score ≥ 15% (major osteoporotic fractures) were invited to a DXA scan. Primary outcome was incident clinical fractures. Intention-to-treat analysis and two per-protocol analyses were performed. A total of 3416 fractures were observed during a median follow-up of 5 years. No significant differences were found in the intention-to-treat analyses with 34,229 women included aged 65-80 years. The per-protocol analyses showed a risk reduction in the group that underwent DXA scanning compared to women in the control group with a FRAX ≥ 15%, in regard to major osteoporotic fractures, hip fractures, and all fractures. The risk reduction was most pronounced for hip fractures (adjusted SHR 0.741, p = 0.007). Compared to an office-based case-finding strategy, the two-step systematic screening strategy had no overall effect on fracture incidence. The two-step strategy seemed, however, to be beneficial in the group of women who were

  17. Reduction of allogeneic red blood cell usage during cardiac surgery by an integrated intra- and postoperative blood salvage strategy: results of a randomized comparison.

    Science.gov (United States)

    Weltert, Luca; Nardella, Saverio; Rondinelli, Maria Beatrice; Pierelli, Luca; De Paulis, Ruggero

    2013-04-01

    The amount of allogeneic blood transfusion may relate to worse outcome in cardiac surgery. The reinfusion of red blood cells (RBCs) lost by patients, including those of chest drains, is a promising strategy to minimize allogeneic transfusions. To verify this hypotheis, 1047 cardiac surgery patients were randomly assigned to either traditional intraoperative blood salvage followed by chest drain insertion or intra- and postoperative strategy with the Haemonetics cardioPAT system. Allogeneic RBC transfusion rate (primary endpoint) and postoperative complications (secondary endpoint) were recorded at the time of discharge from the hospital and at first month follow-up visit, respectively. The cardioPAT arm received 1.20 units of allogeneic RBCs per patient, whereas the control group required 2.11 units per patient, and this difference proved to be highly significant (p=0.02). We observed a comparable 45-day mortality rate but a lower rate of deep vein thrombosis (p=0.04) and atrial fibrillation (p=0.04) in the cardioPAT arm. A significant reduction in patient exposure to allogeneic RBCs was observed in the cardioPAT system arm. Complications were slightly less frequent in the cardioPAT group. The use of the cardioPAT is a safe and effective strategy to reduce allogeneic RBC transfusions in cardiac surgery. © 2012 American Association of Blood Banks.

  18. Enhancement of Biomass and Lipid Productivities of Water Surface-Floating Microalgae by Chemical Mutagenesis

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    Daisuke Nojima

    2017-05-01

    Full Text Available Water surface-floating microalgae have great potential for biofuel applications due to the ease of the harvesting process, which is one of the most problematic steps in conventional microalgal biofuel production. We have collected promising water surface-floating microalgae and characterized their capacity for biomass and lipid production. In this study, we performed chemical mutagenesis of two water surface-floating microalgae to elevate productivity. Floating microalgal strains AVFF007 and FFG039 (tentatively identified as Botryosphaerella sp. and Chlorococcum sp., respectively were exposed to ethyl methane sulfonate (EMS or 1-methyl-3-nitro-1-nitrosoguanidine (MNNG, and pale green mutants (PMs were obtained. The most promising FFG039 PM formed robust biofilms on the surface of the culture medium, similar to those formed by wild type strains, and it exhibited 1.7-fold and 1.9-fold higher biomass and lipid productivities than those of the wild type. This study indicates that the chemical mutation strategy improves the lipid productivity of water surface-floating microalgae without inhibiting biofilm formation and floating ability.

  19. Random resampling masks: a non-Bayesian one-shot strategy for noise reduction in digital holography.

    Science.gov (United States)

    Bianco, V; Paturzo, M; Memmolo, P; Finizio, A; Ferraro, P; Javidi, B

    2013-03-01

    Holographic imaging may become severely degraded by a mixture of speckle and incoherent additive noise. Bayesian approaches reduce the incoherent noise, but prior information is needed on the noise statistics. With no prior knowledge, one-shot reduction of noise is a highly desirable goal, as the recording process is simplified and made faster. Indeed, neither multiple acquisitions nor a complex setup are needed. So far, this result has been achieved at the cost of a deterministic resolution loss. Here we propose a fast non-Bayesian denoising method that avoids this trade-off by means of a numerical synthesis of a moving diffuser. In this way, only one single hologram is required as multiple uncorrelated reconstructions are provided by random complementary resampling masks. Experiments show a significant incoherent noise reduction, close to the theoretical improvement bound, resulting in image-contrast improvement. At the same time, we preserve the resolution of the unprocessed image.

  20. Implementation strategies of internet-based asthma self-management support in usual care. Study protocol for the IMPASSE cluster randomized trial

    Directory of Open Access Journals (Sweden)

    van Gaalen Johanna L

    2012-11-01

    Full Text Available Abstract Background Internet-based self-management (IBSM support cost-effectively improves asthma control, asthma related quality of life, number of symptom-free days, and lung function in patients with mild to moderate persistent asthma. The current challenge is to implement IBSM in clinical practice. Methods/design This study is a three-arm cluster randomized trial with a cluster pre-randomisation design and 12 months follow-up per practice comparing the following three IBSM implementation strategies: minimum strategy (MS: dissemination of the IBSM program; intermediate strategy (IS: MS + start-up support for professionals (i.e., support in selection of the appropriate population and training of professionals; and extended strategy (ES: IS + additional training and ongoing support for professionals. Because the implementation strategies (interventions are primarily targeted at general practices, randomisation will occur at practice level. In this study, we aim to evaluate 14 primary care practices per strategy in the Leiden-The Hague region, involving 140 patients per arm. Patients aged 18 to 50 years, with a physician diagnosis of asthma, prescription of inhaled corticosteroids, and/or montelukast for ≥3 months in the previous year are eligible to participate. Primary outcome measures are the proportion of referred patients that participate in IBSM, and the proportion of patients that have clinically relevant improvement in the asthma-related quality of life. The secondary effect measures are clinical outcomes (asthma control, lung function, usage of airway treatment, and presence of exacerbations; self-management related outcomes (health education impact, medication adherence, and illness perceptions; and patient utilities. Process measures are the proportion of practices that participate in IBSM and adherence of professionals to implementation strategies. Cost-effective measurements are medical costs and healthcare consumption

  1. CRISPR/Cas9-mediated targeted mutagenesis in grape.

    Science.gov (United States)

    Nakajima, Ikuko; Ban, Yusuke; Azuma, Akifumi; Onoue, Noriyuki; Moriguchi, Takaya; Yamamoto, Toshiya; Toki, Seiichi; Endo, Masaki

    2017-01-01

    RNA-guided genome editing using the CRISPR/Cas9 CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) system has been applied successfully in several plant species. However, to date, there are few reports on the use of any of the current genome editing approaches in grape-an important fruit crop with a large market not only for table grapes but also for wine. Here, we report successful targeted mutagenesis in grape (Vitis vinifera L., cv. Neo Muscat) using the CRISPR/Cas9 system. When a Cas9 expression construct was transformed to embryonic calli along with a synthetic sgRNA expression construct targeting the Vitis vinifera phytoene desaturase (VvPDS) gene, regenerated plants with albino leaves were obtained. DNA sequencing confirmed that the VvPDS gene was mutated at the target site in regenerated grape plants. Interestingly, the ratio of mutated cells was higher in lower, older, leaves compared to that in newly appearing upper leaves. This result might suggest either that the proportion of targeted mutagenized cells is higher in older leaves due to the repeated induction of DNA double strand breaks (DSBs), or that the efficiency of precise DSBs repair in cells of old grape leaves is decreased.

  2. Overproduction of Clavulanic Acid by UV Mutagenesis of Streptomyces clavuligerus.

    Science.gov (United States)

    Korbekandi, Hassan; Darkhal, Parisa; Hojati, Zohreh; Abedi, Daryoush; Hamedi, Javad; Pourhosein, Meraj

    2010-01-01

    Clavulanic acid is produced industrially by fermentation of Streptomyces clavuligerus and researches have increased its production by strain improvement, recombinant DNA technology, and media composition and growth condition optimization. The main objective of this study was to increase the level of clavulanic acid production from Streptomyces clavuligerus (DSM 738), using UV irradiation. After incubation, the spores and aerial mycelia were scraped off the agar plate by a sterile loop. After passing through a cotton wool, the serially diluted spore suspension was spread on GYM- agar containing caffeine. The plates were irradiated with UV light, wrapped in aluminum foil and incubated. The colonies were sub-cultured again to express the mutations. An aliquot of the spore suspension prepared from the resulted culture was poured in GYM agar plates and incubated. The plates were overlaid with nutrient-agar containing penicillin G and Klebsiela pneumoniae, and incubated. The inhibition zone diameter was measured and compared with the wild type colony. Repeating this procedure, the overproducer mutants were selected. Concentration of clavulanic acid was determined by HPLC analysis. It was concluded that secondary metabolites, mainly antibiotics containing clavulanic acid, were produced about 6-7 days after the growth, and concentration of clavulanic acid was increased up to two-folds after UV mutagenesis.

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

    Directory of Open Access Journals (Sweden)

    Takashi Nakanishi

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

  4. Overproduction of Clavulanic Acid by UV Mutagenesis of Streptomyces clavuligerus

    Science.gov (United States)

    Korbekandi, Hassan; Darkhal, Parisa; Hojati, Zohreh; Abedi, Daryoush; Hamedi, Javad; Pourhosein, Meraj

    2010-01-01

    Clavulanic acid is produced industrially by fermentation of Streptomyces clavuligerus and researches have increased its production by strain improvement, recombinant DNA technology, and media composition and growth condition optimization. The main objective of this study was to increase the level of clavulanic acid production from Streptomyces clavuligerus (DSM 738), using UV irradiation. After incubation, the spores and aerial mycelia were scraped off the agar plate by a sterile loop. After passing through a cotton wool, the serially diluted spore suspension was spread on GYM- agar containing caffeine. The plates were irradiated with UV light, wrapped in aluminum foil and incubated. The colonies were sub-cultured again to express the mutations. An aliquot of the spore suspension prepared from the resulted culture was poured in GYM agar plates and incubated. The plates were overlaid with nutrient-agar containing penicillin G and Klebsiela pneumoniae, and incubated. The inhibition zone diameter was measured and compared with the wild type colony. Repeating this procedure, the overproducer mutants were selected. Concentration of clavulanic acid was determined by HPLC analysis. It was concluded that secondary metabolites, mainly antibiotics containing clavulanic acid, were produced about 6–7 days after the growth, and concentration of clavulanic acid was increased up to two-folds after UV mutagenesis. PMID:24363725

  5. Recurrent AAV2-related insertional mutagenesis in human hepatocellular carcinomas.

    Science.gov (United States)

    Nault, Jean-Charles; Datta, Shalini; Imbeaud, Sandrine; Franconi, Andrea; Mallet, Maxime; Couchy, Gabrielle; Letouzé, Eric; Pilati, Camilla; Verret, Benjamin; Blanc, Jean-Frédéric; Balabaud, Charles; Calderaro, Julien; Laurent, Alexis; Letexier, Mélanie; Bioulac-Sage, Paulette; Calvo, Fabien; Zucman-Rossi, Jessica

    2015-10-01

    Hepatocellular carcinomas (HCCs) are liver tumors related to various etiologies, including alcohol intake and infection with hepatitis B (HBV) or C (HCV) virus. Additional risk factors remain to be identified, particularly in patients who develop HCC without cirrhosis. We found clonal integration of adeno-associated virus type 2 (AAV2) in 11 of 193 HCCs. These AAV2 integrations occurred in known cancer driver genes, namely CCNA2 (cyclin A2; four cases), TERT (telomerase reverse transcriptase; one case), CCNE1 (cyclin E1; three cases), TNFSF10 (tumor necrosis factor superfamily member 10; two cases) and KMT2B (lysine-specific methyltransferase 2B; one case), leading to overexpression of the target genes. Tumors with viral integration mainly developed in non-cirrhotic liver (9 of 11 cases) and without known risk factors (6 of 11 cases), suggesting a pathogenic role for AAV2 in these patients. In conclusion, AAV2 is a DNA virus associated with oncogenic insertional mutagenesis in human HCC.

  6. Oligonucleotide-directed mutagenesis for precision gene editing.

    Science.gov (United States)

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

    2016-02-01

    Differences in gene sequences, many of which are single nucleotide polymorphisms, underlie some of the most important traits in plants. With humanity facing significant challenges to increase global agricultural productivity, there is an urgent need to accelerate the development of these traits in plants. oligonucleotide-directed mutagenesis (ODM), one of the many tools of Cibus' Rapid Trait Development System (RTDS(™) ) technology, offers a rapid, precise and non-transgenic breeding alternative for trait improvement in agriculture to address this urgent need. This review explores the application of ODM as a precision genome editing technology, with emphasis on using oligonucleotides to make targeted edits in plasmid, episomal and chromosomal DNA of bacterial, fungal, mammalian and plant systems. The process of employing ODM by way of RTDS technology has been improved in many ways by utilizing a fluorescence conversion system wherein a blue fluorescent protein (BFP) can be changed to a green fluorescent protein (GFP) by editing a single nucleotide of the BFP gene (CAC→TAC; H66 to Y66). For example, dependent on oligonucleotide length, applying oligonucleotide-mediated technology to target the BFP transgene in Arabidopsis thaliana protoplasts resulted in up to 0.05% precisely edited GFP loci. Here, the development of traits in commercially relevant plant varieties to improve crop performance by genome editing technologies such as ODM, and by extension RTDS, is reviewed. © 2015 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  7. Agrobacterium tumefaciens-mediated transformation as an efficient tool for insertional mutagenesis of Cercospora zeae-maydis.

    Science.gov (United States)

    Lu, Yuanyuan; Xiao, Shuqin; Wang, Fen; Sun, Jiaying; Zhao, Likun; Yan, Libin; Xue, Chunsheng

    2017-02-01

    An efficient Agrobacterium tumefaciens-mediated transformation (ATMT) approach was developed for the plant pathogenic fungus, Cercospora zeae-maydis, which is the causative agent of gray leaf spot in maize. The transformation was evaluated with five parameters to test the efficiencies of transformation. Results showed that spore germination time, co-cultivation temperature and time were the significant influencing factors in all parameters. Randomly selected transformants were confirmed and the transformants were found to be mitotically stable, with single-copy T-DNA integration in the genome. T-DNA flanking sequences were cloned by thermal asymmetric interlaced PCR. Thus, the ATMT approach is an efficient tool for insertional mutagenesis of C. zeae-maydis. Copyright © 2016 Elsevier B.V. All rights reserved.

  8. COmplex coronary Bifurcation lesions: RAndomized comparison of a strategy using a dedicated self-expanding biolimus-eluting stent versus a culotte strategy using everolimus-eluting stents: primary results of the COBRA trial.

    Science.gov (United States)

    Dubois, Christophe; Bennett, Johan; Dens, Joseph; De Cock, Dries; Desmet, Walter; Belmans, Ann; Ughi, Giovanni J; Sinnaeve, Peter; Vrolix, Mathias; D'hooge, Jan; Adriaenssens, Tom

    2016-04-20

    We aimed to compare healing responses with optical coherence tomography, and clinical and angiographic outcome after treatment of coronary bifurcation lesions with a dedicated stent versus a conventional culotte technique. Forty patients with true and complex coronary bifurcation lesions were randomly assigned to treatment with the Axxess™ bifurcation stent in the proximal main vessel (MV) and additional BioMatrix™ stents in the branches (Biosensors Europe SA, Morges, Switzerland), versus a culotte technique using XIENCE™ stents (Abbott Vascular, Santa Clara, CA, USA). The primary endpoint of percentage of uncovered struts at nine months was similar with the dedicated strategy vs. culotte in the proximal MV (median 17.8 [IQR 3.3-24.7] vs. 6.8 [2.0-20.5]; p=0.19), bifurcation core (9.5 [5.7-19.5] vs. 4.0 [0.7-17.6]; p=0.17), distal MV (2.6 [2.3-18] vs. 2.2 [0.5-6.0]; p=0.09) and side branch (5.7 [1.5-11.5] vs. 1.9 [0-5.8]; p=0.14). As compared with culotte, a strategy using Axxess resulted in a significantly larger lumen in the proximal MV both acutely (minimum lumen diameter 3.03±0.51 vs. 2.71±0.44 mm, p=0.04) and at follow-up (mean lumen area 10.0±2.1 vs. 7.1±1.8 mm2, pstrategies resulted in good clinical outcomes at one year, and no stent thromboses. As compared with a culotte strategy with XIENCE stents, complex bifurcation stenting using a dedicated strategy combining Axxess and BioMatrix stents results in similar stent strut coverage at nine-month follow-up, and a significantly larger lumen and lower angiographic late lumen loss in the proximal MV.

  9. Comparison of three different tourniquet application strategies for minimally invasive total knee arthroplasty: a prospective non-randomized clinical trial.

    Science.gov (United States)

    Huang, Ze Yu; Pei, Fu Xing; Ma, Jun; Yang, Jing; Zhou, Zong Ke; Kang, Peng De; Shen, Bin

    2014-04-01

    It is still controversial on the optimal timing of tourniquet used in total knee arthroplasty (TKA). Most previous studies focused on the comparison of different tourniquet application in controversial TKA, while the aim of our work was to compare three strategies of tourniquet application in minimally invasive TKA. 90 patients were enrolled in this study. Based on the different tourniquet application strategies, they were divided into three groups. Group A: using tourniquet during the whole surgery; Group B: tourniquet inflated before incision and deflated after the hardening of the cement; Group C: using tourniquet during the cementation. Blood loss and serum levels of C-reactive protein, IL-6, creatine kinase and myoglobin were checked preoperatively. The HSS knee score, VAS pain score, range of motion (ROM), limb swelling and hospital stays were also recorded. The mean levels of Hb and Hct were lower in Group C (104.2 ± 10.4 g/L, 31.8 ± 3.2 %) than those in Groups A (111.4 ± 14.4 g/L, p = 0.035; 34.1 ± 4.1 %, p = 0.032) and B (112.8 ± 14.3 g/L, p = 0.013; 34.5 ± 3.7 %, p = 0.011) immediately after the surgery. Compared with Groups A and B, both serum inflammation and muscle damage markers were lower in Group C. There were no significant differences between the groups in terms of HSS knee score, ROM, estimated blood loss, swelling ratio, VAS pain score and hospital stays. Using a tourniquet full time in minimally invasive TKA causes less intraoperative blood loss and more excessive inflammation and muscle damage. However, the advantage of part-time using tourniquet did not show in early functional outcomes.

  10. Successful Strategies for Practice-Based Recruitment of Racial and Ethnic Minority Pregnant Women in a Randomized Controlled Trial: the IDEAS for a Healthy Baby Study.

    Science.gov (United States)

    Goff, Sarah L; Youssef, Yara; Pekow, Penelope S; White, Katharine O; Guhn-Knight, Haley; Lagu, Tara; Mazor, Kathleen M; Lindenauer, Peter K

    2016-12-01

    Racial/ethnic minority patients are often underrepresented in clinical trials. Efforts to address barriers to participation may improve representation, thus enhancing our understanding of how research findings apply to more diverse populations. The IDEAS (Information, Description, Education, Assistance, and Support) for a Healthy Baby study was a randomized controlled trial (RCT) of an intervention to reduce barriers to using publicly reported quality data for low-income, racial/ethnic minority women. We used strategies grounded in a health equity framework to address barriers to recruitment and retention in three domains: preparation, process, and patient-centeredness. "Preparation" included teaching study staff about health inequities, role-playing skills to develop rapport and trust, and partnering with clinic staff. "Processes" included use of electronic registration systems to pre-screen potential candidates and determine when eligible participants were in clinic and an electronic database to track patients through the study. Use of a flexible protocol, stipends, and consideration of literacy levels promoted "patient-centeredness." We anticipated needing to recruit 800 women over 18 months to achieve a completion goal of 650. Using the recruitment and retention strategies outlined above, we recruited 746 women in 15 months, achieving higher recruitment (87.1 %) and retention rates (97.3 %) than we had anticipated. These successful recruitment and retention strategies used for a large RCT promoted inclusivity and accessibility. Researchers seeking to recruit racial and ethnic minority pregnant women in similar settings may find the preparation, process, and patient-centered strategies used in this study applicable for their own studies. ClinicalTrials.gov NCT01784575 , 1R21HS021864-01.

  11. Blood transfusion strategy and risk of postoperative delirium in nursing homes residents with hip fracture. A post hoc analysis based on the TRIFE randomized controlled trial.

    Science.gov (United States)

    Blandfort, Sif; Gregersen, Merete; Borris, Lars Carl; Damsgaard, Else Marie

    2017-06-01

    To investigate whether a liberal blood transfusion strategy [Hb levels ≥11.3 g/dL (7 mmol/L)] reduces the risk of postoperative delirium (POD) on day 10, among nursing home residents with hip fracture, compared to a restrictive transfusion strategy [Hb levels ≥9.7 g/dL (6 mmol/L)]. Furthermore, to investigate whether POD influences mortality within 90 days after hip surgery. This is a post hoc analysis based on The TRIFE - a randomized controlled trial. Frail anemic patients from the Orthopedic Surgical Ward at Aarhus University Hospital were enrolled consecutively between January 18, 2010 and June 6, 2013. These patients (aged ≥65 years) had been admitted from nursing homes for unilateral hip fracture surgery. After surgery, 179 patients were included in this study. On the first day of hospitalization, all enrolled patients were examined for cognitive impairment (assessed by MMSE) and delirium (assessed by CAM). Delirium was also assessed on the tenth postoperative day. The prevalence of delirium was 10 % in patients allocated to a liberal blood transfusion strategy (LB) and 21 % in the group with a restrictive blood transfusion strategy (RB). LB prevents development of delirium on day 10, compared to RB, odds ratio 0.41 (95 % CI 0.17-0.96), p = 0.04. Development of POD on day 10 increased the risk of 90-day death, hazard ratio 3.14 (95 % CI 1.72-5.78), p < 0.001. In nursing home residents undergoing surgery for hip fracture, maintaining hemoglobin level above 11.3 g/dL reduces the rate of POD on day 10 compared to a RB. Development of POD is associated with increased mortality.

  12. Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis.

    Directory of Open Access Journals (Sweden)

    Feixiong Cheng

    2016-09-01

    Full Text Available Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins. We herein reported 712 candidate cellular genes, characterizing distinct topological network and evolutionary signatures, and occupying central hubs in the human interactome. Cell cycle phase-specific network analysis showed that host cell cycle programs played critical roles during viral replication (e.g. MYC and TAF4 regulating G0/1 phase. Moreover, the viral perturbation of host cellular networks reflected disease etiology in that host genes (e.g. CTCF, RHOA, and CDKN1B identified were frequently essential and significantly associated with Mendelian and orphan diseases, or somatic mutations in cancer. Computational drug repositioning framework via incorporating drug-gene signatures from the Connectivity Map into the virus-host interactome identified 110 putative druggable antiviral targets and prioritized several existing drugs (e.g. ajmaline that may be potential for antiviral indication (e.g. anti-Ebola. In summary, this work provides a powerful methodology with a tight integration of gene-trap insertional mutagenesis testing and systems biology to identify new antiviral targets and drugs for the development of broadly acting and targeted clinical antiviral therapeutics.

  13. Need-based intervention is an effective strategy for improving the nutritional status of older people living in a nursing home: a randomized controlled trial.

    Science.gov (United States)

    Lee, Li-Chin; Tsai, Alan C; Wang, Jiun-Yi; Hurng, Baai-Shyun; Hsu, Hui-Chuan; Tsai, Hsin-Jen

    2013-12-01

    Nutrition is a key element in geriatric health. Protein-energy malnutrition is common in institutionalized persons. This study examined the effectiveness of a need-based "routine screening and timely intervention" strategy in improving the nutritional status of persons living in nursing homes. A 24-week randomized, double-blind, controlled trial. A privately managed geriatric nursing home in Taiwan. Ninety-two ≥65-year old persons who were ≤25kg/m(2), >1 month residence, able to self-feed or receive oral feeding, without acute infection and non-bed-ridden. Prospective participants were stratified by gender and then randomly assigned to either the control group (n=45) or the intervention group (n=47). Each subject in the intervention group was given a 50g/day soy-protein-based nutritional supplement if he/she was rated as undernourished according to the Mini Nutritional Assessment (MNA, score ≤24) and BMI ≤24kg/m(2). The supplement contained 9.5g protein, 250kcal energy and all essential micro-nutrients. The supplementation would be suspended once either one of the "at risk" condition was corrected. Nutritional rating with the MNA took place at baseline and every 4 weeks during the trial. Biochemical indicators were measured at baseline, mid-point (week-12) and end-point (week-24). Results were analyzed with the two-sample t-test, and the generalized estimating equations (GEE) controlled for demographic and health-related variables. Of the 92 subjects, 82 completed the trial; 7 withdrew and 3 died during the trial. Results showed that the need-based intervention was an effective and appropriate strategy for improving the nutritional status of persons at risk of undernourishment. The intervention significantly improved body weight, BMI, mid-arm circumference, calf circumference, and serum albumin and cholesterol concentrations at all intervals (all pintervention did not significantly improve hematocrit, hemoglobin or lymphocyte count status. Results suggest

  14. Mutagenesis of bacteriophage T7 and T7 DNA by alkylation damage.

    OpenAIRE

    Masker, W E; Dodson, L A; Maupin, M

    1985-01-01

    We have developed a new assay for in vitro mutagenesis of bacteriophage T7 DNA that measures the generation of mutations in the specific T7 gene that codes for the phage ligase. This assay was used to examine mutagenesis caused by in vitro DNA synthesis in the presence of O6-methylguanosine triphosphate. Reversion of one of the newly generated ligase mutants by ethyl methanesulfonate was also tested.

  15. Mutagenesis of bacteriophage T7 and T7 DNA by alkylation damage.

    Science.gov (United States)

    Masker, W E; Dodson, L A; Maupin, M

    1985-01-01

    We have developed a new assay for in vitro mutagenesis of bacteriophage T7 DNA that measures the generation of mutations in the specific T7 gene that codes for the phage ligase. This assay was used to examine mutagenesis caused by in vitro DNA synthesis in the presence of O6-methylguanosine triphosphate. Reversion of one of the newly generated ligase mutants by ethyl methanesulfonate was also tested. PMID:3903213

  16. Neural-Fuzzy Digital Strategy of Continuous-Time Nonlinear Systems Using Adaptive Prediction and Random-Local-Optimization Design

    Directory of Open Access Journals (Sweden)

    Zhi-Ren Tsai

    2013-01-01

    Full Text Available A tracking problem, time-delay, uncertainty and stability analysis of a predictive control system are considered. The predictive control design is based on the input and output of neural plant model (NPM, and a recursive fuzzy predictive tracker has scaling factors which limit the value zone of measured data and cause the tuned parameters to converge to obtain a robust control performance. To improve the further control performance, the proposed random-local-optimization design (RLO for a model/controller uses offline initialization to obtain a near global optimal model/controller. Other issues are the considerations of modeling error, input-delay, sampling distortion, cost, greater flexibility, and highly reliable digital products of the model-based controller for the continuous-time (CT nonlinear system. They are solved by a recommended two-stage control design with the first-stage (offline RLO and second-stage (online adaptive steps. A theorizing method is then put forward to replace the sensitivity calculation, which reduces the calculation of Jacobin matrices of the back-propagation (BP method. Finally, the feedforward input of reference signals helps the digital fuzzy controller improve the control performance, and the technique works to control the CT systems precisely.

  17. A double-masked Randomized Clinical Trial (RCT) comparing four periodontitis treatment strategies: 5-year clinical results.

    Science.gov (United States)

    Preus, Hans R; Gjermo, Per; Baelum, Vibeke

    2017-10-01

    To test the hypothesis of no difference in the 5-year clinical outcome of therapy between groups of patients treated with conventional over-weeks scaling and root planing or same-day full-mouth-disinfection, with or without adjunctive metronidazole (MTZ). Following a three-month oral hygiene phase, 184 periodontitis patients were randomly allocated to one of four treatment regimens (1) full-mouth disinfection (FDIS)+ MTZ, (2) FDIS +placebo, (3) scaling and root planing+ MTZ and (4) scaling and root planing+placebo. Following active treatment, patients received biannual maintenance; 161 patients completed the five-year follow-up maintenance and examination, where clinical attachment level (CAL), probing pocket depth (PPD), presence of plaque and bleeding were registered. Metronidazole increased the highest CAL recording statistically insignificantly by an average of 0.17 mm while FDIS decreased it by an average of 0.12 mm. The corresponding values for the highest PPD were 0.00 and 0.05 mm, respectively. While single-level analyses showed statistically significant differences, they could not be confirmed with more appropriate analyses and were too small to recommend MTZ, with its risk of patient side effects and environmental consequences, for the treatment of patients with severe periodontitis. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  18. A Randomized Controlled Trial to Evaluate a Potential Hepatitis B Booster Vaccination Strategy Using Combined Hepatitis A and B Vaccine.

    Science.gov (United States)

    Li, Fangjun; Hu, Yuansheng; Zhou, Youming; Chen, Lixin; Xia, Wei; Song, Yufei; Tan, Zhengliang; Gao, Lidong; Yang, Zhong; Zeng, Gang; Han, Xing; Li, Junhua; Li, Jing

    2017-05-01

    Booster doses could play a major role in no responders or low responders to primary hepatitis B (HB) vaccine. Planed time point for hepatitis A vaccination in China provides a good opportunity to carry out HB booster dose by using combined hepatitis A and B vaccine. A randomized, double-blinded clinical trial was conducted to compare the immunogenicity and safety of toddlers 18-24 months of age receiving 3 different vaccination regimens: 2 doses of inactivated hepatitis A vaccine (group 1), 1 dose of inactivated hepatitis A vaccine plus 1 dose of combined hepatitis A and B vaccine (group 2) or 2 doses of combined hepatitis A and B vaccine (group 3). All 3 groups showed 100% seroprotection for antihepatitis A virus antibody after vaccination. Seroprotection rate for anti-HB antibody before vaccination ranged from 79.5% to 92.9% in the 3 groups. After second inoculation, anti-HBs seroprotection increased from 92.9% to 100% in group 2 with postvaccination geometric mean concentration (GMC) of 2258.3 mIU/mL and from 79.5% to 98.9% in group 3 with postvaccination GMC of 2055.3 mIU/mL. The adverse events were not statistically different among groups (P = 0.345). Combined hepatitis A and B vaccine could stimulate high level of both antihepatitis A virus and anti-HBs antibodies and not increase adverse events, providing a new choice for HB booster.

  19. An integrated classifier for computer-aided diagnosis of colorectal polyps based on random forest and location index strategies

    Science.gov (United States)

    Hu, Yifan; Han, Hao; Zhu, Wei; Li, Lihong; Pickhardt, Perry J.; Liang, Zhengrong

    2016-03-01

    Feature classification plays an important role in differentiation or computer-aided diagnosis (CADx) of suspicious lesions. As a widely used ensemble learning algorithm for classification, random forest (RF) has a distinguished performance for CADx. Our recent study has shown that the location index (LI), which is derived from the well-known kNN (k nearest neighbor) and wkNN (weighted k nearest neighbor) classifier [1], has also a distinguished role in the classification for CADx. Therefore, in this paper, based on the property that the LI will achieve a very high accuracy, we design an algorithm to integrate the LI into RF for improved or higher value of AUC (area under the curve of receiver operating characteristics -- ROC). Experiments were performed by the use of a database of 153 lesions (polyps), including 116 neoplastic lesions and 37 hyperplastic lesions, with comparison to the existing classifiers of RF and wkNN, respectively. A noticeable gain by the proposed integrated classifier was quantified by the AUC measure.

  20. No “Magic Bullet”: Exploring Community Mobilization Strategies Used in a Multi-site Community Based Randomized Controlled Trial: Project Accept (HPTN 043)

    Science.gov (United States)

    Tedrow, Virginia A.; Zelaya, Carla E.; Kennedy, Caitlin E.; Morin, Stephen F.; Khumalo-Sakutukwa, Gertrude; Sweat, Michael D.; Celentano, David D.

    2012-01-01

    As community-level interventions become more common in HIV prevention, processes such as community mobilization (CM) are increasingly utilized in public health programs and research. Project Accept, a multi-site community randomized controlled trial, is testing the hypothesis that CM coupled with community-based mobile voluntary counseling and testing and post-test support services will alter community norms and reduce the incidence of HIV. By using a multiple-case study approach, this qualitative study identifies seven major community mobilization strategies used in Project Accept, including stakeholder buy-in, formation of community coalitions, community engagement, community participation, raising community awareness, involvement of leaders, and partnership building, and describes three key elements of mobilization success. PMID:21822627

  1. No "magic bullet": exploring community mobilization strategies used in a multi-site community based randomized controlled trial: Project Accept (HPTN 043).

    Science.gov (United States)

    Tedrow, Virginia A; Zelaya, Carla E; Kennedy, Caitlin E; Morin, Stephen F; Khumalo-Sakutukwa, Gertrude; Sweat, Michael D; Celentano, David D

    2012-07-01

    As community-level interventions become more common in HIV prevention, processes such as community mobilization (CM) are increasingly utilized in public health programs and research. Project Accept, a multi-site community randomized controlled trial, is testing the hypothesis that CM coupled with community-based mobile voluntary counseling and testing and post-test support services will alter community norms and reduce the incidence of HIV. By using a multiple-case study approach, this qualitative study identifies seven major community mobilization strategies used in Project Accept, including stakeholder buy-in, formation of community coalitions, community engagement, community participation, raising community awareness, involvement of leaders, and partnership building, and describes three key elements of mobilization success.

  2. Neck-Related Physical Function, Self-Efficacy, and Coping Strategies in Patients With Cervical Radiculopathy: A Randomized Clinical Trial of Postoperative Physiotherapy.

    Science.gov (United States)

    Wibault, Johanna; Öberg, Birgitta; Dedering, Åsa; Löfgren, Håkan; Zsigmond, Peter; Persson, Liselott; Andell, Maria; R Jonsson, Margareta; Peolsson, Anneli

    2017-06-01

    The purpose of this study was to compare postoperative rehabilitation with structured physiotherapy to the standard approach in patients with cervical radiculopathy (CR) in a prospective randomized study at 6 months follow-up based on measures of neck-related physical function, self-efficacy, and coping strategies. Patients with persistent CR and scheduled for surgery (N = 202) were randomly assigned to structured postoperative physiotherapy or a standard postoperative approach. Structured postoperative physiotherapy combined neck-specific exercises with a behavioral approach. Baseline, 3-month, and 6-month evaluations included questionnaires and clinical examinations. Neck muscle endurance, active cervical range of motion, self-efficacy, pain catastrophizing (CSQ-CAT), perceived control over pain, and ability to decrease pain were analyzed for between-group differences using complete case and per-protocol approaches. No between-group difference was reported at the 6-month follow-up (P = .05-.99), but all outcomes had improved from baseline (P physiotherapy with ≥50% attendance at treatment sessions had larger improvements in CSQ-CAT (P = .04) during the rehabilitation period from 3 to 6 months after surgery compared with the patients who received standard postoperative approach. No between-group difference was found at 6 months after surgery based on measures of neck-related physical function, self-efficacy, and coping strategies. However, the results confirm that neck-specific exercises are tolerated by patients with CR after surgery and may suggest a benefit from combining surgery with structured postoperative physiotherapy for patients with CR. Copyright © 2017. Published by Elsevier Inc.

  3. Effect of a Behavioral Intervention Strategy for Adoption and Maintenance of a Physically Active Lifestyle: The Italian Diabetes and Exercise Study 2 (IDES_2): A Randomized Controlled Trial.

    Science.gov (United States)

    Balducci, Stefano; D'Errico, Valeria; Haxhi, Jonida; Sacchetti, Massimo; Orlando, Giorgio; Cardelli, Patrizia; Vitale, Martina; Bollanti, Lucilla; Conti, Francesco; Zanuso, Silvano; Nicolucci, Antonio; Pugliese, Giuseppe

    2017-11-01

    Adherence to physical activity (PA) recommendations is hampered by the lack of effective strategies to promote behavior change. The Italian Diabetes and Exercise Study 2 (IDES_2) is a randomized controlled trial evaluating a novel behavioral intervention strategy for increasing PA and decreasing sedentary time (SED-time) in patients with type 2 diabetes. The study randomized 300 physically inactive and sedentary patients with type 2 diabetes 1:1 to receive theoretical and practical counseling once yearly for 3 years (intervention group [INT]) or standard care (control group [CON]). Here, we report the 4-month effects on objectively (accelerometer) measured daily light-intensity PA (LPA), moderate-to-vigorous-intensity PA (MVPA), and SED-time, and cardiovascular risk factors. LPA and MVPA both increased, and SED-time decreased in both groups, although changes were significantly more marked in INT participants (approximately twofold for LPA and SED-time and approximately sixfold for MVPA). A significant reduction in HbA1c was observed only in INT subjects. An increase in LPA >0.92 h · day-1 and in MVPA >7.33 min · day-1 and a decrease in SED-time >1.05 h · day-1 were associated with an average decrease in HbA1c of ∼1% and also with significant improvements in fasting glucose, body weight, waist circumference, and hs-CRP. Changes in PA and SED-time were independent predictors of improvements in HbA1c. This behavioral intervention is effective in the short term for increasing LPA and MVPA and reducing SED-time. Significant improvements in cardiometabolic risk profiles were observed in subjects experiencing the most pronounced changes in PA and SED-time, even if below the recommended level. © 2017 by the American Diabetes Association.

  4. Identifying novel mycobacterial stress associated genes using a random mutagenesis screen in Mycobacterium smegmatis.

    Science.gov (United States)

    Viswanathan, Gopinath; Joshi, Shrilaxmi V; Sridhar, Aditi; Dutta, Sayantanee; Raghunand, Tirumalai R

    2015-12-10

    Cell envelope associated components of Mycobacterium tuberculosis (M.tb) have been implicated in stress response, immune modulation and in vivo survival of the pathogen. Although many such factors have been identified, there is a large disparity between the number of genes predicted to be involved in functions linked to the envelope and those described in the literature. To identify and characterise novel stress related factors associated with the mycobacterial cell envelope, we isolated colony morphotype mutants of Mycobacterium smegmatis (M. smegmatis), based on the hypothesis that mutants with unusual colony morphology may have defects in the biosynthesis of cell envelope components. On testing their susceptibility to stress conditions relevant to M.tb physiology, multiple mutants were found to be sensitive to Isoniazid, Diamide and H2O2, indicative of altered permeability due to changes in cell envelope composition. Two mutants showed defects in biofilm formation implying possible roles for the target genes in antibiotic tolerance and/or virulence. These assays identified novel stress associated roles for several mycobacterial genes including sahH, tatB and aceE. Complementation analysis of selected mutants with the M. smegmatis genes and their M.tb homologues showed phenotypic restoration, validating their link to the observed phenotypes. A mutant carrying an insertion in fhaA encoding a forkhead associated domain containing protein, showed reduced survival in THP-1 macrophages, providing in vivo validation to this screen. Taken together, these results suggest that the M.tb homologues of a majority of the identified genes may play significant roles in the pathogenesis of tuberculosis. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. E-learning interventions are comparable to user's manual in a randomized trial of training strategies for the AGREE II

    Directory of Open Access Journals (Sweden)

    Durocher Lisa D

    2011-07-01

    Full Text Available Abstract Background Practice guidelines (PGs are systematically developed statements intended to assist in patient and practitioner decisions. The AGREE II is the revised tool for PG development, reporting, and evaluation, comprised of 23 items, two global rating scores, and a new User's Manual. In this study, we sought to develop, execute, and evaluate the impact of two internet interventions designed to accelerate the capacity of stakeholders to use the AGREE II. Methods Participants were randomized to one of three training conditions. 'Tutorial'--participants proceeded through the online tutorial with a virtual coach and reviewed a PDF copy of the AGREE II. 'Tutorial + Practice Exercise'--in addition to the Tutorial, participants also appraised a 'practice' PG. For the practice PG appraisal, participants received feedback on how their scores compared to expert norms and formative feedback if scores fell outside the predefined range. 'AGREE II User's Manual PDF (control condition'--participants reviewed a PDF copy of the AGREE II only. All participants evaluated a test PG using the AGREE II. Outcomes of interest were learners' performance, satisfaction, self-efficacy, mental effort, time-on-task, and perceptions of AGREE II. Results No differences emerged between training conditions on any of the outcome measures. Conclusions We believe these results can be explained by better than anticipated performance of the AGREE II PDF materials (control condition or the participants' level of health methodology and PG experience rather than the failure of the online training interventions. Some data suggest the online tools may be useful for trainees new to this field; however, this requires further study.

  6. Pathfinding to an optimal strategy of revascularization in primary coronary intervention in patients with multivessel disease: a network meta-analysis of randomized trials.

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    Komócsi, András; Kehl, Dániel; d'Ascenso, Fabrizio; DiNicolantonio, James; Vorobcsuk, András

    2017-03-01

    In ST-segment elevation myocardial infarction (STEMI), current guidelines discourage treatment of the non-culprit lesions at the time of the primary intervention. Latest trials have challenged this strategy suggesting benefit of early complete revascularization. We performed a Bayesian multiple treatment network meta-analysis of randomized clinical trials (RCTs) in STEMI on culprit-only intervention (CO) versus different timing multivessel revascularization, including immediate (IM), same hospitalization (SH) or later staged (ST). Outcome parameters were pooled with a random-effects model. For multiple-treatment meta-analysis, a Bayesian Markov chain Monte Carlo method was used. Eight RCTs involving 2077 patients were identified. ST and IM revascularization was associated with a decrease in major adverse cardiac events (MACEs) compared to culprit-only approach (risk ratio [RR]: 0.43 credible interval [CrI]: 0.22-0.77 and RR: 0.36 CrI: 0.24-0.54, respectively). IM was superior to SH (RR: 0.49 CrI: 0.29-0.80). With regards to myocardial infarction IM was superior to SH (RR: 0.18 CrI: 0.02-0.99). The posterior probability of being the best choice of treatment regarding the frequency of MACEs was 71.2% for IM, 28.5% for ST, 0.3% for SH and 0.05% for culprit-only approach. Results from RCTs indicate that immediate or staged revascularization of non-culprit lesions reduces major adverse events in patients after primary percutaneous coronary intervention. Differences in MACEs suggest superiority of the immediate or staged intervention; however, further randomized trials are needed to determine the optimal timing of revascularization of the non-culprit lesions.

  7. Permissive Hypotension vs. Conventional Resuscitation Strategies in Adult Trauma Patients with Hemorrhagic Shock: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.

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    Tran, Alexandre; Yates, Jeffrey; Lau, Aaron; Lampron, Jacinthe; Matar, Maher

    2018-01-24

    Aggressive fluid resuscitation in trauma promotes deleterious effects such as clot disruption, dilutional coagulopathy and hypothermia. Animal studies suggest that permissive hypotension maintains appropriate organ perfusion, reduces bleeding and improves mortality. This review assesses the efficacy and safety of permissive hypotension in adult trauma patients with hemorrhagic shock. We searched the MEDLINE and EMBASE databases from inception to May 2017 for randomized controlled trials comparing permissive hypotension vs. conventional resuscitation following traumatic injury. We included pre-operative and intraoperative resuscitation strategies. The primary outcome was 30-day or in-hospital mortality. Secondary outcomes included blood product utilization, estimated blood loss and in-hospital complications. Pooling was performed with a random-effects model. We screened 722 abstracts, from which five randomized trials evaluating 1158 patients were included. Blood pressure targets in the intervention arms varied from systolic BP 50 - 70 mmHg or MAP ≥ 50 mmHg as compared to systolic BP 65 - 100 mmHg or MAP ≥ 65 in the control arms. Two studies evaluated only patients with penetrating injury while the remaining three additionally included blunt injuries. Four trials suggested a survival benefit for 30-day or in-hospital mortality with hypotensive resuscitation, although three studies were insufficiently powered to find statistical significance. Studies were of poor to moderate quality due to poor protocol reporting and lack of blinding. The pooled odds ratio was 0.70 (95% CI 0.53 to 0.92), suggesting a survival benefit for permissive hypotension. Those patients received fewer blood products and had lesser estimated blood loss. Permissive hypotension may offer a survival benefit over conventional resuscitation for patients with hemorrhagic injury. It may additionally reduce blood loss and blood product utilization. However, the majority of studies were underpowered

  8. Design considerations of a randomized controlled trial of sedation level during hip fracture repair surgery: a strategy to reduce the incidence of postoperative delirium in elderly patients.

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    Li, Tianjing; Wieland, L Susan; Oh, Esther; Neufeld, Karin J; Wang, Nae-Yuh; Dickersin, Kay; Sieber, Frederick E

    2017-06-01

    Background Delirium is an acute change in mental status characterized by sudden onset, fluctuating course, inattention, disorganized thinking, and abnormal level of consciousness. The objective of the randomized controlled trial "A STrategy to Reduce the Incidence of Postoperative Delirium in Elderly Patients" (STRIDE) is to assess the effectiveness of light versus heavy sedation on delirium and other outcomes in elderly patients undergoing hip fracture repair surgery. Our goal is to describe the design considerations and lessons learned in planning and implementing the STRIDE trial. Methods Discussed are challenges encountered including (1) how to ensure that we quickly identify, assess the eligibility of, and randomize traumatic hip fracture patients; (2) how to implement interventions that involve continuous monitoring and adjustment during the surgery; and (3) how to measure and ascertain the primary outcome, delirium. Results To address the first challenge, we monitored the operating room schedule more actively than anticipated. We constructed and organized eligibility assessment data collection forms by purpose and by source of information needed to complete them. We decided that randomization needs to take place in the operating room. To address the second challenge, we designed and implemented a treatment protocol and covered the bispectral index monitor to prevent the Anesthesiologist/Anesthetist from being influenced by the bispectral index reading while administering the intervention. Finally, clinical assessment of delirium consisted of standardized interviews of the patient using validated instruments, interviews of those caring for the patient, and review of the medical record. A consensus panel made the final determination of a delirium diagnosis. We note that STRIDE is a single-center trial. The decisions we took may have different implications for multi-center trials. Conclusions Lessons learned are likely to provide useful information to others

  9. Combining motivational and volitional strategies to promote unsupervised walking in patients with fibromyalgia: study protocol for a randomized controlled trial.

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    Pastor, María-Ángeles; López-Roig, Sofía; Lledó, Ana; Peñacoba, Cecilia; Velasco, Lilian; Schweiger-Gallo, Inge; Cigarán, Margarita; Ecija, Carmen; Limón, Ramón; Sanz, Yolanda

    2014-04-11

    Fibromyalgia patients are often advised to engage in regular low- to moderate-intensity physical exercise. The need of fibromyalgia patients to walk has been stressed in previous research. Behavioral self-regulation theories suggest that a combination of motivational aspects (to develop or strengthen a behavioral intention: Theory of Planned Behavior) and volitional aspects (engagement of intention in behavior: implementation intentions) is more effective than a single intervention. In this paper, we describe a protocol for identifying the motivational processes (using the Theory of Planned Behavior) involved in the practice of walking (phase I) and for studying the efficacy of an intervention that combines motivational and volitional contents to enhance the acquisition and continuation of this exercise behavior (phase II). The paper also shows the characteristics of eligible individuals (women who do not walk) and ineligible populations (women who walk or do not walk because of comorbidity without medical recommendation to walk). Both groups consist of members of any of four patients' associations in Spain who are between 18 and 70 years of age and meet the London Fibromyalgia Epidemiology Study Screening Questionnaire criteria for fibromyalgia. Furthermore, using this study protocol, we will explore the characteristics of participants (eligible women who agreed to participate in the study) and nonparticipants (eligible women who refused to participate). Two studies will be conducted: Phase I will be a cross-sectional study, and phase II will be a triple-blind, randomized longitudinal study with two treatment groups and one active control group. The questionnaires were sent to a total of 2,227 members of four patients' associations in Spain. A total of 920 participants with fibromyalgia returned the questionnaires, and 582 were ultimately selected to participate. The first data gathered have allowed us to identify the characteristics of the study population and

  10. Pregabalin as a perioperative strategy for pain management in patients undergoing cosmetic surgery. A randomized, double-blind, and placebo-controlled study

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    Lorena Duque

    2008-11-01

    Full Text Available BACKGROUND: Preoperative Gabapentin has demonstrated to be as analgesic strategy in the control of perioperative pain. Pregabalin -an analogue of Gabapentin- has only a few trials demonstrating its effectiveness on this clinical setting. We wanted to assess the effectiveness of pregabalin given not only as a single dose in the preoperative period, but also continuing its administration 75 mg bid up to the fourth day after surgery. METHODS: Previous consent by the Ethical Committee of the University, we enrolled 110 patients undergoing ambulatory liposuction. They were randomized and blindedallocated to receive Pregabalin (75 mg bid versus placebo, starting 12 hours before surgery up to the fourth day after surgery. We use the postoperative pain intensity by numerical rating scale, pain intensity by categorical pain scale and tramadol-ibuprofen request as primary outcomes. RESULTS: We had 9 dropouts during the recruitment and follow up. 24 hours after surgery we had 18/51 (35.3% versus 16/50 (32% (p=0.7. We also found no difference in opioid request at the same time point, being 6.3 mg morphine equivalents in the pregabalin versus 6.7 mg in the Placebo Group. Subsequent evaluations at 48, 72 and 96 hours demonstrated no difference between groups for analgesic request and pain intensity. CONCLUSION: Perioperative use of Pregabalin (75 mg bid does not offer benefit as analgesic strategy in terms of pain intensity and opioid requirement in patients undergoing cosmetic liposuction.

  11. Strategy for recruitment and factors associated with motivation and satisfaction in a randomized trial with 210 healthy volunteers without financial compensation.

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    Luzurier, Quentin; Damm, Cédric; Lion, Fabien; Daniel, Carine; Pellerin, Lucille; Tavolacci, Marie-Pierre

    2015-01-05

    The aim was to describe a strategy for recruitment of healthy volunteers (HV) to a randomized trial that assessed the efficacy of different telephone techniques to assist HV in performing cardiac massage for vital emergency. Participation in the randomized trial was not financially compensated, however HV were offered emergency first-aid training. We also studied factors associated with HV motivation and satisfaction regarding participation in the trial. Strategy for recruitment of 210 HV aged 18 to 60 years was based on: (1) the updated records of all telephone number since January 2000 of HV registered in the Rouen Clinical Investigation Centre HV database, (2) a communication campaign for the general public focussing on posters and media advertisements. Data on the recruitment, socio-demographics, motivation and satisfaction of the 210 HV were collected by anonymous self-administered questionnaire. Of the 210 HV included, 63.3% (n = 133) were recruited from the HV database and 36.7% (n = 77) by the communication campaign. On the one hand, the HV database enabled screening of 1315 HV, 54.8% (n = 721) of whom were reached by phone, 55.2% (n = 398) of these latter accepted to participate in the study and 10.1% of the initial screening (n = 133) were finally included. One the other hand, for the 77 HV not recruited from the HV database, word-of-mouth (56.1%) was the main means of recruitment. The male/female ratio of the 210 HV was 0.5 and mean age 43.5 years (Standard Deviation = 12.4). The main motivations given for participating in the trial were to support research (87.6%) and receive emergency first-aid training (85.7%). Overall satisfaction with the welcome process was significantly higher for older HV (46-60 years) (adjusted odds ratio (AOR): 3.44; 95% confidence interval (95% CI): 1.48-7.99), and for HV in management jobs (AOR: 4.26; 95% CI: 1.22-14.87). Satisfaction with protocol management was higher for women (AOR: 2.33; 95% CI: 1

  12. Study protocol: Cost effectiveness of two strategies to implement the NVOG guidelines on hypertension in pregnancy: An innovative strategy including a computerised decision support system compared to a common strategy of professional audit and feedback, a randomized controlled trial

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    Luitjes Susanne HE

    2010-09-01

    Full Text Available Abstract Background Hypertensive disease in pregnancy remains the leading cause of maternal mortality in the Netherlands. Seventeen percent of the clinical pregnancies are complicated by hypertension and 2% by preeclampsia. The Dutch Society of Obstetrics and Gynaecology (NVOG has developed evidence-based guidelines on the management of hypertension in pregnancy and chronic hypertension. Previous studies showed a low adherence rate to other NVOG guidelines and a large variation in usual care in the different hospitals. An explanation is that the NVOG has no general strategy of practical implementation and evaluation of its guidelines. The development of an effective and cost effective implementation strategy to improve adherence to the guidelines on hypertension in pregnancy is needed. Methods/Design The objective of this study is to assess the cost effectiveness of an innovative implementation strategy of the NVOG guidelines on hypertension including a computerised decision support system (BOS compared to a common strategy of professional audit and feedback. A cluster randomised controlled trial with an economic evaluation alongside will be performed. Both pregnant women who develop severe hypertension or pre-eclampsia and professionals involved in the care for these women will participate. The main outcome measures are a combined rate of major maternal complications and process indicators extracted from the guidelines. A total of 472 patients will be included in both groups. For analysis, descriptive as well as regression techniques will be used. A cost effectiveness and cost utility analysis will be performed according to the intention-to-treat principle and from a societal perspective. Cost effectiveness ratios will be calculated using bootstrapping techniques.

  13. A multicenter randomized clinical trial investigating the cost-effectiveness of treatment strategies with or without antibiotics for uncomplicated acute diverticulitis (DIABOLO trial

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    Fockens Paul

    2010-07-01

    Full Text Available Abstract Background Conservative treatment of uncomplicated or mild diverticulitis usually includes antibiotic therapy. It is, however, uncertain whether patients with acute diverticulitis indeed benefit from antibiotics. In most guidelines issued by professional organizations antibiotics are considered mandatory in the treatment of mild diverticulitis. This advice lacks evidence and is merely based on experts' opinion. Adverse effects of the use of antibiotics are well known, including allergic reactions, development of bacterial resistance to antibiotics and other side-effects. Methods A randomized multicenter pragmatic clinical trial comparing two treatment strategies for uncomplicated acute diverticulitis. I A conservative strategy with antibiotics: hospital admission, supportive measures and at least 48 hours of intravenous antibiotics which subsequently are switched to oral, if tolerated (for a total duration of antibiotic treatment of 10 days. II A liberal strategy without antibiotics: admission only if needed on clinical grounds, supportive measures only. Patients are eligible for inclusion if they have a diagnosis of acute uncomplicated diverticulitis as demonstrated by radiological imaging. Only patients with stages 1a and 1b according to Hinchey's classification or "mild" diverticulitis according to the Ambrosetti criteria are included. The primary endpoint is time-to-full recovery within a 6-month follow-up period. Full recovery is defined as being discharged from the hospital, with a return to pre-illness activities, and VAS score below 4 without the use of daily pain medication. Secondary endpoints are proportion of patients who develop complicated diverticulitis requiring surgery or non-surgical intervention, morbidity, costs, health-related quality of life, readmission rate and acute diverticulitis recurrence rate. In a non-inferiority design 264 patients are needed in each study arm to detect a difference in time

  14. Assessing the effect of an integrated control strategy for schistosomiasis japonica emphasizing bovines in a marshland area of Hubei Province, China: a cluster randomized trial.

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    Xi-Cheng Hong

    Full Text Available INTRODUCTION: More than 80% of schistosomiasis patients in China live in the lake and marshland regions. The purpose of our study is to assess the effect of a comprehensive strategy to control transmission of Schistosoma japonicum in marshland regions. METHODOLOGY/PRINCIPAL FINDINGS: In a cluster randomized controlled trial, we implemented an integrated control strategy in twelve villages from 2009 through 2011 in Gong'an County, Hubei Province. The routine interventions included praziquantel chemotherapy and controlling snails, and were implemented in all villages. New interventions, mainly consisting of building fences to limit the grazing area for bovines, building safe pastures for grazing, improving the residents' health conditions and facilities, were only implemented in six intervention villages. Results showed that the rate of S. japonicum infection in humans, bovines, snails, cow dung and mice in the intervention group decreased from 3.41% in 2008 to 0.81% in 2011, 3.3% to none, 11 of 6,219 to none, 3.9% to none and 31.7% to 1.7%, respectively (P0.05 for all comparisons. Moreover, a generalized linear model showed that there was a higher infection risk in humans in the control group than in the intervention group (OR = 1.250, P = 0.001 and an overall significant downward trend in infection risk during the study period. CONCLUSIONS/SIGNIFICANCE: The integrated control strategy, designed to reduce the role of bovines and humans as sources of S. japonicum infection, was highly effective in controlling the transmission of S. japonicum in marshland regions in China. TRIAL REGISTRATION: Chinese Clinical Trial Registry ChiCTR-PRC-12002405.

  15. Strategies to Make Ramadan Fasting Safer in Type 2 Diabetics: A Systematic Review and Network Meta-analysis of Randomized Controlled Trials and Observational Studies.

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    Lee, Shaun Wen Huey; Lee, Jun Yang; Tan, Christina San San; Wong, Chee Piau

    2016-01-01

    Ramadan is the holy month for Muslims whereby they fast from predawn to after sunset and is observed by all healthy Muslim adults as well as a large population of type 2 diabetic Muslims.To determine the comparative effectiveness of various strategies that have been used for type 2 diabetic Muslim who fast during Ramadan.A systematic review and network meta-analysis of randomized controlled studies (RCT) as well as observational studies for patients with type 2 diabetes who fasted during Ramadan was conducted. Eight databases were searched from January 1980 through October 2015 for relevant studies. Two reviewers independently screened and assessed study for eligibility, assessed the risk of bias, and extracted relevant data. A network meta-analysis for each outcome was fitted separately, combining direct and indirect evidence for each comparison.Twenty-nine studies, 16 RCTs and 13 observational studies each met the inclusion criteria. The most common strategy used was drug changes during the Ramadan period, which found that the use of DPP-4 (Dipeptidyl peptidase inhibitor -4) inhibitors were associated with a reduction in incidence of experiencing hypoglycemia during Ramadan in both RCTs (pooled relative risk: 0.56; 95% confidence interval: 0.44-0.72) as well as in observational studies (pooled relative risk: 0.27; 0.09-0.75). Ramadan-focused education was shown to be beneficial in reducing hypoglycemia in observational studies but not RCTs (0.25 versus 1.00). Network meta-analyses suggest that incretin mimetics can reduce the risk of hypoglycemia by nearly 1.5 times.The newer antidiabetic agents appear to lower the risk of hypoglycemia and improved glycemic control when compared with sulfonylureas. Ramadan-focused education shows to be a promising strategy but more rigorous examination from RCTs are required.

  16. The Effect of a Novel Movement Strategy in Decreasing ACL Risk Factors in Female Adolescent Soccer Players: A Randomized Controlled Trial

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    Celebrini, Richard G.; Eng, Janice J.; Miller, William C.; Ekegren, Christina L.; Johnston, James D.; Depew, Thomas A.; MacIntyre, Donna L.

    2015-01-01

    Objective To determine the effect of a novel movement strategy incorporated within a soccer warm-up on biomechanical risk factors for ACL injury during three sport-specific movement tasks. Design Single-blind, randomized controlled clinical trial. Setting Laboratory setting. Participants 20 top-tier female teenage soccer players. Interventions Subjects were randomized to the Core Position and Control movement strategy (Core-PAC) warm-up or standard warm-up which took place prior to their regular soccer practice over a 6-week period. The Core-PAC focuses on getting the centre of mass closer to the plant foot or base of support. Main Outcome Measures Peak knee flexion angle and abduction moments during a side-hop (SH), side-cut (SC) and unanticipated side-cut (USC) task after the 6-weeks with (intervention group only) and without a reminder to use the Core-PAC strategy. Results The Core-PAC group increased peak flexion angles during the SH task (Mean difference = 6.2°, 95% CI: 1.9–10.5°, effect size = 1.01, P = 0.034) after the 6-week warm-up program without a reminder. In addition, the Core-PAC group demonstrated increased knee flexion angles for the side-cut (Mean difference = 8.5°, 95% CI: 4.8–12.2°, ES = 2.02, P = 0.001) and side-hop (Mean difference = 10.0°, 95% CI: 5.7–14.3°, ES = 1.66, P = 0.001) task after a reminder. No changes in abduction moments were found. Conclusions The results of this study suggest that the Core-PAC may be one method of modifying high-risk soccer-specific movements and can be implemented within a practical, team-based soccer warm-up. The results should be interpreted with caution due to the small sample size. PMID:24184850

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

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    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

  18. Effect of Intensive vs Moderate Alveolar Recruitment Strategies Added to Lung-Protective Ventilation on Postoperative Pulmonary Complications: A Randomized Clinical Trial.

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    Costa Leme, Alcino; Hajjar, Ludhmila Abrahao; Volpe, Marcia S; Fukushima, Julia Tizue; De Santis Santiago, Roberta Ribeiro; Osawa, Eduardo A; Pinheiro de Almeida, Juliano; Gerent, Aline Muller; Franco, Rafael Alves; Zanetti Feltrim, Maria Ignez; Nozawa, Emília; de Moraes Coimbra, Vera Regina; de Moraes Ianotti, Rafael; Hashizume, Clarice Shiguemi; Kalil Filho, Roberto; Auler, Jose Otavio Costa; Jatene, Fabio Biscegli; Gomes Galas, Filomena Regina Barbosa; Amato, Marcelo Britto Passos

    2017-04-11

    Perioperative lung-protective ventilation has been recommended to reduce pulmonary complications after cardiac surgery. The protective role of a small tidal volume (VT) has been established, whereas the added protection afforded by alveolar recruiting strategies remains controversial. To determine whether an intensive alveolar recruitment strategy could reduce postoperative pulmonary complications, when added to a protective ventilation with small VT. Randomized clinical trial of patients with hypoxemia after cardiac surgery at a single ICU in Brazil (December 2011-2014). Intensive recruitment strategy (n=157) or moderate recruitment strategy (n=163) plus protective ventilation with small VT. Severity of postoperative pulmonary complications computed until hospital discharge, analyzed with a common odds ratio (OR) to detect ordinal shift in distribution of pulmonary complication severity score (0-to-5 scale, 0, no complications; 5, death). Prespecified secondary outcomes were length of stay in the ICU and hospital, incidence of barotrauma, and hospital mortality. All 320 patients (median age, 62 years; IQR, 56-69 years; 125 women [39%]) completed the trial. The intensive recruitment strategy group had a mean 1.8 (95% CI, 1.7 to 2.0) and a median 1.7 (IQR, 1.0-2.0) pulmonary complications score vs 2.1 (95% CI, 2.0-2.3) and 2.0 (IQR, 1.5-3.0) for the moderate strategy group. Overall, the distribution of primary outcome scores shifted consistently in favor of the intensive strategy, with a common OR for lower scores of 1.86 (95% CI, 1.22 to 2.83; P = .003). The mean hospital stay for the moderate group was 12.4 days vs 10.9 days in the intensive group (absolute difference, -1.5 days; 95% CI, -3.1 to -0.3; P = .04). The mean ICU stay for the moderate group was 4.8 days vs 3.8 days for the intensive group (absolute difference, -1.0 days; 95% CI, -1.6 to -0.2; P = .01). Hospital mortality (2.5% in the intensive group vs 4.9% in the moderate group; absolute

  19. Bidirectional promoter trapping T-DNA for insertional mutagenesis in Verticillium dahliae.

    Science.gov (United States)

    Deng, Sheng; Wang, Cai-yue; Zhang, Xin; Lin, Ling

    2014-07-01

    Transfer DNA (T-DNA)-based random insertional mutagenesis is a universal forward genetic approach for gene identification and cloning in many phytopathogenic fungi. In a large number of randomly selected transformants, screening for mutants with a specific phenotype is laborious, especially for pathogenicity-defective mutants. To accelerate mutant screening and gene identification, a bidirectional promoter-trapping Ti binary vector, 1300-bisGFP-hyg, was constructed and deployed in this study. More than 6000 Verticillium dahliae transformants were obtained by the mediation of Agrobacterium tumefaciens carrying the vector. One thousand randomly selected transformants were cultured on Czapek-Dox and on Czapek-Dox plus cotton root extract media plates. The cultured transformants with green fluorescent protein (GFP) expression or changes in phenotype were selected and used in virulence or promoter-trapping assays. Based on the virulence assay of 60 transformants, the pathogenicity of 17 of these mutants was compromised. Ten pathogenicity-defective mutants were found with GFP expression, and 6 with expression in Czapek-Dox plus cotton root extract media specifically. Using TAIL-PCR (thermal asymmetric interlaced polymerase chain reaction), the T-DNA insertion sites were identified in 8 GFP-expressing transformants, including 5 pathogenicity-defective mutants and 3 unaffected transformants. Promoters of 6 genes were successfully trapped using the T-DNA method in this study. The nonpathogenic transformant 24C9 was the subject of additional investigation. It displayed strong GFP expression on water agar medium supplemented with cotton root extracts and on cotton seedling stems. The results obtained by Southern blot and quantitative real-time PCR confirmed that the transcription level of VdUGPU (encoding UTP-glucose-1-phosphate uridylyltransferase) was significantly reduced owing to T-DNA insertion in the gene promoter region. These results indicate that the bidirectional

  20. Gene transfer and genome-wide insertional mutagenesis by retroviral transduction in fish stem cells.

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    Qizhi Liu

    Full Text Available Retrovirus (RV is efficient for gene transfer and integration in dividing cells of diverse organisms. RV provides a powerful tool for insertional mutagenesis (IM to identify and functionally analyze genes essential for normal and pathological processes. Here we report RV-mediated gene transfer and genome-wide IM in fish stem cells from medaka and zebrafish. Three RVs were produced for fish cell transduction: rvLegfp and rvLcherry produce green fluorescent protein (GFP and mCherry fluorescent protein respectively under control of human cytomegalovirus immediate early promoter upon any chromosomal integration, whereas rvGTgfp contains a splicing acceptor and expresses GFP only upon gene trapping (GT via intronic in-frame integration and spliced to endogenous active genes. We show that rvLegfp and rvLcherry produce a transduction efficiency of 11~23% in medaka and zebrafish stem cell lines, which is as 30~67% efficient as the positive control in NIH/3T3. Upon co-infection with rvGTgfp and rvLcherry, GFP-positive cells were much fewer than Cherry-positive cells, consistent with rareness of productive gene trapping events versus random integration. Importantly, rvGTgfp infection in the medaka haploid embryonic stem (ES cell line HX1 generated GTgfp insertion on all 24 chromosomes of the haploid genome. Similar to the mammalian haploid cells, these insertion events were presented predominantly in intergenic regions and introns but rarely in exons. RV-transduced HX1 retained the ES cell properties such as stable growth, embryoid body formation and pluripotency gene expression. Therefore, RV is proficient for gene transfer and IM in fish stem cells. Our results open new avenue for genome-wide IM in medaka haploid ES cells in culture.

  1. Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis

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    Bulina, Maria E; Chudakov, Dmitry M; Mudrik, Nikolay N; Lukyanov, Konstantin A

    2002-01-01

    Background Within the family of green fluorescent protein (GFP) homologs, one can mark two main groups, specifically, fluorescent proteins (FPs) and non-fluorescent or chromoproteins (CPs). Structural background of differences between FPs and CPs are poorly understood to date. Results Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595) from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP) were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield (< 0.001). These spectral characteristics allow one to regard DsRed-NF as a true chromoprotein. Conclusions We located a novel point in asCP sequence (position 165) mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed. PMID:11972899

  2. Gene transfer and genome-wide insertional mutagenesis by retroviral transduction in fish stem cells.

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    Liu, Qizhi; Wang, Yunzhi; Lin, Fan; Zhang, Lei; Li, Yan; Ge, Ruowen; Hong, Yunhan

    2015-01-01

    Retrovirus (RV) is efficient for gene transfer and integration in dividing cells of diverse organisms. RV provides a powerful tool for insertional mutagenesis (IM) to identify and functionally analyze genes essential for normal and pathological processes. Here we report RV-mediated gene transfer and genome-wide IM in fish stem cells from medaka and zebrafish. Three RVs were produced for fish cell transduction: rvLegfp and rvLcherry produce green fluorescent protein (GFP) and mCherry fluorescent protein respectively under control of human cytomegalovirus immediate early promoter upon any chromosomal integration, whereas rvGTgfp contains a splicing acceptor and expresses GFP only upon gene trapping (GT) via intronic in-frame integration and spliced to endogenous active genes. We show that rvLegfp and rvLcherry produce a transduction efficiency of 11~23% in medaka and zebrafish stem cell lines, which is as 30~67% efficient as the positive control in NIH/3T3. Upon co-infection with rvGTgfp and rvLcherry, GFP-positive cells were much fewer than Cherry-positive cells, consistent with rareness of productive gene trapping events versus random integration. Importantly, rvGTgfp infection in the medaka haploid embryonic stem (ES) cell line HX1 generated GTgfp insertion on all 24 chromosomes of the haploid genome. Similar to the mammalian haploid cells, these insertion events were presented predominantly in intergenic regions and introns but rarely in exons. RV-transduced HX1 retained the ES cell properties such as stable growth, embryoid body formation and pluripotency gene expression. Therefore, RV is proficient for gene transfer and IM in fish stem cells. Our results open new avenue for genome-wide IM in medaka haploid ES cells in culture.

  3. Interconversion of Anthozoa GFP-like fluorescent and non-fluorescent proteins by mutagenesis

    Directory of Open Access Journals (Sweden)

    Mudrik Nikolay N

    2002-04-01

    Full Text Available Abstract Background Within the family of green fluorescent protein (GFP homologs, one can mark two main groups, specifically, fluorescent proteins (FPs and non-fluorescent or chromoproteins (CPs. Structural background of differences between FPs and CPs are poorly understood to date. Results Here, we applied site-directed and random mutagenesis in order to to transform CP into FP and vice versa. A purple chromoprotein asCP (asFP595 from Anemonia sulcata and a red fluorescent protein DsRed from Discosoma sp. were selected as representatives of CPs and FPs, respectively. For asCP, some substitutions at positions 148 and 165 (numbering in accordance to GFP were found to dramatically increase quantum yield of red fluorescence. For DsRed, substitutions at positions 148, 165, 167, and 203 significantly decreased fluorescence intensity, so that the spectral characteristics of these mutants became more close to those of CPs. Finally, a practically non-fluorescent mutant DsRed-NF was generated. This mutant carried four amino acid substitutions, specifically, S148C, I165N, K167M, and S203A. DsRed-NF possessed a high extinction coefficient and an extremely low quantum yield ( Conclusions We located a novel point in asCP sequence (position 165 mutations at which can result in red fluorescence appearance. Probably, this finding could be applied onto other CPs to generate red and far-red fluorescent mutants. A possibility to transform an FP into CP was demonstrated. Key role of residues adjacent to chromophore's phenolic ring in fluorescent/non-fluorescent states determination was revealed.

  4. Mitochondrial mutagenesis induced by tumor-specific radiation bystander effects.

    LENUS (Irish Health Repository)

    Gorman, Sheeona

    2012-02-01

    The radiation bystander effect is a cellular process whereby cells not directly exposed to radiation display cellular alterations similar to directly irradiated cells. Cellular targets including mitochondria have been postulated to play a significant role in this process. In this study, we utilized the Random Mutation Capture assay to quantify the levels of random mutations and deletions in the mitochondrial genome of bystander cells. A significant increase in the frequency of random mitochondrial mutations was found at 24 h in bystander cells exposed to conditioned media from irradiated tumor explants (p = 0.018). CG:TA mutations were the most abundant lesion induced. A transient increase in the frequency of random mitochondrial deletions was also detected in bystander cells exposed to conditioned media from tumor but not normal tissue at 24 h (p = 0.028). The increase in both point mutations and deletions was transient and not detected at 72 h. To further investigate mitochondrial dysfunction, mitochondrial membrane potential and reactive oxygen species were assessed in these bystander cells. There was a significant reduction in mitochondrial membrane potential and this was positively associated with the frequency of random point mutation and deletions in bystander cells treated with conditioned media from tumor tissue (r = 0.71, p = 0.02). This study has shown that mitochondrial genome alterations are an acute consequence of the radiation bystander effect secondary to mitochondrial dysfunction and suggests that this cannot be solely attributable to changes in ROS levels alone.

  5. Comparison of pharmacological and nonpharmacological treatment strategies in promotion of infertility self-efficacy scale in infertile women: A randomized controlled trial

    Science.gov (United States)

    Pasha, Hajar; Faramarzi, Mahbobeh; Esmailzadeh, Seddigheh; Kheirkhah, Farzan; Salmalian, Hajar

    2013-01-01

    Background: The infertility is associated with psychological consequence including depression, and lack of self-efficacy. Objective: The aim of this study was to compare the pharmacological and no pharmacological strategies in promotion of self-efficacy of infertile women. Materials and Methods: A randomized controlled clinical trial was conducted on 89 infertile women who were recruited from Fatemeh Zahra Infertility and Reproductive Health Research Center and were randomized into three groups; cognitive behavioral therapy (CBT), antidepressant therapy with flouxetine 20 mg daily for 3 month, and a control group. All participants completed Infertility Self-efficacy Inventory (ISE) and the Beck Depression Inventory (BDI) at the beginning and end of the study. Results: The means ISE scores among the CBT, fluoxetine, and control groups at the beginning and end of the study were 6.1±1.6 vs. 7.2±0.9, 6.4±1.4 vs. 6.9±1.3 and 6.1±1.1 vs. 5.9±1.4 respectively. Both CBT and fluoxetine increased the mean of ISE scores more than control group after intervention (pinfertility self-efficacy for women exposed to the intervention compared with those in the control group. Also, there was an improvement in depression. Both fluoxetine and CBT decreased significantly the mean of BDI scores more than the control group; decrease in the CBT group was significantly more than that in the fluoxetine group. Conclusion: CBT can serve as an effective psychosocial intervention for promoting self-efficacy of infertile women. Registration ID in IRCT: IRCT2012061710048N1 PMID:24639784

  6. Using Getting To Outcomes to facilitate the use of an evidence-based practice in VA homeless programs: a cluster-randomized trial of an implementation support strategy.

    Science.gov (United States)

    Chinman, Matthew; McCarthy, Sharon; Hannah, Gordon; Byrne, Thomas Hugh; Smelson, David A

    2017-03-09

    Incorporating evidence-based integrated treatment for dual disorders into typical care settings has been challenging, especially among those serving Veterans who are homeless. This paper presents an evaluation of an effort to incorporate an evidence-based, dual disorder treatment called Maintaining Independence and Sobriety Through Systems Integration, Outreach, and Networking-Veterans Edition (MISSION-Vet) into case management teams serving Veterans who are homeless, using an implementation strategy called Getting To Outcomes (GTO). This Hybrid Type III, cluster-randomized controlled trial assessed the impact of GTO over and above MISSION-Vet Implementation as Usual (IU). Both conditions received standard MISSION-Vet training and manuals. The GTO group received an implementation manual, training, technical assistance, and data feedback. The study occurred in teams at three large VA Medical Centers over 2 years. Within each team, existing sub-teams (case managers and Veterans they serve) were the clusters randomly assigned. The trial assessed MISSION-Vet services delivered and collected via administrative data and implementation barriers and facilitators, via semi-structured interview. No case managers in the IU group initiated MISSION-Vet while 68% in the GTO group did. Seven percent of Veterans with case managers in the GTO group received at least one MISSION-Vet session. Most case managers appreciated the MISSION-Vet materials and felt the GTO planning meetings supported using MISSION-Vet. Case manager interviews also showed that MISSION-Vet could be confusing; there was little involvement from leadership after their initial agreement to participate; the data feedback system had a number of difficulties; and case managers did not have the resources to implement all aspects of MISSION-Vet. This project shows that GTO-like support can help launch new practices but that multiple implementation facilitators are needed for successful execution of a complex evidence

  7. Randomized Comparison of a CrossBoss First Versus Standard Wire Escalation Strategy for Crossing Coronary Chronic Total Occlusions: The CrossBoss First Trial.

    Science.gov (United States)

    Karacsonyi, Judit; Tajti, Peter; Rangan, Bavana V; Halligan, Sean C; Allen, Raymond H; Nicholson, William J; Harvey, James E; Spaedy, Anthony J; Jaffer, Farouc A; Grantham, J Aaron; Salisbury, Adam; Hart, Anthony J; Safley, David M; Lombardi, William L; Hira, Ravi; Don, Creighton; McCabe, James M; Burke, M Nicholas; Alaswad, Khaldoon; Koenig, Gerald C; Sanghvi, Kintur A; Ice, Daniel; Kovach, Richard C; Varghese, Vincent; Murad, Bilal; Baran, Kenneth W; Resendes, Erica; Martinez-Parachini, Jose R; Karatasakis, Aris; Danek, Barbara A; Iwnetu, Rahel; Roesle, Michele; Khalili, Houman; Banerjee, Subhash; Brilakis, Emmanouil S

    2018-02-12

    The authors performed a multicenter, randomized-controlled, clinical trial comparing upfront use of the CrossBoss catheter versus antegrade wire escalation for antegrade crossing of coronary chronic total occlusions. There is equipoise about the optimal initial strategy for crossing coronary chronic total occlusions. The primary endpoints were the time required to cross the chronic total occlusion or abort the procedure and the frequency of procedural major adverse cardiovascular events. The secondary endpoints were technical and procedural success, total procedure time, fluoroscopy time required to cross and total fluoroscopy time, total air kerma radiation dose, total contrast volume, and equipment use. Between 2015 and 2017, 246 patients were randomized to the CrossBoss catheter (n = 122) or wire escalation (n = 124) at 11 U.S. centers. The baseline clinical and angiographic characteristics of the study groups were similar. Technical and procedural success were 87.8% and 84.1%, respectively, and were similar in the 2 groups. Crossing time was similar: 56 min (interquartile range: 33 to 93 min) in the CrossBoss group and 66 min (interquartile range: 36 to 105 min) in the wire escalation group (p = 0.323), as was as the incidence of procedural major adverse cardiovascular events (3.28% vs. 4.03%; p = 1.000). There were no significant differences in the secondary study endpoints. As compared with wire escalation, upfront use of the CrossBoss catheter for antegrade crossing of coronary chronic total occlusions was associated with similar crossing time, similar success and complication rates, and similar equipment use and cost. Copyright © 2018 American College of Cardiology Foundation. All rights reserved.

  8. Comparison of pharmacological and nonpharmacological treatment strategies in promotion of infertility self-efficacy scale in infertile women: A randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Hajar Pasha

    2013-06-01

    Full Text Available Background: The infertility is associated with psychological consequence including depression, and lack of self-efficacy. Objective: The aim of this study was to compare the pharmacological and no pharmacological strategies in promotion of self-efficacy of infertile women. Materials and Methods: A randomized controlled clinical trial was conducted on 89 infertile women who were recruited from Fatemeh Zahra Infertility and Reproductive Health Research Center and were randomized into three groups; cognitive behavioral therapy (CBT, antidepressant therapy with flouxetine 20 mg daily for 3 month, and a control group. All participants completed Infertility Self-efficacy Inventory (ISE and the Beck Depression Inventory (BDI at the beginning and end of the study. Results: The means ISE scores among the CBT, fluoxetine, and control groups at the beginning and end of the study were 6.1±1.6 vs. 7.2±0.9, 6.4±1.4 vs. 6.9±1.3 and 6.1±1.1 vs. 5.9±1.4 respectively. Both CBT and fluoxetine increased the mean of ISE scores more than control group after intervention (p<0.0001, p=0.033; respectively, but increase in the CBT group was significantly greater than flouxetine group. Finally, there was evidence of high infertility self-efficacy for women exposed to the intervention compared with those in the control group. Also, there was an improvement in depression. Both fluoxetine and CBT decreased significantly the mean of BDI scores more than the control group; decrease in the CBT group was significantly more than that in the fluoxetine group. Conclusion: CBT can serve as an effective psychosocial intervention for promoting self-efficacy of infertile women

  9. Gene-trap mutagenesis identifies mammalian genes contributing to intoxication by Clostridium perfringens ε-toxin.

    Directory of Open Access Journals (Sweden)

    Susan E Ivie

    Full Text Available The Clostridium perfringens ε-toxin is an extremely potent toxin associated with lethal toxemias in domesticated ruminants and may be toxic to humans. Intoxication results in fluid accumulation in various tissues, most notably in the brain and kidneys. Previous studies suggest that the toxin is a pore-forming toxin, leading to dysregulated ion homeostasis and ultimately cell death. However, mammalian host factors that likely contribute to ε-toxin-induced cytotoxicity are poorly understood. A library of insertional mutant Madin Darby canine kidney (MDCK cells, which are highly susceptible to the lethal affects of ε-toxin, was used to select clones of cells resistant to ε-toxin-induced cytotoxicity. The genes mutated in 9 surviving resistant cell clones were identified. We focused additional experiments on one of the identified genes as a means of validating the experimental approach. Gene expression microarray analysis revealed that one of the identified genes, hepatitis A virus cellular receptor 1 (HAVCR1, KIM-1, TIM1, is more abundantly expressed in human kidney cell lines than it is expressed in human cells known to be resistant to ε-toxin. One human kidney cell line, ACHN, was found to be sensitive to the toxin and expresses a larger isoform of the HAVCR1 protein than the HAVCR1 protein expressed by other, toxin-resistant human kidney cell lines. RNA interference studies in MDCK and in ACHN cells confirmed that HAVCR1 contributes to ε-toxin-induced cytotoxicity. Additionally, ε-toxin was shown to bind to HAVCR1 in vitro. The results of this study indicate that HAVCR1 and the other genes identified through the use of gene-trap mutagenesis and RNA interference strategies represent important targets for investigation of the process by which ε-toxin induces cell death and new targets for potential therapeutic intervention.

  10. 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.

  11. Effectiveness of a combination strategy for linkage and retention in adult HIV care in Swaziland: The Link4Health cluster randomized trial.

    Directory of Open Access Journals (Sweden)

    Margaret L McNairy

    2017-11-01

    Full Text Available Gaps in the HIV care continuum contribute to poor health outcomes and increase HIV transmission. A combination of interventions targeting multiple steps in the continuum is needed to achieve the full beneficial impact of HIV treatment.Link4Health, a cluster-randomized controlled trial, evaluated the effectiveness of a combination intervention strategy (CIS versus the standard of care (SOC on the primary outcome of linkage to care within 1 month plus retention in care at 12 months after HIV-positive testing. Ten clusters of HIV clinics in Swaziland were randomized 1:1 to CIS versus SOC. The CIS included point-of-care CD4+ testing at the time of an HIV-positive test, accelerated antiretroviral therapy (ART initiation for treatment-eligible participants, mobile phone appointment reminders, health educational packages, and noncash financial incentives. Secondary outcomes included each component of the primary outcome, mean time to linkage, assessment for ART eligibility, ART initiation and time to ART initiation, viral suppression defined as HIV-1 RNA < 1,000 copies/mL at 12 months after HIV testing among patients on ART ≥6 months, and loss to follow-up and death at 12 months after HIV testing. A total of 2,197 adults aged ≥18 years, newly tested HIV positive, were enrolled from 19 August 2013 to 21 November 2014 (1,096 CIS arm; 1,101 SOC arm and followed for 12 months. The median participant age was 31 years (IQR 26-39, and 59% were women. In an intention-to-treat analysis, 64% (705/1,096 of participants at the CIS sites achieved the primary outcome versus 43% (477/1,101 at the SOC sites (adjusted relative risk [RR] 1.52, 95% CI 1.19-1.96, p = 0.002. Participants in the CIS arm versus the SOC arm had the following secondary outcomes: linkage to care regardless of retention at 12 months (RR 1.08, 95% CI 0.97-1.21, p = 0.13, mean time to linkage (2.5 days versus 7.5 days, p = 0.189, retention in care at 12 months regardless of time to linkage (RR

  12. The "Sarcopenia and Physical fRailty IN older people: multi-componenT Treatment strategies" (SPRINTT) randomized controlled trial: design and methods.

    Science.gov (United States)

    Landi, Francesco; Cesari, Matteo; Calvani, Riccardo; Cherubini, Antonio; Di Bari, Mauro; Bejuit, Raphael; Mshid, Jerome; Andrieu, Sandrine; Sinclair, Alan J; Sieber, Cornel C; Vellas, Bruno; Topinkova, Eva; Strandberg, Timo; Rodriguez-Manas, Leocadio; Lattanzio, Fabrizia; Pahor, Marco; Roubenoff, Ronenn; Cruz-Jentoft, Alfonso J; Bernabei, Roberto; Marzetti, Emanuele

    2017-02-01

    The sustainability of health and social care systems is threatened by a growing population of older persons with heterogeneous needs related to multimorbidity, frailty, and increased risk of functional impairment. Since disability is difficult to reverse in old age and is extremely burdensome for individuals and society, novel strategies should be devised to preserve adequate levels of function and independence in late life. The development of mobility disability, an early event in the disablement process, precedes and predicts more severe forms of inability. Its prevention is, therefore, critical to impede the transition to overt disability. For this reason, the Sarcopenia and Physical fRailty IN older people: multi-componenT Treatment strategies (SPRINTT) project is conducting a randomized controlled trial (RCT) to test a multicomponent intervention (MCI) specifically designed to prevent mobility disability in high-risk older persons. SPRINTT is a phase III, multicenter RCT aimed at comparing the efficacy of a MCI, based on long-term structured physical activity, nutritional counseling/dietary intervention, and an information and communication technology intervention, versus a healthy aging lifestyle education program designed to prevent mobility disability in 1500 older persons with physical frailty and sarcopenia who will be followed for up to 36 months. The primary outcome of the SPRINTT trial is mobility disability, operationalized as the inability to walk for 400 m within 15 min, without sitting, help of another person, or the use of a walker. Secondary outcomes include changes in muscle mass and strength, persistent mobility disability, falls and injurious falls, disability in activities of daily living, nutritional status, cognition, mood, the use of healthcare resources, cost-effectiveness analysis, quality of life, and mortality rate. SPRINTT results are expected to promote significant advancements in the management of frail older persons at high risk

  13. A strategy of symptom-limited exercise with regadenoson-as-needed for stress myocardial perfusion imaging: a randomized controlled trial.

    Science.gov (United States)

    Parker, Matthew W; Morales, Donna Chelle; Slim, Hanna B; Ahlberg, Alan W; Katten, Deborah M; Cyr, Giselle; Mathur, Shishir; Ardestani, Afrooz; Barmpouletos, Dimitrios; Iyah, Geeta Swamy; Borer, Steven M; Heller, Gary V

    2013-04-01

    Ambulatory patients with uncertain functional capacity may benefit from combined exercise and vasodilator stress protocols for myocardial perfusion imaging (MPI). The safety and MPI image quality with regadenoson administered during symptom-limited exercise have not been prospectively evaluated. A total of 140 patients (mean age 61 years, 48% female) referred for exercise with vasodilator stress MPI were randomized 2:1 to a strategy of exercise with regadenoson-as-necessary (Ex-Reg, n = 96) or dipyridamole with exercise (Dip-Ex, n = 44) after Duke Activity Status Index (DASI) scoring (median score 28 vs 24, P = .09). Ex-Reg subjects commenced treadmill exercise and regadenoson was administered only if the subject was unable to reach standard endpoints. Dip-Ex subjects received dipyridamole prior to symptom-limited exercise. Hemodynamics were recorded throughout. Subjects completed symptom questionnaires and MPI image quality was assessed by blinded read. Ex-Reg subjects were more likely to achieve ≥85% age-predicted maximum heart rate than Dip-Ex subjects (57% vs 32%, P regadenoson and none had symptomatic hemodynamic changes. Severe side effects or adverse events occurred in 16% of Ex-Reg and 24% of Dip-Ex subjects (P = .12). MPI image quality was "good" or "excellent" in 88% of Ex-Reg subjects and 86% of Dip-Ex subjects (P = .33). A strategy of exercise with regadenoson-as-needed for MPI offers similar safety and side effect profile with similar image quality compared to dipyridamole with exercise, with reduced pharmaceutical use.

  14. An interactive education session and follow-up support as a strategy to improve clinicians' goal-writing skills: a randomized controlled trial.

    Science.gov (United States)

    Marsland, Elisabeth; Bowman, Julia

    2010-02-01

    Recent research indicates that allied health clinicians have difficulty articulating client needs and priorities into specific and measurable goals. As a result, a number of strategies to facilitate improvement in allied health clinicians' goal-setting skills have been recommended in the literature. In order to assist clinicians develop the skills required to set SMART goals, it is necessary that the strategies are rigorously tested. To determine if a 50-minute education session and 3-month email and telephone support programme improves clinicians' SMART goal-writing skill and accurately predicts improved goal-writing behaviour. Concealed random allocation of participants (n = 120) into two parallel groups: (1) intervention group received education on writing goals using the SMART Goal Evaluation Method as part of a workshop on outcome measurement and received 3 months of follow-up support (n = 60); and (2) control group attended a workshop on evidence-based practice (n = 60). Education and follow-up support improved clinicians' SMART goal-writing skills at both the 3- and 6-month review (Yates chi(2) = 4.324, d.f. = 1, P = 0.0375). Structural equation modelling revealed education and follow-up support is an accurate predictor of SMART goal-setting behaviour change at both 3 months (standardized regression weights = 0.21; P = 0.014) and 6 months (standardized regression weights = 0.19; P = 0.02) post intervention. Changes were modest and developed over a 6-month period. This study provides empirical evidence that a programme of educating clinicians in a standardized method of goal setting and providing follow-up support improves allied health clinicians' SMART goal-writing skills.

  15. CRISPR-Cas9 Targeted Mutagenesis Leads to Simultaneous Modification of Different Homoeologous Gene Copies in Polyploid Oilseed Rape (Brassica napus).

    Science.gov (United States)

    Braatz, Janina; Harloff, Hans-Joachim; Mascher, Martin; Stein, Nils; Himmelbach, Axel; Jung, Christian

    2017-06-01

    In polyploid species, altering a trait by random mutagenesis is highly inefficient due to gene redundancy. We have stably transformed tetraploid oilseed rape (Brassica napus) with a CRISPR-Cas9 construct targeting two ALCATRAZ (ALC) homoeologs. ALC is involved in valve margin development and, thus, contributes to seed shattering from mature fruits. Knocking out ALC would increase shatter resistance to avoid seed loss during mechanical harvest. We obtained a transgenic T1 plant with four alc mutant alleles by the use of a single target sequence. All mutations were stably inherited to the T2 progeny. The T2 generation was devoid of any wild-type alleles, proving that the underlying T1 was a nonchimeric double heterozygote. T-DNA and ALC loci were not linked, as indicated by random segregation in the T2 generation. Hence, we could select double mutants lacking the T-DNA already in the first offspring generation. However, whole-genome sequencing data revealed at least five independent insertions of vector backbone sequences. We did not detect any off-target effects in two genome regions homologous to the target sequence. The simultaneous alteration of multiple homoeologs by CRISPR-Cas9 mutagenesis without any background mutations will offer new opportunities for using mutant genotypes in rapeseed breeding. © 2017 American Society of Plant Biologists. All Rights Reserved.

  16. Efficient generation of recombinant RNA viruses using targeted recombination-mediated mutagenesis of bacterial artificial chromosomes containing full-length cDNA

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Risager, Peter Christian; Fahnøe, Ulrik

    2013-01-01

    Background Infectious cDNA clones are a prerequisite for directed genetic manipulation of RNA viruses. Here, a strategy to facilitate manipulation and rescue of classical swine fever viruses (CSFVs) from full-length cDNAs present within bacterial artificial chromosomes (BACs) is described....... This strategy allows manipulation of viral cDNA by targeted recombination-mediated mutagenesis within bacteria. Results A new CSFV-BAC (pBeloR26) derived from the Riems vaccine strain has been constructed and subsequently modified in the E2 coding sequence, using the targeted recombination strategy to enable...... rescue of chimeric pestiviruses (vR26_E2gif and vR26_TAV) with potential as new marker vaccine candidates. Sequencing of the BACs revealed a high genetic stability during passages within bacteria. The complete genome sequences of rescued viruses, after extensive passages in mammalian cells showed...

  17. Sub-lethal antibiotic treatment leads to multidrug resistance via radical-induced mutagenesis

    Science.gov (United States)

    Kohanski, Michael A.; DePristo, Mark A.; Collins, James J.

    2010-01-01

    Summary Antibiotic resistance arises through mechanisms such as selection of naturally occurring resistant mutants and horizontal gene transfer. Recently, oxidative stress has been implicated as one of the mechanisms whereby bactericidal antibiotics kill bacteria. Here we show that sub-lethal levels of bactericidal antibiotics induce mutagenesis, resulting in heterogeneous increases in the minimum inhibitory concentration for a range of antibiotics, irrespective of the drug target. This increase in mutagenesis correlates with an increase in ROS, and is prevented by the ROS scavenger thiourea and by anaerobic conditions, indicating that sub-lethal concentrations of antibiotics induce mutagenesis by stimulating the production of ROS. We demonstrate that these effects can lead to mutant strains that are sensitive to the applied antibiotic but resistant to other antibiotics. This work establishes a radical-based molecular mechanism whereby sub-lethal levels of antibiotics can lead to multidrug resistance, which has important implications for the widespread use and misuse of antibiotics. PMID:20159551

  18. 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.

  19. Distance learning strategies for weight management utilizing social media: A comparison of phone conference call versus social media platform. Rationale and design for a randomized study.

    Science.gov (United States)

    Willis, Erik A; Szabo-Reed, Amanda N; Ptomey, Lauren T; Steger, Felicia L; Honas, Jeffery J; Al-Hihi, Eyad M; Lee, Robert; Vansaghi, Lisa; Washburn, Richard A; Donnelly, Joseph E

    2016-03-01

    Management of obesity in the context of the primary care physician visit is of limited efficacy in part because of limited ability to engage participants in sustained behavior change between physician visits. Therefore, healthcare systems must find methods to address obesity that reach beyond the walls of clinics and hospitals and address the issues of lifestyle modification in a cost-conscious way. The dramatic increase in technology and online social networks may present healthcare providers with innovative ways to deliver weight management programs that could have an impact on health care at the population level. A randomized study will be conducted on 70 obese adults (BMI 30.0-45.0 kg/m(2)) to determine if weight loss (6 months) is equivalent between weight management interventions utilizing behavioral strategies by either a conference call or social media approach. The primary outcome, body weight, will be assessed at baseline and 6 months. Secondary outcomes including waist circumference, energy and macronutrient intake, and physical activity will be assessed on the same schedule. In addition, a cost analysis and process evaluation will be completed. Copyright © 2016 Elsevier Inc. All rights reserved.

  20. A trial to determine whether septic shock-reversal is quicker in pediatric patients randomized to an early goal-directed fluid-sparing strategy versus usual care (SQUEEZE): study protocol for a pilot randomized controlled trial.

    Science.gov (United States)

    Parker, Melissa J; Thabane, Lehana; Fox-Robichaud, Alison; Liaw, Patricia; Choong, Karen

    2016-11-22

    Current pediatric septic shock resuscitation guidelines from the American College of Critical Care Medicine focus on the early and goal-directed administration of intravascular fluid followed by vasoactive medication infusions for persistent and fluid-refractory shock. However, accumulating adult and pediatric data suggest that excessive fluid administration is associated with worse patient outcomes and even increased risk of death. The optimal amount of intravascular fluid required in early pediatric septic shock resuscitation prior to the initiation of vasoactive support remains unanswered. The SQUEEZE Pilot Trial is a pragmatic, two-arm, parallel-group, open-label, prospective pilot randomized controlled trial. Participants are children aged 29 days to under 18 years with suspected or confirmed septic shock and a need for ongoing resuscitation. Eligible participants are enrolled under an exception to consent process and randomly assigned via concealed allocation to either the Usual Care (control) or Fluid Sparing (intervention) resuscitation strategy. The primary objective of this pilot trial is to determine feasibility, based on the ability to enroll participants and to adhere to the study protocol. The primary outcome measure by which success will be determined is participant enrollment rate ("pass" defined as at least two participants/site/month, recognizing that enrollment may be slower during the run-in phase). Secondary objectives include assessing (1) appropriateness of eligibility criteria, and (2) completeness of clinical outcomes to inform the endpoints for the planned multisite trial. To support the nested translational study, SQUEEZE-D, we will also evaluate the feasibility of describing cell-free DNA (a procoagulant molecule with prognostic utility) in blood samples obtained from children enrolled into the SQUEEZE Pilot Trial at baseline and at 24 h. The optimal degree of fluid resuscitation and the timing of initiation of vasoactive support in

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

    CERN Document Server

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

    2014-01-01

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

  2. A pragmatic cluster randomized clinical trial of diabetes prevention strategies for women with gestational diabetes: design and rationale of the Gestational Diabetes' Effects on Moms (GEM) study.

    Science.gov (United States)

    Ferrara, Assiamira; Hedderson, Monique M; Albright, Cheryl L; Brown, Susan D; Ehrlich, Samantha F; Caan, Bette J; Sternfeld, Barbara; Gordon, Nancy P; Schmittdiel, Julie A; Gunderson, Erica P; Mevi, Ashley A; Tsai, Ai-Lin; Ching, Jenny; Crites, Yvonne; Quesenberry, Charles P

    2014-01-15

    Women with gestational diabetes (GDM) are at high risk of developing diabetes later in life. After a GDM diagnosis, women receive prenatal care to control their blood glucose levels via diet, physical activity and medications. Continuing such lifestyle skills into early motherhood may reduce the risk of diabetes in this high risk population. In the Gestational Diabetes' Effects on Moms (GEM) study, we are evaluating the comparative effectiveness of diabetes prevention strategies for weight management designed for pregnant/postpartum women with GDM and delivered at the health system level. The GEM study is a pragmatic cluster randomized clinical trial of 44 medical facilities at Kaiser Permanente Northern California randomly assigned to either the intervention or usual care conditions, that includes 2,320 women with a GDM diagnosis between March 27, 2011 and March 30, 2012. A Diabetes Prevention Program-derived print/telephone lifestyle intervention of 13 telephonic sessions tailored to pregnant/postpartum women was developed. The effectiveness of this intervention added to usual care is to be compared to usual care practices alone, which includes two pages of printed lifestyle recommendations sent to postpartum women via mail. Primary outcomes include the proportion of women who reach a postpartum weight goal and total weight change. Secondary outcomes include postpartum glycemia, blood pressure, depression, percent of calories from fat, total caloric intake and physical activity levels. Data were collected through electronic medical records and surveys at baseline (soon after GDM diagnosis), 6 weeks (range 2 to 11 weeks), 6 months (range 12 to 34 weeks) and 12 months postpartum (range 35 to 64 weeks). There is a need for evidence regarding the effectiveness of lifestyle modification for the prevention of diabetes in women with GDM, as well as confirmation that a diabetes prevention program delivered at the health system level is able to successfully reach this

  3. A randomized trial of a strategy for increasing high-density lipoprotein cholesterol levels: effects on progression of coronary heart disease and clinical events.

    Science.gov (United States)

    Whitney, Edwin J; Krasuski, Richard A; Personius, Bradley E; Michalek, Joel E; Maranian, Ara M; Kolasa, Mark W; Monick, Erik; Brown, B Gregory; Gotto, Antonio M

    2005-01-18

    The high-density lipoprotein (HDL) cholesterol level is a strong predictor of cardiovascular events in epidemiologic studies. Until recently, it has been less extensively studied as a therapeutic target. To assess the angiographic and clinical effects of a pharmacologic strategy to increase HDL cholesterol levels. Randomized, double-blind, placebo-controlled trial conducted from 1993 to 1996. Outpatient specialty clinic of a large U.S. military medical center. 143 military retirees younger than 76 years of age with low HDL cholesterol levels and angiographically evident coronary disease. Gemfibrozil, niacin, and cholestyramine or corresponding placebos, with aggressive dietary and lifestyle intervention at baseline. Change from baseline to 30 months and a composite measure of clinical events that included hospitalization for angina, myocardial infarction, transient ischemic attack and stroke, death, and cardiovascular procedures. At baseline, mean (+/-SD) lipid values were as follows: total cholesterol, 5.1 +/- 0.8 mmol/L (196 +/- 31 mg/dL); low-density lipoprotein (LDL) cholesterol, 3.3 +/- 0.7 mmol/L (128 +/- 27 mg/dL); and HDL cholesterol, 0.9 +/- 0.2 mmol/L (34 +/- 6 mg/dL). Compared with placebo, the pharmacologically treated group experienced a 20% (95% CI, 14.8% to 24.3%) decrease in total cholesterol level, a 36% (CI, 28.4% to 43.5%) increase in HDL cholesterol level, a 26% (CI, 19.1% to 33.7%) decrease in LDL cholesterol level, and a 50% (CI, 40.5% to 59.2%) reduction in triglyceride levels. Focal coronary stenosis increased by 1.4% in the placebo group but decreased by 0.8% in the drug group (difference, -2.2 percentage points [CI, -4.2 to -0.1 percentage points]). A composite cardiovascular event end point was reached in 26% of patients in the placebo group and 13% of those in the drug group (difference, 13.7 percentage points [CI, 0.9 to 26.5 percentage points]). Side effects, particularly flushing and gastrointestinal intolerance, were more common in

  4. Economic evaluation of price discounts and skill-building strategies on purchase and consumption of healthy food and beverages: The SHELf randomized controlled trial.

    Science.gov (United States)

    Le, Ha N D; Gold, Lisa; Abbott, Gavin; Crawford, David; McNaughton, Sarah A; Mhurchu, Cliona Ni; Pollard, Christina; Ball, Kylie

    2016-06-01

    Pricing strategies are a promising approach for promoting healthier dietary choices. However, robust evidence of the cost-effectiveness of pricing manipulations on dietary behaviour is limited. We aimed to assess the cost-effectiveness of a 20% price reduction on fruits and vegetables and a combined skills-based behaviour change and price reduction intervention. Cost-effectiveness analysis from a societal perspective was undertaken for the randomized controlled trial Supermarket Healthy Eating for Life (SHELf). Female shoppers in Melbourne, Australia were randomized to: (1) skill-building (n = 160); (2) price reductions (n = 161); (3) combined skill-building and price reduction (n = 161); or (4) control group (n = 161). The intervention was implemented for three months followed by a six month follow-up. Costs were measured in 2012 Australian dollars. Fruit and vegetable purchasing and consumption were measured in grams/week. At three months, compared to control participants, price reduction participants increased vegetable purchases by 233 g/week (95% CI 4 to 462, p = 0.046) and fruit purchases by 364 g/week (95% CI 95 to 633, p = 0.008). Participants in the combined group purchased 280 g/week more fruits (95% CI 27 to 533, p = 0.03) than participants in the control group. Increases were not maintained six-month post intervention. No effect was noticed in the skill-building group. Compared to the control group, the price reduction intervention cost an additional A$2.3 per increased serving of vegetables purchased per week or an additional A$3 per increased serving of fruit purchased per week. The combined intervention cost an additional A$12 per increased serving of fruit purchased per week compared to the control group. A 20% discount on fruits and vegetables was effective in promoting overall fruit and vegetable purchases during the period the discount was active and may be cost-effective. The price discount program gave better value for money

  5. A combination intervention strategy to improve linkage to and retention in HIV care following diagnosis in Mozambique: A cluster-randomized study.

    Directory of Open Access Journals (Sweden)

    Batya Elul

    2017-11-01

    Full Text Available Concerning gaps in the HIV care continuum compromise individual and population health. We evaluated a combination intervention strategy (CIS targeting prevalent barriers to timely linkage and sustained retention in HIV care in Mozambique.In this cluster-randomized trial, 10 primary health facilities in the city of Maputo and Inhambane Province were randomly assigned to provide the CIS or the standard of care (SOC. The CIS included point-of-care CD4 testing at the time of diagnosis, accelerated ART initiation, and short message service (SMS health messages and appointment reminders. A pre-post intervention 2-sample design was nested within the CIS arm to assess the effectiveness of CIS+, an enhanced version of the CIS that additionally included conditional non-cash financial incentives for linkage and retention. The primary outcome was a combined outcome of linkage to care within 1 month and retention at 12 months after diagnosis. From April 22, 2013, to June 30, 2015, we enrolled 2,004 out of 5,327 adults ≥18 years of age diagnosed with HIV in the voluntary counseling and testing clinics of participating health facilities: 744 (37% in the CIS group, 493 (25% in the CIS+ group, and 767 (38% in the SOC group. Fifty-seven percent of the CIS group achieved the primary outcome versus 35% in the SOC group (relative risk [RR]CIS vs SOC = 1.58, 95% CI 1.05-2.39. Eighty-nine percent of the CIS group linked to care on the day of diagnosis versus 16% of the SOC group (RRCIS vs SOC = 9.13, 95% CI 1.65-50.40. There was no significant benefit of adding financial incentives to the CIS in terms of the combined outcome (55% of the CIS+ group achieved the primary outcome, RRCIS+ vs CIS = 0.96, 95% CI 0.81-1.16. Key limitations include the use of existing medical records to assess outcomes, the inability to isolate the effect of each component of the CIS, non-concurrent enrollment of the CIS+ group, and exclusion of many patients newly diagnosed with HIV.The CIS

  6. Improved self-management skills in Chinese diabetes patients through a comprehensive health literacy strategy: study protocol of a cluster randomized controlled trial.

    Science.gov (United States)

    Xu, Wang Hong; Rothman, Russell L; Li, Rui; Chen, Yingyao; Xia, Qinghua; Fang, Hong; Gao, Junling; Yan, Yujie; Zhou, Peng; Jiang, Yu; Liu, Yinan; Zhou, Fangjia; Wang, Wei; Chen, Minling; Liu, Xiao Yu; Liu, Xiao Na

    2014-12-20

    Diabetes self-management often involves the interpretation and application of oral, written, or quantitative information. Numerous diabetes patients in China have limited health literacy, which likely leads to poorer clinical outcomes. This study is designed to examine the efficacy and cost-effectiveness of addressing health literacy to improve self-management skills and glycemic control in Chinese diabetes patients. This is a cluster randomized controlled trial (RCT) conducted in 20 community healthcare sites in Shanghai, China. Overall, 800 diabetes patients will be randomized into intervention and control arms and will have a baseline hemoglobin A1c (HbA1c) assay and undergo a baseline survey which includes measures of health literacy and diabetes numeracy using revised Chinese versions of the Health Literacy Management Scale and Diabetes Numeracy Test Scale. During the 1-year period of intervention, while the control group will receive usual care, the intervention group will be supplemented with a comprehensive health literacy strategy which includes i) training healthcare providers in effective health communication skills that address issues related to low literacy, and ii) use of an interactive Diabetes Education Toolkit to improve patient understanding and behaviors. Assessments will be conducted at both patient and healthcare provider levels, and will take place upon admission and after 3, 6, 12, and 24 months of intervention. The primary outcome will be the improvement in HbA1c between Intervention group and Control group patients. Secondary outcomes at the patient level will include improvement in i) clinical outcomes (blood pressure, fasting lipids, body mass index, weight, smoking status), ii) patient reported self-management behaviors, and iii) patient-reported self-efficacy. Outcomes at the provider level will include: i) provider satisfaction and ii) intensity and type of care provided. The effects of the intervention will be examined in

  7. Improved thermostability and enzyme activity of a recombinant phyA mutant phytase from Aspergillus niger N25 by directed evolution and site-directed mutagenesis.

    Science.gov (United States)

    Tang, Zizhong; Jin, Weiqiong; Sun, Rong; Liao, Yan; Zhen, Tianrun; Chen, Hui; Wu, Qi; Gou, Lin; Li, Chenlei

    2018-01-01

    We previously constructed three recombinant phyA mutant strains (PP-NPm-8, PP-NPep-6A and I44E/T252R-PhyA), showing improved catalytic efficiency or thermostability of Aspergillus niger N25 phytase, by error-prone PCR or site-directed mutagenesis. In this study, directed evolution and site-directed mutagenesis were further applied to improve the modified phytase properties. After one-round error-prone PCR for phytase gene of PP-NPep-6A, a single transformant, T195L/Q368E/F376Y, was obtained with the significant improvements in catalytic efficiency and thermostability. The phytase gene of T195L/Q368E/F376Y, combined with the previous mutant phytase genes of PP-NPep-6A, PP-NPm-8 and I44E/T252R-PhyA, was then sequentially modified by DNA shuffling. Three genetically engineered strains with desirable properties were then obtained, namedQ172R, Q172R/K432R andQ368E/K432R. Among them, Q172R/K432R showed the highest thermostability with the longest half-life and the greatest remaining phytase activity after heat treatment, while Q368E/K432R showed the highest catalytic activity. Five substitutions (Q172R, T195L, Q368E, F376Y, K432R) identified from random mutagenesis were added sequentially to the phytase gene of PP-NPep-6A to investigate how the mutant sites influence the properties of phytase. Characterization and structural analysis demonstrated that these mutations could produce cumulative or synergistic improvements in thermostability or catalytic efficiency of phytase. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Integral strategy to supportive care in breast cancer survivors through occupational therapy and a m-health system: design of a randomized clinical trial.

    Science.gov (United States)

    Lozano-Lozano, Mario; Martín-Martín, Lydia; Galiano-Castillo, Noelia; Álvarez-Salvago, Francisco; Cantarero-Villanueva, Irene; Fernández-Lao, Carolina; Sánchez-Salado, Carmen; Arroyo-Morales, Manuel

    2016-11-25

    Technological support using e-health mobile applications (m-health) is a promising strategy to improve the adherence to healthy lifestyles in breast cancer survivors (excess in energy intake or low physical activity are determinants of the risk of recurrence, second cancers and cancer mortality). Moreover, cancer rehabilitation programs supervised by health professionals are needed due to the inherent characteristics of these breast cancer patients. Our main objective is to compare the clinical efficacy of a m-health lifestyle intervention system alone versus an integral strategy to improve Quality of Life in breast cancer survivors. This therapeutic superiority study will use a two-arm, assessor blinded parallel RCT design. Women will be eligible if: they are diagnosed of stage I, II or III-A breast cancer; are between 25 and 75 years old; have a Body Mass Index > 25 kg/m(2); they have basic ability to use mobile apps; they had completed adjuvant therapy except for hormone therapy; and they have some functional shoulder limitations. Participants will be randomized to one of the following groups: integral group will use a mobile application (BENECA APP) and will receive a face-to-face rehabilitation (8-weeks); m-health group will use the BENECA app for 2-months and will received usual care information. Study endpoints will be assessed after 8 weeks and 6 months. The primary outcome will be Quality of Life measured by The European Organization for Research and Treatment of Cancer Quality of Life Questionnaire Core and breast module. The secondary outcomes: body composition; upper-body functionality (handgrip, Disability of the Arm, Shoulder and Hand questionnaire, goniometry); cognitive function (Wechsler Adult Intelligence Scale, Trail Making Test); anxiety and depression (Hospital Anxiety and Depression Scale); physical fitness (Short version of the Minnesota Leisure Time Physical Activity Questionnaire, Self-Efficacy Scale for Physical Activity

  9. A cluster randomized Hybrid Type III trial testing an implementation support strategy to facilitate the use of an evidence-based practice in VA homeless programs.

    Science.gov (United States)

    Smelson, David A; Chinman, Matthew; McCarthy, Sharon; Hannah, Gordon; Sawh, Leon; Glickman, Mark

    2015-05-28

    The Housing and Urban Development-Veterans Affairs Supportive Housing (HUD-VASH) program is one of the largest initiatives to end Veteran homelessness. However, mental health and substance use disorders continue to reduce client stability and impede program success. HUD-VASH programs do not consistently employ evidence-based practices that address co-occurring mental health and substance use disorders. This paper presents a study protocol to evaluate the implementation of an evidence-based, co-occurring disorder treatment called Maintaining Independence and Sobriety Through Systems Integration, Outreach, and Networking-Veterans Edition (MISSION-Vet) in HUD-VASH using an implementation strategy called Getting To Outcomes (GTO). In three large VA Medical Centers, this Hybrid Type III trial will randomize case managers and their clients by HUD-VASH sub-teams to receive either MISSION-Vet Implementation as Usual (IU-standard training and access to the MISSION-Vet treatment manuals) or MISSION-Vet implementation augmented by GTO. In addition to testing GTO, effectiveness of the treatment (MISSION-Vet) will be assessed using existing Veteran-level data from the HUD-VASH data monitoring system. This project will compare GTO and IU case managers and their clients on the following variables: (1) fidelity to the MISSION-Vet intervention; (2) proportion of time the Veteran is housed; (3) mental health, substance use, and functional outcomes among Veterans; and (4) factors key to the successful deployment of a new treatment as specified by the Reach, Effectiveness, Adoption, Implementation, and Maintenance (RE-AIM) model. This project is an important step for developing an implementation strategy to increase adoption of evidence-based practice use in VA homeless programs, and to further examine efficacy of MISSION-Vet in HUD-VASH. This project has important implications for program managers, policy makers, and researchers within the homelessness field. VA Central IRB approval

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

    Science.gov (United States)

    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. PMID:27832146

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

    Directory of Open Access Journals (Sweden)

    Raymond Teck Ho Lee

    Full Text Available 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.

  12. Potential for Controlling Cholera Using a Ring Vaccination Strategy: Re-analysis of Data from a Cluster-Randomized Clinical Trial.

    Directory of Open Access Journals (Sweden)

    Mohammad Ali

    2016-09-01

    Full Text Available Vaccinating a buffer of individuals around a case (ring vaccination has the potential to target those who are at highest risk of infection, reducing the number of doses needed to control a disease. We explored the potential vaccine effectiveness (VE of oral cholera vaccines (OCVs for such a strategy.This analysis uses existing data from a cluster-randomized clinical trial in which OCV or placebo was given to 71,900 participants in Kolkata, India, from 27 July to 10 September 2006. Cholera surveillance was then conducted on 144,106 individuals living in the study area, including trial participants, for 5 y following vaccination. First, we explored the risk of cholera among contacts of cholera patients, and, second, we measured VE among individuals living within 25 m of cholera cases between 8 and 28 d after onset of the index case. For the first analysis, individuals living around each index case identified during the 5-y period were assembled using a ring to define cohorts of individuals exposed to cholera index cases. An index control without cholera was randomly selected for each index case from the same population, matched by age group, and individuals living around each index control were assembled using a ring to define cohorts not exposed to cholera cases. Cholera attack rates among the exposed and non-exposed cohorts were compared using different distances from the index case/control to define the rings and different time frames to define the period at risk. For the VE analysis, the exposed cohorts were further stratified according to the level of vaccine coverage into high and low coverage strata. Overall VE was assessed by comparing the attack rates between high and low vaccine coverage strata irrespective of individuals' vaccination status, and indirect VE was assessed by comparing the attack rates among unvaccinated members between high and low vaccine coverage strata. Cholera risk among the cohort exposed to cholera cases was 5

  13. Improvement of Coenzyme Q10 Production: Mutagenesis Induced by High Hydrostatic Pressure Treatment and Optimization of Fermentation Conditions

    Directory of Open Access Journals (Sweden)

    Yahong Yuan

    2012-01-01

    Full Text Available Coenzyme Q10 (CoQ10, ubiquinone, a potent antioxidative dietary supplement, was produced by submerged fermentation using Agrobacterium tumefaciens instead of chemical synthesis or solvent extraction. Agrobacterium tumefaciens 1.2554 was subjected to mutagenesis using a series of treatments including high hydrostatic pressure (HHP treatment, UV irradiation, and diethyl sulfate (DES treatment to obtain mutant strains showing higher CoQ10 production than wild-type strains. A mutant strain PK38 with four genetic markers was isolated: the specific CoQ10 content of the mutant strain increased by 52.83% compared with the original strain. Effects of carbon and nitrogen sources on CoQ10 production with PK38 were studied. Sucrose at concentration of 30 g/l was tested as the best carbon source, and yeast extract at concentration of 30 g/l supplemented with 10 g/l of ammonium sulfate was identified to be the most favorable for CoQ10 production using PK38. Fed-batch culture strategy was then used for increasing production of CoQ10 in 5-l fermentor. Using the exponential feeding fed-batch culture of sucrose, cell growth and CoQ10 formation were significantly improved. With this strategy, the final cell biomass, CoQ10 production, and specific CoQ10 production increased by 126.11, 173.12, and 22.76%, respectively, compared to those of batch culture.

  14. Unexpectedly high leprosy seroprevalence detected using a random surveillance strategy in midwestern Brazil: A comparison of ELISA and a rapid diagnostic test.

    Science.gov (United States)

    Frade, Marco Andrey C; de Paula, Natália A; Gomes, Ciro M; Vernal, Sebastian; Bernardes Filho, Fred; Lugão, Helena B; de Abreu, Marilda M M; Botini, Patrícia; Duthie, Malcolm S; Spencer, John S; Soares, Rosa Castália F R; Foss, Norma T

    2017-02-01

    Leprosy diagnosis is mainly based on clinical evaluation, although this approach is difficult, especially for untrained physicians. We conducted a temporary campaign to detect previously unknown leprosy cases in midwestern Brazil and to compare the performance of different serological tests. A mobile clinic was stationed at the main bus terminal in Brasília, Brazil. Volunteers were quizzed and given a clinical exam to allow categorization as either patients, known contacts of patients or non-contacts, and blood was collected to determine anti-PGL-I and anti-LID-1 antibody titers by ELISA and by the NDO-LID rapid test. New cases of leprosy and the impact of performing this broad random surveillance strategy were evaluated. Accuracy values and concordance between the test results were evaluated among all groups. Four hundred thirty-four individuals were evaluated, and 44 (10.1%) were diagnosed with leprosy. Borderline forms were the most frequent presentation. Both tests presented higher positivity in those individuals with multibacillary disease. Serological tests demonstrated specificities arround 70% for anti-PGL-1 and anti-LID ELISA; and arround 40% for NDO-LID. Sensitivities ranged from 48 to 62%. A substantial agreement between NDO-LID and ELISA with concomitant positive results was found within leprosy patients (Kappa index = 0.79 CI95% 0.36-1.22). The unexpectedly high leprosy prevalence in this population indicates ongoing community-based exposure to Mycobacterium leprae antigens and high rates of subclinical infection. All tests showed low specificity and sensitivity values and therefore cannot be considered for use as stand-alone diagnostics. Rather, considering their positivity among MB patients and non-patients, these tests can be considered effective tools for screening and identifying individuals at high risk who might benefit from regular monitoring.

  15. Effect of dose and dosing rate on the mutagenesis of nitric oxide in ...

    African Journals Online (AJOL)

    Effect of dose and dosing rate on the mutagenesis of nitric oxide in supF shuttle vector. Ji Hye Kim1 and ... Purpose: To determine how the dose and rate of NO• treatment affects mutagenic responses. Methods: Shuttle vector pSP189 was ... form a strong oxidant and nitrating agent, peroxynitrite (ONOO-), which can initiate.

  16. Highly efficient CRISPR/Cas9-mediated targeted mutagenesis of multiple genes in Populus.

    Science.gov (United States)

    Liu, Ting-ting; Fan, Di; Ran, Ling-yu; Jiang, Yuan-zhong; Liu, Rui; Luo, Ke-ming

    2015-10-01

    The typeⅡCRISPR/Cas9 system (Clustered regularly interspaced short palindromic repeats /CRISPR-associated 9) has been widely used in bacteria, yeast, animals and plants as a targeted genome editing technique. In previous work, we have successfully knocked out the endogenous phytoene dehydrogenase (PDS) gene in Populus tomentosa Carr. using this system. To study the effect of target design on the efficiency of CRISPR/Cas9-mediated gene knockout in Populus, we analyzed the efficiency of mutagenesis using different single-guide RNA (sgRNA) that target PDS DNA sequence. We found that mismatches between the sgRNA and the target DNA resulted in decreased efficiency of mutagenesis and even failed mutagenesis. Moreover, complementarity between the 3' end nucleotide of sgRNA and target DNA is especially crucial for efficient mutagenesis. Further sequencing analysis showed that two PDS homologs in Populus, PtPDS1 and PtPDS2, could be knocked out simultaneously using this system with 86.4% and 50% efficiency, respectively. These results indicated the possibility of introducing mutations in two or more endogenous genes efficiently and obtaining multi-mutant strains of Populus using this system. We have indeed generated several knockout mutants of transcription factors and structural genes in Populus, which establishes a foundation for future studies of gene function and genetic improvement of Populus.

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

    NARCIS (Netherlands)

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

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

  18. 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.

  19. Mutagenesis effects of X-irradiation on the germination, growth and ...

    African Journals Online (AJOL)

    The time of exposure and mutagenesis effects of X-ray on the germination, growth and development of maize (Zea mays) seeds have been investigated employing a nuclear source, (90Sr as X-ray source; 3mA, 70kv). Five sects of zea mays seeds in different packs were irradiated in different times of exposure and later ...

  20. Bromination of deoxycytidine by eosinophil peroxidase: A mechanism for mutagenesis by oxidative damage of nucleotide precursors

    OpenAIRE

    Henderson, Jeffrey P.; Byun, Jaeman; Williams, Michelle V.; McCormick, Michael L.; Parks, William C.; Ridnour, Lisa A.; Heinecke, Jay W.

    2001-01-01

    Oxidants generated by eosinophils during chronic inflammation may lead to mutagenesis in adjacent epithelial cells. Eosinophil peroxidase, a heme enzyme released by eosinophils, generates hypobromous acid that damages tissue in inflammatory conditions. We show that human eosinophils use eosinophil peroxidase to produce 5-bromodeoxycytidine. Flow cytometric, immunohistochemical, and mass spectrometric analyses all demonstrated that 5-bromodeoxycytidine generated by ...

  1. Mutagenesis Objective Search and Selection Tool (MOSST: an algorithm to predict structure-function related mutations in proteins

    Directory of Open Access Journals (Sweden)

    Asenjo Juan A

    2011-04-01

    Full Text Available Abstract Background Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships. Results A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein

  2. Comprehensive Essentiality Analysis of the Mycobacterium tuberculosis Genome via Saturating Transposon Mutagenesis.

    Science.gov (United States)

    DeJesus, Michael A; Gerrick, Elias R; Xu, Weizhen; Park, Sae Woong; Long, Jarukit E; Boutte, Cara C; Rubin, Eric J; Schnappinger, Dirk; Ehrt, Sabine; Fortune, Sarah M; Sassetti, Christopher M; Ioerger, Thomas R

    2017-01-17

    For decades, identifying the regions of a bacterial chromosome that are necessary for viability has relied on mapping integration sites in libraries of random transposon mutants to find loci that are unable to sustain insertion. To date, these studies have analyzed subsaturated libraries, necessitating the application of statistical methods to estimate the likelihood that a gap in transposon coverage is the result of biological selection and not the stochasticity of insertion. As a result, the essentiality of many genomic features, particularly small ones, could not be reliably assessed. We sought to overcome this limitation by creating a completely saturated transposon library in Mycobacterium tuberculosis In assessing the composition of this highly saturated library by deep sequencing, we discovered that a previously unknown sequence bias of the Himar1 element rendered approximately 9% of potential TA dinucleotide insertion sites less permissible for insertion. We used a hidden Markov model of essentiality that accounted for this unanticipated bias, allowing us to confidently evaluate the essentiality of features that contained as few as 2 TA sites, including open reading frames (ORF), experimentally identified noncoding RNAs, methylation sites, and promoters. In addition, several essential regions that did not correspond to known features were identified, suggesting uncharacterized functions that are necessary for growth. This work provides an authoritative catalog of essential regions of the M. tuberculosis genome and a statistical framework for applying saturating mutagenesis to other bacteria. Sequencing of transposon-insertion mutant libraries has become a widely used tool for probing the functions of genes under various conditions. The Himar1 transposon is generally believed to insert with equal probabilities at all TA dinucleotides, and therefore its absence in a mutant library is taken to indicate biological selection against the corresponding mutant

  3. Efficient gene-driven germ-line point mutagenesis of C57BL/6J mice

    Directory of Open Access Journals (Sweden)

    Hughes Lori A

    2005-11-01

    Full Text Available Abstract Background Analysis of an allelic series of point mutations in a gene, generated by N-ethyl-N-nitrosourea (ENU mutagenesis, is a valuable method for discovering the full scope of its biological function. Here we present an efficient gene-driven approach for identifying ENU-induced point mutations in any gene in C57BL/6J mice. The advantage of such an approach is that it allows one to select any gene of interest in the mouse genome and to go directly from DNA sequence to mutant mice. Results We produced the Cryopreserved Mutant Mouse Bank (CMMB, which is an archive of DNA, cDNA, tissues, and sperm from 4,000 G1 male offspring of ENU-treated C57BL/6J males mated to untreated C57BL/6J females. Each mouse in the CMMB carries a large number of random heterozygous point mutations throughout the genome. High-throughput Temperature Gradient Capillary Electrophoresis (TGCE was employed to perform a 32-Mbp sequence-driven screen for mutations in 38 PCR amplicons from 11 genes in DNA and/or cDNA from the CMMB mice. DNA sequence analysis of heteroduplex-forming amplicons identified by TGCE revealed 22 mutations in 10 genes for an overall mutation frequency of 1 in 1.45 Mbp. All 22 mutations are single base pair substitutions, and nine of them (41% result in nonconservative amino acid substitutions. Intracytoplasmic sperm injection (ICSI of cryopreserved spermatozoa into B6D2F1 or C57BL/6J ova was used to recover mutant mice for nine of the mutations to date. Conclusions The inbred C57BL/6J CMMB, together with TGCE mutation screening and ICSI for the recovery of mutant mice, represents a valuable gene-driven approach for the functional annotation of the mammalian genome and for the generation of mouse models of human genetic diseases. The ability of ENU to induce mutations that cause various types of changes in proteins will provide additional insights into the functions of mammalian proteins that may not be detectable by knockout mutations.

  4. A cluster-randomized controlled trial of strategies to increase adolescents' physical activity and motivation during physical education lessons: the Motivating Active Learning in Physical Education (MALP) trial

    National Research Council Canada - National Science Library

    Rosenkranz, Richard R; Lubans, David R; Peralta, Louisa R; Bennie, Andrew; Sanders, Taren; Lonsdale, Chris

    2012-01-01

    ... intervention studies have examined motivational strategies in PE. The purpose of this study was to compare the effect of three motivational strategies, each based on Self-Determination Theory (SDT...

  5. Gene-scrambling mutagenesis: generation and analysis of insertional mutations in the alginate regulatory region of Pseudomonas aeruginosa.

    Science.gov (United States)

    Mohr, C D; Deretic, V

    1990-11-01

    A novel method for random mutagenesis of targeted chromosomal regions in Pseudomona aeruginosa was developed. This method can be used with a cloned DNA fragment of indefinite size that contains a putative gene of interest. Cloned DNA is digested to produce small fragments that are then randomly reassembled into long DNA inserts by using cosmid vectors and lambda packaging reaction. This DNA is then transferred into P. aeruginosa and forced into the chromosome via homologous recombination, producing in a single step a random set of insertional mutants along a desired region of the chromosome. Application of this method to extend the analysis of the alginate regulatory region, using a cloned 6.2-kb fragment with the algR gene and the previously uncharacterized flanking regions, produced several insertional mutations. One mutation was obtained in algR, a known transcriptional regulatory of mucoidy in P. aeruginosa. The null mutation of algR was generated in a mucoid derivative of the standard genetic strain PAO responsive to different environmental factors. This mutation was used to demonstrate that the algR gene product was not essential for the regulation of its promoters. Additional insertions were obtained in regions downstream and upstream of algR. A mutation that did not affect mucoidy was generated in a gene located 1 kb upstream of algR. This gene was transcribed in the direction opposite that of algR transcription and encoded a polypeptide of 47 kDa. Partial nucleotide sequence analysis revealed strong homology of its predicted gene product with the human and yeast argininosuccinate lyases. An insertion downstream of algR produced a strain showing reduced induction of mucoidy in response to growth on nitrate as the nitrogen source.

  6. Use of pentapeptide-insertion scanning mutagenesis for functional mapping of the plum pox virus helper component proteinase suppressor of gene silencing.

    Science.gov (United States)

    Varrelmann, Mark; Maiss, Edgar; Pilot, Ruth; Palkovics, Laszlo

    2007-03-01

    Helper component proteinase (HC-Pro) of Plum pox virus is a multifunctional potyvirus protein that has been examined intensively. In addition to its involvement in aphid transmission, genome amplification and long-distance movement, it is also one of the better-studied plant virus suppressors of RNA silencing. The first systematic analysis using pentapeptide-insertion scanning mutagenesis of the silencing suppression function of a potyvirus HC-Pro is presented here. Sixty-three in-frame insertion mutants, each containing five extra amino acids inserted randomly within the HC-Pro protein, were analysed for their ability to suppress transgene-induced RNA silencing using Agrobacterium infiltration in transgenic Nicotiana benthamiana plants expressing green fluorescent protein. A functional map was obtained, consisting of clearly defined regions with different classes of silencing-suppression activity (wild-type, restricted and disabled). This map confirmed that the N-terminal part of the protein, which is indispensable for aphid transmission, is dispensable for silencing suppression and supports the involvement of the central region in silencing suppression, in addition to its role in maintenance of genome amplification and synergism with other viruses. Moreover, evidence is provided that the C-terminal part of the protein, previously known to be necessary mainly for proteolytic activity, also participates in silencing suppression. Pentapeptide-insertion scanning mutagenesis has been shown to be a fast and powerful tool to functionally characterize plant virus proteins.

  7. Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates.

    Science.gov (United States)

    Sanchis, Joaquin; Fernández, Layla; Carballeira, J Daniel; Drone, Jullien; Gumulya, Yosephine; Höbenreich, Horst; Kahakeaw, Daniel; Kille, Sabrina; Lohmer, Renate; Peyralans, Jérôme J-P; Podtetenieff, John; Prasad, Shreenath; Soni, Pankaj; Taglieber, Andreas; Wu, Sheng; Zilly, Felipe E; Reetz, Manfred T

    2008-11-01

    Saturation mutagenesis constitutes a powerful method in the directed evolution of enzymes. Traditional protocols of whole plasmid amplification such as Stratagene's QuikChange sometimes fail when the templates are difficult to amplify. In order to overcome such restrictions, we have devised a simple two-primer, two-stage polymerase chain reaction (PCR) method which constitutes an improvement over existing protocols. In the first stage of the PCR, both the mutagenic primer and the antiprimer that are not complementary anneal to the template. In the second stage, the amplified sequence is used as a megaprimer. Sites composed of one or more residues can be randomized in a single PCR reaction, irrespective of their location in the gene sequence.The method has been applied to several enzymes successfully, including P450-BM3 from Bacillus megaterium, the lipases from Pseudomonas aeruginosa and Candida antarctica and the epoxide hydrolase from Aspergillus niger. Here, we show that megaprimer size as well as the direction and design of the antiprimer are determining factors in the amplification of the plasmid. Comparison of the results with the performances of previous protocols reveals the efficiency of the improved method.

  8. Enhancement of the lipid productivity and fatty acid methyl ester profile of Chlorella vulgaris by two rounds of mutagenesis.

    Science.gov (United States)

    Sarayloo, Ehsan; Simsek, Salim; Unlu, Yigit Sabri; Cevahir, Gul; Erkey, Can; Kavakli, Ibrahim Halil

    2017-12-02

    In this study, we applied a second round of random mutagenesis using ethyl methanesulfonate to further increase the lipid productivity of a Chlorella vulgaris mutant strain. We generated a mutant (UV715-EMS25) with a lipid content and biomass that were respectively 67% and 35% higher than those of the wild type (WT). The highest achieved lipid productivity in UV715-EMS25 was 91 mg L-1 day-1. Gas chromatography-mass spectrophotometric analysis revealed that the fatty acid methyl ester content of the mutant was 3.9-fold higher compared with that of WT cells. Amounts of saturated and monounsaturated fatty acids were also higher in the mutant, while the total amounts of polyunsaturated fatty acids were lower. Finally, the mutant displayed superior lipid productivity compared with the WT during pilot-scale cultivation in a flat panel photobioreactor. All these results demonstrate that UV715-EMS25 is highly suitable for biodiesel production. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Transposon mutagenesis identifies chromatin modifiers cooperating with Ras in thyroid tumorigenesis and detects ATXN7 as a cancer gene.

    Science.gov (United States)

    Montero-Conde, Cristina; Leandro-Garcia, Luis J; Chen, Xu; Oler, Gisele; Ruiz-Llorente, Sergio; Ryder, Mabel; Landa, Iñigo; Sanchez-Vega, Francisco; La, Konnor; Ghossein, Ronald A; Bajorin, Dean F; Knauf, Jeffrey A; Riordan, Jesse D; Dupuy, Adam J; Fagin, James A

    2017-06-20

    Oncogenic RAS mutations are present in 15-30% of thyroid carcinomas. Endogenous expression of mutant Ras is insufficient to initiate thyroid tumorigenesis in murine models, indicating that additional genetic alterations are required. We used Sleeping Beauty (SB) transposon mutagenesis to identify events that cooperate with Hras(G12V) in thyroid tumor development. Random genomic integration of SB transposons primarily generated loss-of-function events that significantly increased thyroid tumor penetrance in Tpo-Cre/homozygous FR-Hras(G12V) mice. The thyroid tumors closely phenocopied the histological features of human RAS-driven, poorly differentiated thyroid cancers. Characterization of transposon insertion sites in the SB-induced tumors identified 45 recurrently mutated candidate cancer genes. These mutation profiles were remarkably concordant with mutated cancer genes identified in a large series of human poorly differentiated and anaplastic thyroid cancers screened by next-generation sequencing using the MSK-IMPACT panel of cancer genes, which we modified to include all SB candidates. The disrupted genes primarily clustered in chromatin remodeling functional nodes and in the PI3K pathway. ATXN7, a component of a multiprotein complex with histone acetylase activity, scored as a significant SB hit. It was recurrently mutated in advanced human cancers and significantly co-occurred with RAS or NF1 mutations. Expression of ATXN7 mutants cooperated with oncogenic RAS to induce thyroid cell proliferation, pointing to ATXN7 as a previously unrecognized cancer gene.

  10. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger.

    Science.gov (United States)

    Hu, Wei; Li, Wenjian; Chen, Hao; Liu, Jing; Wang, Shuyang; Chen, Jihong

    2017-01-01

    The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.

  11. Changes in transcript levels of starch hydrolysis genes and raising citric acid production via carbon ion irradiation mutagenesis of Aspergillus niger.

    Directory of Open Access Journals (Sweden)

    Wei Hu

    Full Text Available The filamentous ascomycete Aspergillus niger is well known for its ability to accumulate citric acid for the hydrolysis of starchy materials. To improve citric acid productivity, heavy ion beam mutagenesis was utilized to produce mutant A.niger strains with enhanced production of citric acid in this work. It was demonstrated that a mutant HW2 with high concentration of citric acid was isolated after carbon ion irradiation with the energy of 80Mev/μ, which was obvious increase higher than the original strain from liquefied corn starch as a feedstock. More importantly, with the evidence from the expression profiles of key genes and enzyme activity involved in the starch hydrolysis process between original strain and various phenotype mutants, our results confirmed that different transcript levels of key genes involving in starch hydrolysis process between original strain and mutants could be a significant contributor to different citric acid concentration in A.niger, such as, amyR and glaA, which therefore opened a new avenue for constructing genetically engineered A.niger mutants for high-yield citric acid accumulation in the future. As such, this work demonstrated that heavy ion beam mutagenesis presented an efficient alternative strategy to be developed to generate various phenotype microbe species mutants for functional genes research.

  12. ENU Mutagenesis Screen to Establish Motor Phenotypes in Wild-Type Mice and Modifiers of a Pre-Existing Motor Phenotype in Tau Mutant Mice

    Directory of Open Access Journals (Sweden)

    Xin Liu

    2011-01-01

    Full Text Available Modifier screening is a powerful genetic tool. While not widely used in the vertebrate system, we applied these tools to transgenic mouse strains that recapitulate key aspects of Alzheimer’s disease (AD, such as tau-expressing mice. These are characterized by a robust pathology including both motor and memory impairment. The phenotype can be modulated by ENU mutagenesis, which results in novel mutant mouse strains and allows identifying the underlying gene/mutation. Here we discuss this strategy in detail. We firstly obtained pedigrees that modify the tau-related motor phenotype, with mapping ongoing. We further obtained transgene-independent motor pedigrees: (i hyperactive, circling ENU 37 mice with a causal mutation in the Tbx1 gene—the complete knock-out of Tbx1 models DiGeorge Syndrome; (ii ENU12/301 mice that show sudden jerky movements and tremor constantly; they have a causal mutation in the Kcnq1 gene, modelling aspects of the Romano-Ward and Jervell and Lange-Nielsen syndromes; and (iii ENU16/069 mice with tremor and hypermetric gait that have a causal mutation in the Mpz (Myelin Protein Zero gene, modelling Charcot-Marie-Tooth disease type 1 (CMT1B. Together, we provide evidence for a real potential of an ENU mutagenesis to dissect motor functions in wild-type and tau mutant mice.

  13. Scarless and site-directed mutagenesis in Salmonella enteritidis chromosome

    Directory of Open Access Journals (Sweden)

    Berghman Luc R

    2007-09-01

    Full Text Available Abstract Background A variety of techniques have been described which introduce scarless, site-specific chromosomal mutations. These techniques can be applied to make point mutations or gene deletions as well as insert heterologous DNA into bacterial vectors for vaccine development. Most methods use a multi-step approach that requires cloning and/or designing repeat sequences to facilitate homologous recombination. We have modified previously published techniques to develop a simple, efficient PCR-based method for scarless insertion of DNA into Salmonella enteritidis chromosome. Results The final product of this mutation strategy is the insertion of DNA encoding a foreign epitope into the S. enteritidis genome without the addition of any unwanted sequence. This experiment was performed by a two-step mutation process via PCR fragments, Red recombinase and counter-selection with the I-SceI enzyme site. First, the I-SceI site and kanamycin resistance gene were introduced into the genome of cells expressing Red recombinase enzymes. Next, this sequence was replaced by a chosen insertion sequence. DNA fragments used for recombination were linear PCR products which consisted of the foreign insertion sequence flanked by homologous sequences of the target gene. Described herein is the insertion of a section of the M2e epitope (LM2 of Influenza A virus, a domain of CD154 (CD154s or a combination of both into the outer membrane protein LamB of S. enteritidis. Conclusion We have successfully used this method to produce multiple mutants with no antibiotic gene on the genome or extra sequence except those nucleotides required for expression of epitope regions. This method is advantageous over other protocols in that it does not require cloning or creating extra duplicate regions to facilitate homologous recombination, contains a universal construct in which an epitope of choice can be placed to check for cell surface expression, and shows high efficiency when

  14. Potential high-frequency off-target mutagenesis induced by CRISPR/Cas9 in Arabidopsis and its prevention.

    Science.gov (United States)

    Zhang, Qiang; Xing, Hui-Li; Wang, Zhi-Ping; Zhang, Hai-Yan; Yang, Fang; Wang, Xue-Chen; Chen, Qi-Jun

    2018-02-23

    We present novel observations of high-specificity SpCas9 variants, sgRNA expression strategies based on mutant sgRNA scaffold and tRNA processing system, and CRISPR/Cas9-mediated T-DNA integrations. Specificity of CRISPR/Cas9 tools has been a major concern along with the reports of their successful applications. We report unexpected observations of high frequency off-target mutagenesis induced by CRISPR/Cas9 in T1 Arabidopsis mutants although the sgRNA was predicted to have a high specificity score. We also present evidence that the off-target effects were further exacerbated in the T2 progeny. To prevent the off-target effects, we tested and optimized two strategies in Arabidopsis, including introduction of a mCherry cassette for a simple and reliable isolation of Cas9-free mutants and the use of highly specific mutant SpCas9 variants. Optimization of the mCherry vectors and subsequent validation found that fusion of tRNA with the mutant rather than the original sgRNA scaffold significantly improves editing efficiency. We then examined the editing efficiency of eight high-specificity SpCas9 variants in combination with the improved tRNA-sgRNA fusion strategy. Our results suggest that highly specific SpCas9 variants require a higher level of expression than their wild-type counterpart to maintain high editing efficiency. Additionally, we demonstrate that T-DNA can be inserted into the cleavage sites of CRISPR/Cas9 targets with high frequency. Altogether, our results suggest that in plants, continuous attention should be paid to off-target effects induced by CRISPR/Cas9 in current and subsequent generations, and that the tools optimized in this report will be useful in improving genome editing efficiency and specificity in plants and other organisms.

  15. The Bypass Angioplasty Revascularization Investigation 2 Diabetes randomized trial of different treatment strategies in type 2 diabetes mellitus with stable ischemic heart disease: impact of treatment strategy on cardiac mortality and myocardial infarction

    National Research Council Canada - National Science Library

    Chaitman, Bernard R; Hardison, Regina M; Adler, Dale; Gebhart, Suzanne; Grogan, Mary; Ocampo, Salvador; Sopko, George; Ramires, Jose A; Schneider, David; Frye, Robert L

    2009-01-01

    ...-cause mortality rates with insulin sensitization versus insulin provision therapy and with a strategy of prompt initial coronary revascularization and intensive medical therapy or intensive medical...

  16. Improving ethanol fermentation performance of Saccharomyces cerevisiae in very high-gravity fermentation through chemical mutagenesis and meiotic recombination

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Jing-Jing; Ding, Wen-Tao; Zhang, Guo-Chang; Wang, Jing-Yu [Tianjin Univ. (China). Dept. of Biochemical Engineering

    2011-08-15

    Genome shuffling is an efficient way to improve complex phenotypes under the control of multiple genes. For the improvement of strain's performance in very high-gravity (VHG) fermentation, we developed a new method of genome shuffling. A diploid ste2/ste2 strain was subjected to EMS (ethyl methanesulfonate) mutagenesis followed by meiotic recombination-mediated genome shuffling. The resulting haploid progenies were intrapopulation sterile and therefore haploid recombinant cells with improved phenotypes were directly selected under selection condition. In VHG fermentation, strain WS1D and WS5D obtained by this approach exhibited remarkably enhanced tolerance to ethanol and osmolarity, increased metabolic rate, and 15.12% and 15.59% increased ethanol yield compared to the starting strain W303D, respectively. These results verified the feasibility of the strain improvement strategy and suggested that it is a powerful and high throughput method for development of Saccharomyces cerevisiae strains with desired phenotypes that is complex and cannot be addressed with rational approaches. (orig.)

  17. High-Throughput Sequencing and Mutagenesis to Accelerate the Domestication of Microlaena stipoides as a New Food Crop

    Science.gov (United States)

    Shapter, Frances M.; Cross, Michael; Ablett, Gary; Malory, Sylvia; Chivers, Ian H.; King, Graham J.; Henry, Robert J.

    2013-01-01

    Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae), was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD97) of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops. PMID:24367532

  18. High-throughput sequencing and mutagenesis to accelerate the domestication of Microlaena stipoides as a new food crop.

    Directory of Open Access Journals (Sweden)

    Frances M Shapter

    Full Text Available Global food demand, climatic variability and reduced land availability are driving the need for domestication of new crop species. The accelerated domestication of a rice-like Australian dryland polyploid grass, Microlaena stipoides (Poaceae, was targeted using chemical mutagenesis in conjunction with high throughput sequencing of genes for key domestication traits. While M. stipoides has previously been identified as having potential as a new grain crop for human consumption, only a limited understanding of its genetic diversity and breeding system was available to aid the domestication process. Next generation sequencing of deeply-pooled target amplicons estimated allelic diversity of a selected base population at 14.3 SNP/Mb and identified novel, putatively mutation-induced polymorphisms at about 2.4 mutations/Mb. A 97% lethal dose (LD₉₇ of ethyl methanesulfonate treatment was applied without inducing sterility in this polyploid species. Forward and reverse genetic screens identified beneficial alleles for the domestication trait, seed-shattering. Unique phenotypes observed in the M2 population suggest the potential for rapid accumulation of beneficial traits without recourse to a traditional cross-breeding strategy. This approach may be applicable to other wild species, unlocking their potential as new food, fibre and fuel crops.

  19. An efficient method for multiple site-directed mutagenesis using type IIs restriction enzymes.

    Science.gov (United States)

    Zhang, Zhiqiang; Xu, Kun; Xin, Ying; Zhang, Zhiying

    2015-05-01

    Site-directed mutagenesis (SDM) methods are very important in modern molecular biology, biochemistry, and protein engineering. Here, we present a novel SDM method that can be used for multiple mutation generation using type IIs restriction enzymes. This approach is faster and more convenient than the overlap polymerase chain reaction (PCR) method due to its having fewer reaction steps and being cheaper than, but as convenient as, enzymatic assembly. We illustrate the usefulness of our method by introducing three mutations into the bacterial Streptococcus thermophilus Cas9 (bStCas9) gene, converting the humanized S. thermophilus Cas9 (hStCas9) gene into nuclease dead or H847A nickase mutants and generating sunnyTALEN mutagenesis from a wild-type TALEN backbone. Copyright © 2015 Elsevier Inc. All rights reserved.

  20. Transposon mutagenesis identifies genes that cooperate with mutant Pten in breast cancer progression

    Science.gov (United States)

    Rangel, Roberto; Lee, Song-Choon; Hon-Kim Ban, Kenneth; Guzman-Rojas, Liliana; Mann, Michael B.; Newberg, Justin Y.; McNoe, Leslie A.; Selvanesan, Luxmanan; Ward, Jerrold M.; Rust, Alistair G.; Chin, Kuan-Yew; Black, Michael A.; Jenkins, Nancy A.; Copeland, Neal G.

    2016-01-01

    Triple-negative breast cancer (TNBC) has the worst prognosis of any breast cancer subtype. To better understand the genetic forces driving TNBC, we performed a transposon mutagenesis screen in a phosphatase and tensin homolog (Pten) mutant mice and identified 12 candidate trunk drivers and a much larger number of progression genes. Validation studies identified eight TNBC tumor suppressor genes, including the GATA-like transcriptional repressor TRPS1. Down-regulation of TRPS1 in TNBC cells promoted epithelial-to-mesenchymal transition (EMT) by deregulating multiple EMT pathway genes, in addition to increasing the expression of SERPINE1 and SERPINB2 and the subsequent migration, invasion, and metastasis of tumor cells. Transposon mutagenesis has thus provided a better understanding of the genetic forces driving TNBC and discovered genes with potential clinical importance in TNBC. PMID:27849608

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

    Directory of Open Access Journals (Sweden)

    Robyn N. Hall

    2012-02-01

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

  2. Cell-mediated mutagenesis and cell transformation of mammalian cells by chemical carcinogens. [Rats, hamsters

    Energy Technology Data Exchange (ETDEWEB)

    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.

  3. Model of SOS-induced mutagenesis in bacteria Escherichia coli under ultraviolet irradiation.

    Science.gov (United States)

    Belov, Oleg V; Krasavin, Evgeny A; Parkhomenko, Alexander Yu

    2009-12-07

    A mathematical model of the mutation process in bacteria Escherichia coli induced by ultraviolet radiation is developed. Our model is based on the experimental data characterizing the main processes of the bacterial SOS response. Here we have modeled a whole sequence of the events leading to the fixation of the primary DNA lesion as a point mutation. A quantitative analysis of the key ways of the SOS mutagenesis was performed in terms of modern system biology. The dynamic changes of the basic SOS protein concentrations and the process of the translesion synthesis by the modified replication complex are described quantitatively. We have also demonstrated the applicability of the developed model to the description of the mutagenesis in individual genes. As an example, an estimation of the mutation frequency in E. coli's lacI gene is performed.

  4. Altered lipid accumulation in Nannochloropsis salina CCAP849/3 following EMS and UV induced mutagenesis

    Directory of Open Access Journals (Sweden)

    T.A. Beacham

    2015-09-01

    Full Text Available Microalgae have potential as a chemical feed stock in a range of industrial applications. Nannochloropsis salina was subject to EMS mutagenesis and the highest lipid containing cells selected using fluorescence-activated cell sorting. Assessment of growth, lipid content and fatty acid composition identified mutant strains displaying a range of altered traits including changes in the PUFA content and a total FAME increase of up to 156% that of the wild type strain. Combined with a reduction in growth this demonstrated a productivity increase of up to 76%. Following UV mutagenesis, lipid accumulation of the mutant cultures was elevated to more than 3 fold that of the wild type strain, however reduced growth rates resulted in a reduction in overall productivity. Changes observed are indicative of alterations to the regulation of the omega 6 Kennedy pathway. The importance of these variations in physiology for industrial applications such as biofuel production is discussed.

  5. Bromination of deoxycytidine by eosinophil peroxidase: A mechanism for mutagenesis by oxidative damage of nucleotide precursors

    Science.gov (United States)

    Henderson, Jeffrey P.; Byun, Jaeman; Williams, Michelle V.; McCormick, Michael L.; Parks, William C.; Ridnour, Lisa A.; Heinecke, Jay W.

    2001-01-01

    Oxidants generated by eosinophils during chronic inflammation may lead to mutagenesis in adjacent epithelial cells. Eosinophil peroxidase, a heme enzyme released by eosinophils, generates hypobromous acid that damages tissue in inflammatory conditions. We show that human eosinophils use eosinophil peroxidase to produce 5-bromodeoxycytidine. Flow cytometric, immunohistochemical, and mass spectrometric analyses all demonstrated that 5-bromodeoxycytidine generated by eosinophil peroxidase was taken up by cultured cells and incorporated into genomic DNA as 5-bromodeoxyuridine. Although previous studies have focused on oxidation of chromosomal DNA, our observations suggest another mechanism for oxidative damage of DNA. In this scenario, peroxidase-catalyzed halogenation of nucleotide precursors yields products that subsequently can be incorporated into DNA. Because the thymine analog 5-BrUra mispairs with guanine in DNA, generation of brominated pyrimidines by eosinophils might constitute a mechanism for cytotoxicity and mutagenesis at sites of inflammation. PMID:11172002

  6. Altered lipid accumulation in Nannochloropsis salina CCAP849/3 following EMS and UV induced mutagenesis.

    Science.gov (United States)

    Beacham, T A; Macia, V Mora; Rooks, P; White, D A; Ali, S T

    2015-09-01

    Microalgae have potential as a chemical feed stock in a range of industrial applications. Nannochloropsis salina was subject to EMS mutagenesis and the highest lipid containing cells selected using fluorescence-activated cell sorting. Assessment of growth, lipid content and fatty acid composition identified mutant strains displaying a range of altered traits including changes in the PUFA content and a total FAME increase of up to 156% that of the wild type strain. Combined with a reduction in growth this demonstrated a productivity increase of up to 76%. Following UV mutagenesis, lipid accumulation of the mutant cultures was elevated to more than 3 fold that of the wild type strain, however reduced growth rates resulted in a reduction in overall productivity. Changes observed are indicative of alterations to the regulation of the omega 6 Kennedy pathway. The importance of these variations in physiology for industrial applications such as biofuel production is discussed.

  7. Controlling mutation: intervening in evolution as a therapeutic strategy.

    Science.gov (United States)

    Cirz, Ryan T; Romesberg, Floyd E

    2007-01-01

    Mutation is the driving force behind many processes linked to human disease, including cancer, aging, and the evolution of drug resistance. Mutations have traditionally been considered the inevitable consequence of replicating large genomes with polymerases of finite fidelity. Observations over the past several decades, however, have led to a new perspective on the process of mutagenesis. It has become clear that, under some circumstances, mutagenesis is a regulated process that requires the induction of pro-mutagenic enzymes and that, at least in bacteria, this induction may facilitate evolution. Herein, we review what is known about induced mutagenesis in bacteria as well as evidence that it contributes to the evolution of antibiotic resistance. Finally, we discuss the possibility that components of induced mutation pathways might be targeted for inhibition as a novel therapeutic strategy to prevent the evolution of antibiotic resistance.

  8. Self-Regulated Strategy Development at Tier 2 for Second-Grade Students with Writing and Behavioral Difficulties: A Randomized Controlled Trial

    Science.gov (United States)

    Lane, Kathleen Lynne; Harris, Karen; Graham, Steve; Driscoll, Steven; Sandmel, Karin; Morphy, Paul; Hebert, Michael; House, Emily; Schatschneider, Christopher

    2011-01-01

    We examined the extent to which strategies instruction, using the Self-Regulated Strategy Development (SRSD) model, would enhance the writing, engagement during writing, and behavior of 44 second-grade students identified as having behavioral and writing difficulties. This study occurred within a comprehensive, integrated, three-tiered model of…

  9. Hands4U: the effects of a multifaceted implementation strategy on hand eczema prevalence in a healthcare setting. Results of a randomized controlled trial

    NARCIS (Netherlands)

    Meer, E.W. van der; Boot, C.R.; Gulden, J.W.J. van der; Knol, D.L.; Jungbauer, F.H.; Coenraads, P.J.; Anema, J.R.

    2015-01-01

    BACKGROUND: Healthcare workers have an increased risk of developing hand eczema. A multifaceted implementation strategy was developed to implement a guideline to prevent hand eczema among healthcare workers. OBJECTIVES: To investigate the effects of the implementation strategy on self-reported hand

  10. Hands4U: the effects of a multifaceted implementation strategy on hand eczema prevalence in a healthcare setting. Results of a randomized controlled trial

    NARCIS (Netherlands)

    van der Meer, E.W.C.; Boot, C.R.L.; van der Gulden, J.W.J.; Knol, D.L.; Jungbauer, F.H.W.; Coenraads, P.J.; Anema, J.R.

    2015-01-01

    Background Healthcare workers have an increased risk of developing hand eczema. A multifaceted implementation strategy was developed to implement a guideline to prevent hand eczema among healthcare workers. Objectives To investigate the effects of the implementation strategy on self-reported hand

  11. Hands4U : the effects of a multifaceted implementation strategy on hand eczema prevalence in a healthcare setting. Results of a randomized controlled trial

    NARCIS (Netherlands)

    van der Meer, Esther W. C.; Boot, Cecile R. L.; van der Gulden, Joost W. J.; Knol, Dirk L.; Jungbauer, Frank H. W.; Coenraads, Pieter Jan; Anema, Johannes R.

    Background. Healthcare workers have an increased risk of developing hand eczema. A multifaceted implementation strategy was developed to implement a guideline to prevent hand eczema among healthcare workers. Objectives. To investigate the effects of the implementation strategy on self-reported hand

  12. Prevention of mutagenesis: new potential mechanisms of metformin action in neoplastic cells.

    Science.gov (United States)

    Bost, Frédéric; Ben-Sahra, Issam; Tanti, Jean-François

    2012-04-01

    Several experimental and epidemiologic studies have shown that the antidiabetes drug metformin has antitumor properties. The report by Algire and colleagues in this issue of the journal (beginning on page 536) shows for the first time that metformin reduces mutagenesis induced by reactive oxygen species. This report offers new perspectives on metformin in cancer prevention and provides a new mechanism for the reduction of cancer risk in diabetic patients treated with this drug. 2012 AACR

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

    OpenAIRE

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

    2006-01-01

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

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

    OpenAIRE

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

    2008-01-01

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

  15. mtDNA Mutagenesis Disrupts Pluripotent Stem Cell Function by Altering Redox Signaling

    Directory of Open Access Journals (Sweden)

    Riikka H. Hämäläinen

    2015-06-01

    Full Text Available mtDNA mutagenesis in somatic stem cells leads to their dysfunction and to progeria in mouse. The mechanism was proposed to involve modification of reactive oxygen species (ROS/redox signaling. We studied the effect of mtDNA mutagenesis on reprogramming and stemness of pluripotent stem cells (PSCs and show that PSCs select against specific mtDNA mutations, mimicking germline and promoting mtDNA integrity despite their glycolytic metabolism. Furthermore, mtDNA mutagenesis is associated with an increase in mitochondrial H2O2, reduced PSC reprogramming efficiency, and self-renewal. Mitochondria-targeted ubiquinone, MitoQ, and N-acetyl-L-cysteine efficiently rescued these defects, indicating that both reprogramming efficiency and stemness are modified by mitochondrial ROS. The redox sensitivity, however, rendered PSCs and especially neural stem cells sensitive to MitoQ toxicity. Our results imply that stem cell compartment warrants special attention when the safety of new antioxidants is assessed and point to an essential role for mitochondrial redox signaling in maintaining normal stem cell function.

  16. Improvements to the Kunkel mutagenesis protocol for constructing primary and secondary phage-display libraries.

    Science.gov (United States)

    Huang, Renhua; Fang, Pete; Kay, Brian K

    2012-09-01

    Site-directed mutagenesis is routinely performed in protein engineering experiments. One method, termed Kunkel mutagenesis, is frequently used for constructing libraries of peptide or protein variants in M13 bacteriophage, followed by affinity selection of phage particles. To make this method more efficient, the following two modifications were introduced: culture was incubated at 25°C for phage replication, which yielded two- to sevenfold more single-stranded DNA template compared to growth at 37°C, and restriction endonuclease recognition sites were used to remove non-recombinants. With both of the improvements, we could construct primary libraries of high complexity and that were 99-100% recombinant. Finally, with a third modification to the standard protocol of Kunkel mutagenesis, two secondary (mutagenic) libraries of a fibronectin type III (FN3) monobody were constructed with DNA segments that were amplified by error-prone and asymmetric PCR. Two advantages of this modification are that it bypasses the lengthy steps of restriction enzyme digestion and ligation, and that the pool of phage clones, recovered after affinity selection, can be used directly to generate a secondary library. Screening one of the two mutagenic libraries yielded variants that bound two- to fourfold tighter to human Pak1 kinase than the starting clone. The protocols described in this study should accelerate the discovery of phage-displayed recombinant affinity reagents. Copyright © 2012 Elsevier Inc. All rights reserved.

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

    Science.gov (United States)

    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 naïve recipient cells. Kinetic studies revealed that it required up to one hour 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 one hour of exposure to the signal in the bystander cells to induce mutations. Bystander signal was fairly stable in the medium, requiring 12–24 hours 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. PMID:19695271

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

    Energy Technology Data Exchange (ETDEWEB)

    Zhang Ying; Zhou Junqing; Baldwin, Joseph [Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO (United States); Held, Kathryn D. [Department of Radiation Oncology, Massachusetts General Hospital, Boston, MA (United States); Prise, Kevin M. [Centre for Cancer Research and Cell Biology, Queen' s University Belfast, Belfast (United Kingdom); Redmond, Robert W. [Wellman Center for Photomedicine, Massachusetts General Hospital, Boston, MA (United States); Liber, Howard L., E-mail: howard.liber@colostate.edu [Environmental and Radiological Health Sciences, Colorado State University, Fort Collins, CO (United States); University of Colorado Cancer Center, Denver, CO (United States)

    2009-12-01

    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 {gamma}-ray exposures.

  19. In vitro Inactivation of Latent HSV by Targeted Mutagenesis Using an HSV-specific Homing Endonuclease

    Directory of Open Access Journals (Sweden)

    Martine Aubert

    2014-01-01

    Full Text Available Following acute infection, herpes simplex virus (HSV establishes latency in sensory neurons, from which it can reactivate and cause recurrent disease. Available antiviral therapies do not affect latent viral genomes; therefore, they do not prevent reactivation following therapy cessation. One possible curative approach involves the introduction of DNA double strand breaks in latent HSV genomes by rare-cutting endonucleases, leading to mutagenesis of essential viral genes. We tested this approach in an in vitro HSV latency model using the engineered homing endonuclease (HE HSV1m5, which recognizes a sequence in the HSV-1 gene UL19, encoding the virion protein VP5. Coexpression of the 3′-exonuclease Trex2 with HEs increased HE-mediated mutagenesis frequencies up to sixfold. Following HSV1m5/Trex2 delivery with adeno-associated viral (AAV vectors, the target site was mutated in latent HSV genomes with no detectable cell toxicity. Importantly, HSV production by latently infected cells after reactivation was decreased after HSV1m5/Trex2 exposure. Exposure to histone deacetylase inhibitors prior to HSV1m5/Trex2 treatment increased mutagenesis frequencies of latent HSV genomes another two- to fivefold, suggesting that chromatin modification may be a useful adjunct to gene-targeting approaches. These results support the continuing development of HEs and other nucleases (ZFNs, TALENs, CRISPRs for cure of chronic viral infections.

  20. In vitro Inactivation of Latent HSV by Targeted Mutagenesis Using an HSV-specific Homing Endonuclease.

    Science.gov (United States)

    Aubert, Martine; Boyle, Nicole M; Stone, Daniel; Stensland, Laurence; Huang, Meei-Li; Magaret, Amalia S; Galetto, Roman; Rawlings, David J; Scharenberg, Andrew M; Jerome, Keith R

    2014-02-04

    Following acute infection, herpes simplex virus (HSV) establishes latency in sensory neurons, from which it can reactivate and cause recurrent disease. Available antiviral therapies do not affect latent viral genomes; therefore, they do not prevent reactivation following therapy cessation. One possible curative approach involves the introduction of DNA double strand breaks in latent HSV genomes by rare-cutting endonucleases, leading to mutagenesis of essential viral genes. We tested this approach in an in vitro HSV latency model using the engineered homing endonuclease (HE) HSV1m5, which recognizes a sequence in the HSV-1 gene UL19, encoding the virion protein VP5. Coexpression of the 3'-exonuclease Trex2 with HEs increased HE-mediated mutagenesis frequencies up to sixfold. Following HSV1m5/Trex2 delivery with adeno-associated viral (AAV) vectors, the target site was mutated in latent HSV genomes with no detectable cell toxicity. Importantly, HSV production by latently infected cells after reactivation was decreased after HSV1m5/Trex2 exposure. Exposure to histone deacetylase inhibitors prior to HSV1m5/Trex2 treatment increased mutagenesis frequencies of latent HSV genomes another two- to fivefold, suggesting that chromatin modification may be a useful adjunct to gene-targeting approaches. These results support the continuing development of HEs and other nucleases (ZFNs, TALENs, CRISPRs) for cure of chronic viral infections.Molecular Therapy-Nucleic Acids (2014) 3, e1; doi:10.1038/mtna.2013.75; published online 4 February 2014.

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

    Science.gov (United States)

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

    2016-06-01

    Custom-designed nuclease technologies such as the clustered regularly interspaced short palindromic repeat (CRISPR)-associated (Cas) system provide attractive genome editing tools for insect functional genetics. The targeted gene mutagenesis mediated by the CRISPR/Cas9 system has been achieved in several insect orders including Diptera, Lepidoptera and Coleoptera. However, little success has been reported in agricultural pests due to the lack of genomic information and embryonic microinjection techniques in these insect species. Here we report that the CRISPR/Cas9 system induced efficient gene mutagenesis in an important Lepidopteran pest Spodoptera litura. We targeted the S. litura Abdominal-A (Slabd-A) gene which is an important embryonic development gene and plays a significant role in determining the identities of the abdominal segments of insects. Direct injection of Cas9 messenger RNA and Slabd-A-specific single guide RNA (sgRNA) into S. litura embryos successfully induced the typical abd-A deficient phenotype, which shows anomalous segmentation and ectopic pigmentation during the larval stage. A polymerase chain reaction-based analysis revealed that the Cas9/sgRNA complex effectively induced a targeted mutagenesis in S. litura. These results demonstrate that the CRISPR/Cas9 system is a powerful tool for genome manipulation in Lepidopteran pests such as S. litura. © 2016 Institute of Zoology, Chinese Academy of Sciences.

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

    Directory of Open Access Journals (Sweden)

    Moskowitz Ivan

    2009-03-01

    Full Text Available Abstract Background ENU-mutagenesis is a powerful technique to identify genes regulating mammalian development. To functionally annotate the distal region of mouse chromosome 4, we performed an ENU-mutagenesis screen using a balancer chromosome targeted to this region of the genome. Results We isolated 11 lethal lines that map to the region of chromosome 4 between D4Mit117 and D4Mit281. These lines form 10 complementation groups. The majority of lines die during embryonic development between E5.5 and E12.5 and display defects in gastrulation, cardiac development, and craniofacial development. One line displayed postnatal lethality and neurological defects, including ataxia and seizures. Conclusion These eleven mutants allow us to query gene function within the distal region of mouse chromosome 4 and demonstrate that new mouse models of mammalian developmental defects can easily and quickly be generated and mapped with the use of ENU-mutagenesis in combination with balancer chromosomes. The low number of mutations isolated in this screen compared with other balancer chromosome screens indicates that the functions of genes in different regions of the genome vary widely.

  3. 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.

  4. 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.

  5. Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

    National Research Council Canada - National Science Library

    Svitashev, Sergei; Young, Joshua K; Schwartz, Christine; Gao, Huirong; Falco, S Carl; Cigan, A Mark

    2015-01-01

    Targeted mutagenesis, editing of endogenous maize (Zea mays) genes, and site-specific insertion of a trait gene using clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas...

  6. Site-directed, Ligase-Independent Mutagenesis (SLIM): a single-tube methodology approaching 100% efficiency in 4 h

    OpenAIRE

    Chiu, Joyce; March, Paul E.; Lee, Ryan; Tillett, Daniel

    2004-01-01

    Site-directed, Ligase-Independent Mutagenesis (SLIM) is a novel PCR-mediated mutagenesis approach that can accommodate all three sequence modification types (insertion, deletion and substitution). The method utilizes an inverse PCR amplification of the template by two tailed long primers and two short primers in a single reaction with all steps carried out in one tube. The tailed primers are designed to contain the desired mutation on complementary overhangs at the terminus of PCR products. U...

  7. Tissue-specific mutagenesis by N-butyl-N-(4-hydroxybutyl)nitrosamine as the basis for urothelial carcinogenesis.

    Science.gov (United States)

    He, Zhiming; Kosinska, Wieslawa; Zhao, Zhong-Lin; Wu, Xue-Ru; Guttenplan, Joseph B

    2012-02-18

    Bladder cancer is one of the few cancers that have been linked to carcinogens in the environment and tobacco smoke. Of the carcinogens tested in mouse chemical carcinogenesis models, N-butyl-N-(4-hydroxybutyl)nitrosamine (BBN) is one that reproducibly causes high-grade, invasive cancers in the urinary bladder, but not in any other tissues. However, the basis for such a high-level tissue-specificity has not been explored. Using mutagenesis in lacI (Big Blue™) mice, we show here that BBN is a potent mutagen and it causes high-level of mutagenesis specifically in the epithelial cells (urothelial) of the urinary bladder. After a 2-6-week treatment of 0.05% BBN in the drinking water, mutagenesis in urothelial cells of male and female mice was about two orders of magnitude greater than the spontaneous mutation background. In contrast, mutagenesis in smooth muscle cells of the urinary bladder was about five times lower than in urothelial tissue. No appreciable increase in mutagenesis was observed in kidney, ureter, liver or forestomach. In lacI (Big Blue™) rats, BBN mutagenesis was also elevated in urothelial cells, albeit not nearly as profoundly as in mice. This provides a potential explanation as to why rats are less prone than mice to the formation of aggressive form of bladder cancer induced by BBN. Our results suggest that the propensity to BBN-triggered mutagenesis of urothelial cells underlies its heightened susceptibility to this carcinogen and that mutagenesis induced by BBN represents a novel model for initiation of bladder carcinogenesis. Copyright © 2011 Elsevier B.V. All rights reserved.

  8. Misuse of randomization

    DEFF Research Database (Denmark)

    Liu, Jianping; Kjaergard, Lise Lotte; Gluud, Christian

    2002-01-01

    The quality of randomization of Chinese randomized trials on herbal medicines for hepatitis B was assessed. Search strategy and inclusion criteria were based on the published protocol. One hundred and seventy-six randomized clinical trials (RCTs) involving 20,452 patients with chronic hepatitis B....../150) of the studies were imbalanced at the 0.05 level of probability for the two treatments and 13.3% (20/150) imbalanced at the 0.01 level in the randomization. It is suggested that there may exist misunderstanding of the concept and the misuse of randomization based on the review....

  9. [IXR1 and HMO1 genes jointly control the level of spontaneous mutagenesis in yeast Saccharomyces cerevisiae].

    Science.gov (United States)

    Fedorov, D V; Koval'tsova, S V; Peshekhonov, V T; Korolev, V G

    2010-06-01

    The yeast genes IXR1 and HMO1 encode proteins belonging to the family of chromatin nonhistone proteins, which are able to recognize and bind to irregular DNA structures. The full deletion of gene IXR1 leads to an increase in cell resistance to the lethal action of UV light, gamma-rays, and MMS, increases spontaneous mutagenesis and significantlly decreases the level of UV-induced mutations. It was earlier demonstrated in our works that the hmo 1 mutation renders cells sensitive to the lethal action of cisplatin and virtually does not affect the sensitivity to UV light. Characteristically, the rates of spontaneous and UV-induced mutagenesis in the mutant are increased. Epistatic analysis of the double mutation hmo 1 ixr1 demonstrated that the interaction of these genes in relation to the lethal effect of cisplatin and UV light, as well as UV-induced mutagenesis, is additive. This suggests that the products of genes HMO1 and IXR1 participate in different repair pathways. The ixr1 mutation significantly increases the rate of spontaneous mutagenesis mediated by replication errors, whereas mutation hmo 1 increases the rate of repair mutagenesis. In wild-type cells, the level of spontaneous mutagenesis was nearly one order of magnitude lower than that obtained in cells of the double mutant. Consequently, the combined activity of the Hmo 1 and the Ixr1 proteins provides efficient correction of both repair and replication errors.

  10. A pragmatic cluster randomized clinical trial of diabetes prevention strategies for women with gestational diabetes: design and rationale of the Gestational Diabetes' Effects on Moms (GEM) study

    National Research Council Canada - National Science Library

    Ferrara, Assiamira; Hedderson, Monique M; Albright, Cheryl L; Brown, Susan D; Ehrlich, Samantha F; Caan, Bette J; Sternfeld, Barbara; Gordon, Nancy P; Schmittdiel, Julie A; Gunderson, Erica P; Mevi, Ashley A; Tsai, Ai-Lin; Ching, Jenny; Crites, Yvonne; Quesenberry, Jr, Charles P

    2014-01-01

    .... In the Gestational Diabetes' Effects on Moms (GEM) study, we are evaluating the comparative effectiveness of diabetes prevention strategies for weight management designed for pregnant/postpartum women with GDM and delivered at the health system level...

  11. Effectiveness and Cost-effectiveness of School-based Dissemination Strategies of an Internet-based Program for the Prevention and Early Intervention in Eating Disorders: A Randomized Trial.

    Science.gov (United States)

    Moessner, Markus; Minarik, Carla; Ozer, Fikret; Bauer, Stephanie

    2016-04-01

    Only little is known about costs and effects (i.e., success) of dissemination strategies, although cost-effective dissemination strategies are crucial for the transfer of interventions into routine care. This study investigates the effects and cost-effectiveness of five school-based dissemination strategies for an Internet-based intervention for the prevention and early intervention of eating disorders. Three-hundred ninety-five schools were randomly assigned to one of five dissemination strategies. Strategies varied with respect to intensity from only sending advertisement materials and asking the school to distribute them among students to organizing presentations and workshops at schools. Effects were defined as the number of page visits, the number of screenings conducted, and the number of registrations to the Internet-based intervention. More expensive strategies proved to be more cost-effective. Cost per page visit ranged from 2.83€ (introductory presentation plus workshop) to 20.37€ (dissemination by student representatives/peers). Costs per screening ranged from 3.30€ (introductory presentation plus workshop) to 75.66€ (dissemination by student representatives/peers), and costs per registration ranged from 6.86€ (introductory presentation plus workshop) to 431.10€ (advertisement materials only). Dissemination of an Internet-based intervention for prevention and early intervention is challenging and expensive. More intense, expensive strategies with personal contact proved to be more cost-effective. The combination of an introductory presentation on eating disorders and a workshop in the high school was most effective and had the best cost-effectiveness ratio. The sole distribution of advertisement materials attracted hardly any participants to the Internet-based program.

  12. A Randomized Trial Comparison of the Effects of Verbal and Pictorial Naturalistic Communication Strategies on Spoken Language for Young Children with Autism

    Science.gov (United States)

    Schreibman, Laura; Stahmer, Aubyn C.

    2014-01-01

    Presently there is no consensus on the specific behavioral treatment of choice for targeting language in young nonverbal children with autism. This randomized clinical trial compared the effectiveness of a verbally-based intervention, Pivotal Response Training (PRT) to a pictorially-based behavioral intervention, the Picture Exchange Communication…

  13. Recurrence of pulmonary vein conduction and atrial fibrillation after pulmonary vein isolation for atrial fibrillation: a randomized trial of the ostial versus the extraostial ablation strategy

    DEFF Research Database (Denmark)

    Nilsson, Brian; Chen, Xu; Pehrson, Steen

    2006-01-01

    . METHODS: A total of 100 consecutive patients (age 56 +/- 10; 71 men) with symptomatic AF (paroxysmal, 51; persistent, 49) were randomized to segmental ostial (n = 54) or circumferential extraostial (n = 46) PV isolation. A circular catheter positioned at the ostium of each target PV guided the ostial PV...... who underwent ostial PV isolation (P paroxysmal AF (65% and 46%, respectively; P = .26). CONCLUSIONS: Overall...

  14. Comparison of the rhythm control treatment strategy versus the rate control strategy in patients with permanent or long-standing persistent atrial fibrillation and heart failure treated with cardiac resynchronization therapy - a pilot study of Cardiac Resynchronization in Atrial Fibrillation Trial (Pilot-CRAfT): study protocol for a randomized controlled trial.

    Science.gov (United States)

    Ciszewski, Jan; Maciag, Aleksander; Kowalik, Ilona; Syska, Pawel; Lewandowski, Michal; Farkowski, Michal M; Borowiec, Anna; Chwyczko, Tomasz; Pytkowski, Mariusz; Szwed, Hanna; Sterlinski, Maciej

    2014-10-04

    The only subgroups of patients with heart failure and atrial fibrillation in which the efficacy of cardiac resynchronization therapy has been scientifically proven are patients with indications for right ventricular pacing and patients after atrioventricular junction ablation. However it is unlikely that atrioventricular junction ablation would be a standard procedure in the majority of the heart failure patients with cardiac resynchronization therapy and concomitant atrial fibrillation due to the irreversible character of the procedure and a spontaneous sinus rhythm resumption that occurs in about 10% of these patients. Pilot-CRAfT is the first randomized controlled trial evaluating the efficacy of a rhythm control strategy in atrial fibrillation patients with cardiac resynchronization therapy devices. The aim of this prospective, single center randomized controlled pilot study is to answer the question whether the patients with cardiac resynchronization therapy and permanent atrial fibrillation would benefit from a strategy to restore and maintain sinus rhythm (that is 'rhythm control' strategy) in comparison to rate control strategy. The study population consists of 60 patients with heart failure and concomitant long-standing persistent or permanent atrial fibrillation who underwent a cardiac resynchronization therapy device implantation at least 3 months before qualification. Study participants are randomly assigned to the rhythm control strategy (including electrical cardioversion and pharmacotherapy) or to the rate control group whose goal is to control ventricular rate. The follow-up time is 12 months. The primary endpoint is the ratio of effectively captured biventricular beats. The secondary endpoints include peak oxygen consumption, six-minute walk test distance, heart failure symptom escalation, reverse remodelling of the heart on echo and quality of life. NCT01850277 registered on 22 April 2013 (ClinicalTrials.gov).

  15. Randomized comparison of ticagrelor versus prasugrel in patients with acute coronary syndrome and planned invasive strategy--design and rationale of the iNtracoronary Stenting and Antithrombotic Regimen: Rapid Early Action for Coronary Treatment (ISAR-REACT) 5 trial.

    Science.gov (United States)

    Schulz, Stefanie; Angiolillo, Dominick J; Antoniucci, David; Bernlochner, Isabell; Hamm, Christian; Jaitner, Juliane; Laugwitz, Karl-Ludwig; Mayer, Katharina; von Merzljak, Barbara; Morath, Tanja; Neumann, Franz-Josef; Richardt, Gert; Ruf, Judith; Schömig, Gisela; Schühlen, Helmut; Schunkert, Heribert; Kastrati, Adnan

    2014-02-01

    In acute coronary syndromes (ACS), a dual antiplatelet regimen with an adenosine diphosphate (ADP) receptor antagonist plus aspirin has become the cornerstone of treatment. The third-generation thienopyridine prasugrel and the cyclopentyl-triazolo-pyrimidine ticagrelor provide a greater, more rapid and consistent platelet inhibition compared to their predecessor clopidogrel. Based on their advantages over clopidogrel in two landmark studies, both drugs received a class I recommendation for their use in ACS patients with and without ST segment elevation. Due to differences in ACS populations and conditions investigated, the relative merits of ticagrelor versus prasugrel in the treatment of ACS patients with planned invasive strategy cannot be reliably estimated from independent trials. To date, no direct head-to-head comparison of ticagrelor and prasugrel in terms of clinical outcome exists. The aim of this multicenter, randomized, open-label trial is to assess whether ticagrelor is superior to prasugrel in ACS patients with planned invasive strategy.

  16. A mariner transposon-based signature-tagged mutagenesis system for the analysis of oral infection by Listeria monocytogenes.

    Science.gov (United States)

    Cummins, Joanne; Casey, Pat G; Joyce, Susan A; Gahan, Cormac G M

    2013-01-01

    Listeria monocytogenes is a Gram-positive foodborne pathogen and the causative agent of listerosis a disease that manifests predominately as meningitis in the non-pregnant individual or infection of the fetus and spontaneous abortion in pregnant women. Common-source outbreaks of foodborne listeriosis are associated with significant morbidity and mortality. However, relatively little is known concerning the mechanisms that govern infection via the oral route. In order to aid functional genetic analysis of the gastrointestinal phase of infection we designed a novel signature-tagged mutagenesis (STM) system based upon the invasive L. monocytogenes 4b serotype H7858 strain. To overcome the limitations of gastrointestinal infection by L. monocytogenes in the mouse model we created a H7858 strain that is genetically optimised for oral infection in mice. Furthermore our STM system was based upon a mariner transposon to favour numerous and random transposition events throughout the L. monocytogenes genome. Use of the STM bank to investigate oral infection by L. monocytogenes identified 21 insertion mutants that demonstrated significantly reduced potential for infection in our model. The sites of transposon insertion included lmOh7858_0671 (encoding an internalin homologous to Lmo0610), lmOh7858_0898 (encoding a putative surface-expressed LPXTG protein homologous to Lmo0842), lmOh7858_2579 (encoding the HupDGC hemin transport system) and lmOh7858_0399 (encoding a putative fructose specific phosphotransferase system). We propose that this represents an optimised STM system for functional genetic analysis of foodborne/oral infection by L. monocytogenes.

  17. A mariner transposon-based signature-tagged mutagenesis system for the analysis of oral infection by Listeria monocytogenes.

    Directory of Open Access Journals (Sweden)

    Joanne Cummins

    Full Text Available Listeria monocytogenes is a Gram-positive foodborne pathogen and the causative agent of listerosis a disease that manifests predominately as meningitis in the non-pregnant individual or infection of the fetus and spontaneous abortion in pregnant women. Common-source outbreaks of foodborne listeriosis are associated with significant morbidity and mortality. However, relatively little is known concerning the mechanisms that govern infection via the oral route. In order to aid functional genetic analysis of the gastrointestinal phase of infection we designed a novel signature-tagged mutagenesis (STM system based upon the invasive L. monocytogenes 4b serotype H7858 strain. To overcome the limitations of gastrointestinal infection by L. monocytogenes in the mouse model we created a H7858 strain that is genetically optimised for oral infection in mice. Furthermore our STM system was based upon a mariner transposon to favour numerous and random transposition events throughout the L. monocytogenes genome. Use of the STM bank to investigate oral infection by L. monocytogenes identified 21 insertion mutants that demonstrated significantly reduced potential for infection in our model. The sites of transposon insertion included lmOh7858_0671 (encoding an internalin homologous to Lmo0610, lmOh7858_0898 (encoding a putative surface-expressed LPXTG protein homologous to Lmo0842, lmOh7858_2579 (encoding the HupDGC hemin transport system and lmOh7858_0399 (encoding a putative fructose specific phosphotransferase system. We propose that this represents an optimised STM system for functional genetic analysis of foodborne/oral infection by L. monocytogenes.

  18. Effectiveness of Kenya's Community Health Strategy in delivering community-based maternal and newborn health care in Busia County, Kenya: non-randomized pre-test post test study.

    Science.gov (United States)

    Wangalwa, Gilbert; Cudjoe, Bennett; Wamalwa, David; Machira, Yvonne; Ofware, Peter; Ndirangu, Meshack; Ilako, Festus

    2012-01-01

    Maternal mortality ratio and neonatal mortality rate trends in Kenya have remained unacceptably high in a decade. In 2007, the Ministry of Public Health and Sanitation adopted a community health strategy to reverse the poor health outcomes in order to meet Millennium Development Goals 4 and 5. It aims at strengthening community participation and its ability to take action towards health. The study aimed at evaluating the effectiveness of the strategy in improving maternal and neonatal health outcomes in Kenya. Between 2008 and 2010, the African Medical and Research Foundation implemented a community-based maternal and newborn care intervention package in Busia County using the community health strategy approach. An interventional, non-randomized pre-test post test study design was used to evaluate change in essential maternal and neonatal care practices among mothers with children aged 0 - 23 months. There was statistically significant (p < 0.05) increase in attendance of at least four antenatal care visits (39% to 62%), deliveries by skilled birth attendants (31% to 57%), receiving intermittent preventive treatment (23% to 57%), testing for HIV during pregnancy (73% to 90%) and exclusive breastfeeding (20% to 52%). The significant increase in essential maternal and neonatal care practices demonstrates that, community health strategy is an appropriate platform to deliver community based interventions. The findings will be used by actors in the child survival community to improve current approaches, policies and practice in maternal and neonatal care.

  19. Anesthetic strategy during endovascular therapy: General anesthesia or conscious sedation? (GOLIATH - General or Local Anesthesia in Intra Arterial Therapy) A single-center randomized trial

    DEFF Research Database (Denmark)

    Simonsen, Claus Z; Sørensen, Leif H; Juul, Niels

    2016-01-01

    RATIONALE: Endovascular therapy after acute ischemic stroke due to large vessel occlusion is now standard of care. There is equipoise as to what kind of anesthesia patients should receive during the procedure. Observational studies suggest that general anesthesia is associated with worse outcomes...... compared to conscious sedation. However, the findings may have been biased. Randomized clinical trials are needed to determine whether the choice of anesthesia may influence outcome. AIM AND HYPOTHESIS: The objective of GOLIATH (General or Local Anestesia in Intra Arterial Therapy) is to examine whether....... Patients with acute ischemic stroke, scheduled for endovascular therapy, are randomized to receive either general anesthesia or conscious sedation. STUDY OUTCOMES: The primary outcome measure is infarct growth after 48-72 h (determined by serial diffusion-weighted magnetic resonance imaging). Secondary...

  20. A Randomized Trial of the Self-Management Training and Regulation Strategy (STARS): A Selective Intervention for Students with Disruptive Behaviors

    Science.gov (United States)

    Thompson, Aaron M.

    2012-01-01

    To attain academic goals, school personnel must effectively manage 20% of students who engage in the disruptive behaviors that interrupt instruction, create teacher stress, and contribute to poor student outcomes. Without effective strategies, school personnel often respond to disruptive students with ineffective authoritarian tactics,…

  1. An Invasive or Conservative Strategy in Patients With Diabetes Mellitus and Non-ST-Segment Elevation Acute Coronary Syndromes A Collaborative Meta-Analysis of Randomized Trials

    NARCIS (Netherlands)

    O'Donoghue, Michelle L.; Vaidya, Ajay; Afsal, Rizwan; Alfredsson, Joakim; Boden, William E.; Braunwald, Eugene; Cannon, Christopher P.; Clayton, Tim C.; de Winter, Robbert J.; Fox, Keith A. A.; Lagerqvist, Bo; McCullough, Peter A.; Murphy, Sabina A.; Spacek, Rudolf; Swahn, Eva; Windhausen, Fons; Sabatine, Marc S.

    2012-01-01

    Objectives The purpose of this study was to conduct a meta-analysis to examine an invasive or conservative strategy in diabetic versus nondiabetic patients. Background Diabetic patients are at increased risk of cardiovascular events after an acute coronary syndrome, yet it remains unknown whether

  2. No “Magic Bullet”: Exploring Community Mobilization Strategies Used in a Multi-site Community Based Randomized Controlled Trial: Project Accept (HPTN 043)

    OpenAIRE

    Tedrow, Virginia A.; Zelaya, Carla E.; Kennedy, Caitlin E.; Morin, Stephen F.; Khumalo-Sakutukwa, Gertrude; Sweat, Michael D.; Celentano, David D.

    2012-01-01

    As community-level interventions become more common in HIV prevention, processes such as community mobilization (CM) are increasingly utilized in public health programs and research. Project Accept, a multi-site community randomized controlled trial, is testing the hypothesis that CM coupled with community-based mobile voluntary counseling and testing and post-test support services will alter community norms and reduce the incidence of HIV. By using a multiple-case study approach, this qualit...

  3. An Innovative Multiphased Strategy to Recruit Underserved Adults into a Randomized Trial of a Community-Based Diabetes Risk Reduction Program

    OpenAIRE

    Santoyo-Olsson, Jasmine; Cabrera, Julissa; Freyre, Rachel; Grossman, Melanie; Alvarez, Natalie; Mathur, Deepika; Guerrero, Maria; Delgadillo, Adriana T.; Kanaya, Alka M.; Stewart, Anita L.

    2011-01-01

    Purpose: To conduct and evaluate a two-phased community-based approach to recruit lower socioeconomic status, minority, or Spanish-speaking adults at risk of developing diabetes to a randomized trial of a lifestyle intervention program delivered by a public health department. Design: Within geographic areas comprising our target population, 4 community organizations provided local space for conducting the study and program. Phase I—outreach in venues surrounding these organizations—included d...

  4. A randomized trial comparison of the effects of verbal and pictorial naturalistic communication strategies on spoken language for young children with autism

    OpenAIRE

    Schreibman, L; Stahmer, AC

    2014-01-01

    Presently there is no consensus on the specific behavioral treatment of choice for targeting language in young nonverbal children with autism. This randomized clinical trial compared the effectiveness of a verbally-based intervention, Pivotal Response Training (PRT) to a pictorially-based behavioral intervention, the Picture Exchange Communication System (PECS) on the acquisition of spoken language by young (2-4 years), nonverbal or minimally verbal (≤9 words) children with autism. Thirty-nin...

  5. Modeling insertional mutagenesis using gene length and expression in murine embryonic stem cells.

    Directory of Open Access Journals (Sweden)

    Alex S Nord

    2007-07-01

    Full Text Available High-throughput mutagenesis of the mammalian genome is a powerful means to facilitate analysis of gene function. Gene trapping in embryonic stem cells (ESCs is the most widely used form of insertional mutagenesis in mammals. However, the rules governing its efficiency are not fully understood, and the effects of vector design on the likelihood of gene-trapping events have not been tested on a genome-wide scale.In this study, we used public gene-trap data to model gene-trap likelihood. Using the association of gene length and gene expression with gene-trap likelihood, we constructed spline-based regression models that characterize which genes are susceptible and which genes are resistant to gene-trapping techniques. We report results for three classes of gene-trap vectors, showing that both length and expression are significant determinants of trap likelihood for all vectors. Using our models, we also quantitatively identified hotspots of gene-trap activity, which represent loci where the high likelihood of vector insertion is controlled by factors other than length and expression. These formalized statistical models describe a high proportion of the variance in the likelihood of a gene being trapped by expression-dependent vectors and a lower, but still significant, proportion of the variance for vectors that are predicted to be independent of endogenous gene expression.The findings of significant expression and length effects reported here further the understanding of the determinants of vector insertion. Results from this analysis can be applied to help identify other important determinants of this important biological phenomenon and could assist planning of large-scale mutagenesis efforts.

  6. 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.

  7. Increased efficiency of targeted mutagenesis by CRISPR/Cas9 in plants using heat stress.

    Science.gov (United States)

    LeBlanc, Chantal; Zhang, Fei; Mendez, Josefina; Lozano, Yamile; Chatpar, Krishna; Irish, Vivian F; Jacob, Yannick

    2018-01-01

    The CRISPR/Cas9 system has greatly improved our ability to engineer targeted mutations in eukaryotic genomes. While CRISPR/Cas9 appears to work universally, the efficiency of targeted mutagenesis and the adverse generation of off-target mutations vary greatly between different organisms. In this study, we report that Arabidopsis plants subjected to heat stress at 37°C show much higher frequencies of CRISPR-induced mutations compared to plants grown continuously at the standard temperature (22°C). Using quantitative assays relying on green fluorescent protein (GFP) reporter genes, we found that targeted mutagenesis by CRISPR/Cas9 in Arabidopsis is increased by approximately 5-fold in somatic tissues and up to 100-fold in the germline upon heat treatment. This effect of temperature on the mutation rate is not limited to Arabidopsis, as we observed a similar increase in targeted mutations by CRISPR/Cas9 in Citrus plants exposed to heat stress at 37°C. In vitro assays demonstrate that Cas9 from Streptococcus pyogenes (SpCas9) is more active in creating double-stranded DNA breaks at 37°C than at 22°C, thus indicating a potential contributing mechanism for the in vivo effect of temperature on CRISPR/Cas9. This study reveals the importance of temperature in modulating SpCas9 activity in eukaryotes, and provides a simple method to increase on-target mutagenesis in plants using CRISPR/Cas9. © 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.

  8. Alleles conferring improved fiber quality from EMS mutagenesis of elite cotton genotypes.

    Science.gov (United States)

    Patel, Jinesh D; Wright, Robert J; Auld, Dick; Chandnani, Rahul; Goff, Valorie H; Ingles, Jennifer; Pierce, Gary J; Torres, Manuel J; Paterson, Andrew H

    2014-04-01

    Genetic improvements for many fiber traits are obtained by mutagenesis of elite cottons, mitigating genetic uniformity in this inbred polyploid by contributing novel alleles important to ongoing crop improvement. The elite gene pool of cotton (Gossypium spp.) has less diversity than those of most other major crops, making identification of novel alleles important to ongoing crop improvement. A total of 3,164 M5 lines resulting from ethyl methanesulfonate (EMS) mutagenesis of two G. hirsutum breeding lines, TAM 94L-25 and Acala 1517-99, were characterized for basic components of fiber quality and selected yield components. Across all measured traits, the ranges of phenotypic values among the mutant lines were consistently larger than could be explained by chance (5.27-10.1 for TAM 94 L-25 and 5.29-7.94 standard deviations for Acala 1517-99-derived lines). Multi-year replicated studies confirmed a genetic basis for these differences, showing significant correlations between lines across years and environments. A subset of 157 lines selected for superior fiber qualities, including fiber elongation (22 lines), length (22), lint percent (17), fineness (23), Rd value (21), strength (19), uniformity (21) and multiple attributes in a selection index (26) were compared to 55 control lines in replicated trials in both Texas and Georgia. For all traits, mutant lines showing substantial and statistically significant improvements over control lines were found, in most cases from each of the two genetic backgrounds. This indicates that genetic improvements for a wide range of fiber traits may be obtained from mutagenesis of elite cottons. Indeed, lines selected for one fiber trait sometimes conferred additional attributes, suggesting pleiotropic effects of some mutations and offering multiple benefits for the incorporation of some alleles into mainstream breeding programs.

  9. CRISPR/Cas9-mediated targeted mutagenesis in the liverwort Marchantia polymorpha L.

    Science.gov (United States)

    Sugano, Shigeo S; Shirakawa, Makoto; Takagi, Junpei; Matsuda, Yoriko; Shimada, Tomoo; Hara-Nishimura, Ikuko; Kohchi, Takayuki

    2014-03-01

    Targeted genome modification technologies are key tools for functional genomics. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease Cas9 system (CRISPR/Cas9) is an emerging technology for targeted genome modification. The CRISPR/Cas9 system consists of a short guide RNA (gRNA), which specifies the target genome sequence, and the Cas9 protein, which has endonuclease activity. The CRISPR/Cas9 system has been applied to model animals and flowering plants, including rice, sorghum, wheat, tobacco and Arabidopsis. Here, we report the application of CRISPR/Cas9 to targeted mutagenesis in the liverwort Marchantia polymorpha L., which has emerged as a model species for studying land plant evolution. The U6 promoter of M. polymorpha was identified and cloned to express the gRNA. The target sequence of the gRNA was designed to disrupt the gene encoding auxin response factor 1 (ARF1) in M. polymorpha. Using Agrobacterium-mediated transformation, we isolated stable mutants in the gametophyte generation of M. polymorpha. CRISPR/Cas9-based site-directed mutagenesis in vivo was achieved using either the Cauliflower mosaic virus 35S or M. polymorpha EF1α promoter to express Cas9. Isolated mutant individuals showing an auxin-resistant phenotype were not chimeric. Moreover, stable mutants were produced by asexual reproduction of T1 plants. Multiple arf1 alleles were easily established using CRIPSR/Cas9-based targeted mutagenesis. Our results provide a rapid and simple approach for molecular genetics in M. polymorpha, and raise the possibility that CRISPR/Cas9 may be applied to a wide variety of plant species.

  10. Mechanism of DNA alkylation-induced transcriptional stalling, lesion bypass, and mutagenesis.

    Science.gov (United States)

    Xu, Liang; Wang, Wei; Wu, Jiabin; Shin, Ji Hyun; Wang, Pengcheng; Unarta, Ilona Christy; Chong, Jenny; Wang, Yinsheng; Wang, Dong

    2017-08-22

    Alkylated DNA lesions, induced by both exogenous chemical agents and endogenous metabolites, interfere with the efficiency and accuracy of DNA replication and transcription. However, the molecular mechanisms of DNA alkylation-induced transcriptional stalling and mutagenesis remain unknown. In this study, we systematically investigated how RNA polymerase II (pol II) recognizes and bypasses regioisomeric O 2 -, N 3-, and O 4 -ethylthymidine ( O 2 -, N 3-, and O 4 -EtdT) lesions. We observed distinct pol II stalling profiles for the three regioisomeric EtdT lesions. Intriguingly, pol II stalling at O 2 -EtdT and N 3-EtdT sites is exacerbated by TFIIS-stimulated proofreading activity. Assessment for the impact of the EtdT lesions on individual fidelity checkpoints provided further mechanistic insights, where the transcriptional lesion bypass routes for the three EtdT lesions are controlled by distinct fidelity checkpoints. The error-free transcriptional lesion bypass route is strongly favored for the minor-groove O 2 -EtdT lesion. In contrast, a dominant error-prone route stemming from GMP misincorporation was observed for the major-groove O 4 -EtdT lesion. For the N 3-EtdT lesion that disrupts base pairing, multiple transcriptional lesion bypass routes were found. Importantly, the results from the present in vitro transcriptional studies are well correlated with in vivo transcriptional mutagenesis analysis. Finally, we identified a minor-groove-sensing motif from pol II (termed Pro-Gate loop). The Pro-Gate loop faces toward the minor groove of RNA:DNA hybrid and is involved in modulating the translocation of minor-groove alkylated DNA template after nucleotide incorporation opposite the lesion. Taken together, this work provides important mechanistic insights into transcriptional stalling, lesion bypass, and mutagenesis of alkylated DNA lesions.

  11. Construction, characterization, and mutagenesis of an anti-fluorescein single chain antibody idiotype family.

    Science.gov (United States)

    Denzin, L K; Voss, E W

    1992-05-05

    In addition to crystallographic studies that determined antigen contact residues for monoclonal anti-fluorescein (Fl) antibody 4-4-20 (Ka = 2.5 x 10(10) M-1), primary structure comparisons revealed idiotypically cross-reactive monoclonal antibodies (mAbs) 9-40 (Ka = 4.4 x 10(7) M-1), 12-40 (Ka = 4.0 x 10(8) M-1), and 5-14 (Ka = 2.4 x 10(8) M-1) possessed identical Fl contact residues, with the exception of L34His for L34Arg. Site-specific mutagenesis of single chain antibody (SCA) 4-4-20 in which L34Arg was changed to L34His resulted in approximately 1000- and 3-fold decreases in binding affinity and Qmax (maximum quenching of bound Fl), respectively, which suggested that L34Arg was directly involved in increased binding affinity and fluorescence quenching. Therefore, substitution of Arg for His at residue L34 in mAbs 9-40, 12-40, and 5-14 should result in increased binding affinity and Qmax. To facilitate site-specific mutagenesis studies, single chain derivatives of mAbs 9-40, 12-40, and 5-14 were constructed. Following expression in Escherichia coli, characterization of the SCAs demonstrated that when compared with the respective parental mAb, the SCAs possessed identical binding affinities and similar Qmax and lambda max (absorption profiles of bound Fl) values. These results validated SCA 9-40, 12-40, and 5-14 for use in site-directed mutagenesis studies. Results of mutagenesis studies indicated that substitution of L34Arg into the active sites of 9-40, 12-40, and 5-14 was not enough to produce 4-4-20-like binding characteristics. Therefore, the following single chain mutants were constructed: 9-40L34Arg/L46Val, 12-40L34Arg/L46Val and 5-14L34Arg/L46Val, 9-40L34Arg/L46Val/H101Asp and 4-4-20H101Ala. Results demonstrated that these mutations were not able to render the mutant SCAs with increased binding affinity and fluorescence quenching values. Collectively, these results suggest that the combining sites of mAb 9-40, 12-40, and 5-14 may possess different active

  12. Scaffolding functions of arrestin-2 revealed by crystal structure and mutagenesis.

    Science.gov (United States)

    Milano, Shawn K; Pace, Helen C; Kim, You-Me; Brenner, Charles; Benovic, Jeffrey L

    2002-03-12

    Arrestin binding to activated, phosphorylated G protein-coupled receptors (GPCRs) represents a critical step in regulation of light- and hormone-dependent signaling. Nonvisual arrestins, such as arrestin-2, interact with multiple proteins for the purpose of propagating and terminating signaling events. Using a combination of X-ray crystallography, molecular modeling, mutagenesis, and binding analysis, we reveal structural features of arrestin-2 that may enable simultaneous binding to phosphorylated receptor, SH3 domains, phosphoinositides, and beta-adaptin. The structure of full-length arrestin-2 thus provides a uniquely oriented scaffold for assembly of multiple, diverse molecules involved in GPCR signal transduction.

  13. The significance of disulfide bonding in biological activity of HB-EGF, a mutagenesis approach

    OpenAIRE

    Hoskins, J.T.; Zhou, Z.; Harding, P A

    2008-01-01

    A site-directed mutagenesis approach was taken to disrupt each of 3 disulfide bonds within human HB-EGF by substituting serine for both cysteine residues that contribute to disulfide bonding. Each HB-EGF disulfide analogue (HB-EGF-Cys/Ser108/121, HB-EGF-Cys/Ser116/132, and HB-EGF-Cys/Ser134/143) was cloned under the regulation of the mouse metallothionein (MT) promoter and stably expressed in mouse fibroblasts. HB-EGF immunoreactive proteins with Mr of 6.5, 21 and 24kDa were observed from lys...

  14. Facile Affinity Maturation of Antibody Variable Domains Using Natural Diversity Mutagenesis

    Directory of Open Access Journals (Sweden)

    Kathryn E. Tiller

    2017-09-01

    Full Text Available The identification of mutations that enhance antibody affinity while maintaining high antibody specificity and stability is a time-consuming and laborious process. Here, we report an efficient methodology for systematically and rapidly enhancing the affinity of antibody variable domains while maximizing specificity and stability using novel synthetic antibody libraries. Our approach first uses computational and experimental alanine scanning mutagenesis to identify sites in the complementarity-determining regions (CDRs that are permissive to mutagenesis while maintaining antigen binding. Next, we mutagenize the most permissive CDR positions using degenerate codons to encode wild-type residues and a small number of the most frequently occurring residues at each CDR position based on natural antibody diversity. This mutagenesis approach results in antibody libraries with variants that have a wide range of numbers of CDR mutations, including antibody domains with single mutations and others with tens of mutations. Finally, we sort the modest size libraries (~10 million variants displayed on the surface of yeast to identify CDR mutations with the greatest increases in affinity. Importantly, we find that single-domain (VHH antibodies specific for the α-synuclein protein (whose aggregation is associated with Parkinson’s disease with the greatest gains in affinity (>5-fold have several (four to six CDR mutations. This finding highlights the importance of sampling combinations of CDR mutations during the first step of affinity maturation to maximize the efficiency of the process. Interestingly, we find that some natural diversity mutations simultaneously enhance all three key antibody properties (affinity, specificity, and stability while other mutations enhance some of these properties (e.g., increased specificity and display trade-offs in others (e.g., reduced affinity and/or stability. Computational modeling reveals that improvements in affinity

  15. Induction of apomixis and fixation of heterosis in Egyptian rice Hybrid1 line using colchicine mutagenesis

    OpenAIRE

    Reda M. Gaafar; Adel R. El Shanshoury; Ahmad A. El Hisseiwy; Mahmoud A. AbdAlhak; Aimn F. Omar; Mohammad M. Abd El Wahab; Randa S. Nofal

    2017-01-01

    It is known that hybrid rice yields 15–20% over inbred varieties in first generation because of heterosis. However, heterosis is normally broken due to segregation. Applying apomixis produces plants as a clone of mother plant and overcomes the problem of breaking heterosis. In order to fix heterosis in the Egyptian rice Hybrid1, their seeds were mutagenized in 0.2% colchicine for two time periods 24 and 50 h. After colchicine mutagenesis, rice seedlings were grown in the field till maturation...

  16. A calcium antagonist vs a non-calcium antagonist hypertension treatment strategy for patients with coronary artery disease. The International Verapamil-Trandolapril Study (INVEST): a randomized controlled trial.

    Science.gov (United States)

    Pepine, Carl J; Handberg, Eileen M; Cooper-DeHoff, Rhonda M; Marks, Ronald G; Kowey, Peter; Messerli, Franz H; Mancia, Giuseppe; Cangiano, José L; Garcia-Barreto, David; Keltai, Matyas; Erdine, Serap; Bristol, Heather A; Kolb, H Robert; Bakris, George L; Cohen, Jerome D; Parmley, William W

    2003-12-03

    Despite evidence of efficacy of antihypertensive agents in treating hypertensive patients, safety and efficacy of antihypertensive agents for coronary artery disease (CAD) have been discerned only from subgroup analyses in large trials. To compare mortality and morbidity outcomes in patients with hypertension and CAD treated with a calcium antagonist strategy (CAS) or a non-calcium antagonist strategy (NCAS). Randomized, open label, blinded end point study of 22 576 hypertensive CAD patients aged 50 years or older, which was conducted September 1997 to February 2003 at 862 sites in 14 countries. Patients were randomly assigned to either CAS (verapamil sustained release) or NCAS (atenolol). Strategies specified dose and additional drug regimens. Trandolapril and/or hydrochlorothiazide was administered to achieve blood pressure goals according to guidelines from the sixth report of the Joint National Committee on Prevention, Detection, Evaluation, and Treatment of High Blood Pressure (JNC VI) of less than 140 mm Hg (systolic) and less than 90 mm Hg (diastolic); and less than 130 mm Hg (systolic) and less than 85 mm Hg (diastolic) if diabetes or renal impairment was present. Trandolapril was also recommended for patients with heart failure, diabetes, or renal impairment. Primary: first occurrence of death (all cause), nonfatal myocardial infarction, or nonfatal stroke; other: cardiovascular death, angina, adverse experiences, hospitalizations, and blood pressure control at 24 months. At 24 months, in the CAS group, 6391 patients (81.5%) were taking verapamil sustained release; 4934 (62.9%) were taking trandolapril; and 3430 (43.7%) were taking hydrochlorothiazide. In the NCAS group, 6083 patients (77.5%) were taking atenolol; 4733 (60.3%) were taking hydrochlorothiazide; and 4113 (52.4%) were taking trandolapril. After a follow-up of 61 835 patient-years (mean, 2.7 years per patient), 2269 patients had a primary outcome event with no statistically significant

  17. Impact of communication strategies to increase knowledge, acceptability, and uptake of a new Woman's Condom in urban Lusaka, Zambia: study protocol for a randomized controlled trial.

    Science.gov (United States)

    Pinchoff, Jessie; Chowdhuri, Rachna Nag; Taruberekera, Noah; Ngo, Thoai D

    2016-12-13

    Globally, 220 million women experience an unmet need for family planning. A newly designed female condom, the Woman's Condom (WC), has been developed featuring an improved design. It is the first dual-protection, female-initiated contraceptive that is a premium, higher price point product. However, market availability alone will not increase uptake. In February 2016 the WC will be distributed with a strong media campaign and interpersonal communication (IPC) outreach intervention. The impact of these on knowledge, acceptability, and use of the WC will be measured. A baseline survey of 2314 randomly selected 18- to 24-year-old sexually active men and women has been conducted. The WC and mass media will be introduced throughout 40 urban wards in and surrounding Lusaka, Zambia. The baseline survey will serve as a quasi-control arm to determine the impact of introducing the WC with mass media. Half of the wards will be randomly allocated to additionally receive the IPC intervention. A single-blind randomized controlled trial will determine the impact of the IPC intervention on knowledge, uptake, and use of the WC. After one year, another 2314 individuals will be randomly selected to participate in the endline survey. We hypothesize that (1) the distribution and media campaign of the WC will increase overall condom use in selected urban wards, and specifically use of the WC; (2) the IPC intervention will significantly impact knowledge, acceptability, and use of the WC. The primary outcome measures are use of the WC, use of any condom, and willingness to use the WC. Secondary outcomes include measures of knowledge, acceptability, and choice of contraception. Odds ratios will be estimated to measure the effect of the intervention on the outcomes with 95% confidence intervals. All analyses will be based on the intention-to-treat principle. Increasing uptake of dual prevention measures (such as the WC) may reduce incidence of sexually transmitted infections/HIV and

  18. Study protocol for a cluster randomized controlled trial to evaluate a referral strategy for axial spondyloarthritis in young primary care patients with chronic low back pain; an impact study.

    Science.gov (United States)

    van Hoeven, Lonneke; Vergouwe, Yvonne; Koes, Bart W; Hazes, Johanna M W; Weel, Angelique E A M

    2016-07-12

    Axial spondyloarthritis (axSpA) is a disabling inflammatory joint disease with chronic low back pain (CLBP) as leading symptom. Recognizing axSpA in the large amount of CLBP patients is difficult for general practioners (GP). This evaluation aims to assess the effect of a referral strategy for axSpA in young primary care patients with CLBP by comparing the use of the strategy with usual care. The effect is measured at three different levels; by patient reported outcomes (the clinical effect), process and costs evaluation. This study design is a cluster randomized controlled trial with GP as clusters. GPs throughout the Netherlands are invited to participate and randomized to either the intervention or the control group. Patients from participating GPs are invited to participate if they have ever been registered with low back pain, without radiation (ICPC L03) and aged 18-45 years. To be included in the study, patients need to have current low back pain and chronic low back pain (>12 weeks). In the intervention arm a referral strategy for axSpA will be applied in CLBP patients, in the control arm care as usual will be provided for CLBP patients. The referral strategy consists of four easy to use variables. All are questions about the back pain complaints of the patients. Data is prospectively collected in an online database at baseline (T0), 4 months (T1), 12 months (T2) and 24 months (T3). After time point T1 (4 months) patients from the control group will also receive the intervention i.e. the application of a referral strategy for axSpA. The effect of the referral strategy is measured at three different levels, by patient outcomes (e.g. pain scores, quality of life), process measures (e.g. number of axSpA diagnoses by rheumatologists) and by costs (work productivity and health care resources use). Our primary outcome is the Roland Morris Disability Questionnaire after 4 months, secondary outcomes are pain and quality of life. Costs will be assessed before

  19. Evaluating a multicomponent social behaviour change communication strategy to reduce intimate partner violence among married couples: study protocol for a cluster randomized trial in Nepal.

    Science.gov (United States)

    Clark, Cari Jo; Spencer, Rachael A; Shrestha, Binita; Ferguson, Gemma; Oakes, J Michael; Gupta, Jhumka

    2017-01-13

    Intimate partner violence (IPV) is a significant public health issue that affects 1 in 3 women globally and a similarly large number of women in Nepal. Over the past decade, important policy and programmatic steps have been taken to address violence against women in Nepal. There remains a dearth of evidence on the effectiveness of primary violence prevention strategies. The Change Starts at Home study begins to fill this gap by utilizing a multi-component social behaviour change communication (SBCC) strategy involving a radio drama and community mobilization to shift attitudes, norms and behaviours that underpin IPV perpetration in Nepal. The study uses a concurrent mixed-methods design. The quantitative aspect of the evaluation is a pair-matched, repeated cross-sectional 2-armed, single-blinded cluster trial (RCT: N = 36 clusters, 1440 individuals), comparing a social behaviour change communication (SBCC) strategy to radio programming alone for its impact on physical and / or sexual IPV at the end of programming (12 months' post-baseline) and 6-months post the cessation of project activities (18-months post baseline). The qualitative aspects of the design include several longitudinal approaches to understand the impact of the intervention and to examine mechanisms of change including in-depth interviews with participants (N = 18 couples), and focus group discussions with community leaders (N = 3 groups), and family members of participants (N = 12 groups). Treatment effects will be estimated with generalized logistic mixed models specified to compare differences in primary outcome from baseline to 12-month follow-up, and baseline to 18-months follow-up in accordance with intention-to-treat principles. The study rigorously evaluates the effectiveness of a promising strategy to prevent IPV. The results of the trial will be immediately useful for governmental, nongovernmental, and donor funded programs targeting partner violence or social norms that

  20. Evaluating a multicomponent social behaviour change communication strategy to reduce intimate partner violence among married couples: study protocol for a cluster randomized trial in Nepal

    Directory of Open Access Journals (Sweden)

    Cari Jo Clark

    2017-01-01

    Full Text Available Abstract Background Intimate partner violence (IPV is a significant public health issue that affects 1 in 3 women globally and a similarly large number of women in Nepal. Over the past decade, important policy and programmatic steps have been taken to address violence against women in Nepal. There remains a dearth of evidence on the effectiveness of primary violence prevention strategies. The Change Starts at Home study begins to fill this gap by utilizing a multi-component social behaviour change communication (SBCC strategy involving a radio drama and community mobilization to shift attitudes, norms and behaviours that underpin IPV perpetration in Nepal. Methods/Design The study uses a concurrent mixed-methods design. The quantitative aspect of the evaluation is a pair-matched, repeated cross-sectional 2-armed, single-blinded cluster trial (RCT: N = 36 clusters, 1440 individuals, comparing a social behaviour change communication (SBCC strategy to radio programming alone for its impact on physical and / or sexual IPV at the end of programming (12 months’ post-baseline and 6-months post the cessation of project activities (18-months post baseline. The qualitative aspects of the design include several longitudinal approaches to understand the impact of the intervention and to examine mechanisms of change including in-depth interviews with participants (N = 18 couples, and focus group discussions with community leaders (N = 3 groups, and family members of participants (N = 12 groups. Treatment effects will be estimated with generalized logistic mixed models specified to compare differences in primary outcome from baseline to 12-month follow-up, and baseline to 18-months follow-up in accordance with intention-to-treat principles. Discussion The study rigorously evaluates the effectiveness of a promising strategy to prevent IPV. The results of the trial will be immediately useful for governmental, nongovernmental, and donor funded

  1. Meta-analysis of coronary computed tomography angiography versus standard of care strategy for the evaluation of low risk chest pain: are randomized controlled trials and cohort studies showing the same evidence?

    Science.gov (United States)

    El-Hayek, Georges; Benjo, Alexandre; Uretsky, Seth; Al-Mallah, Mouaz; Cohen, Randy; Bamira, Daniel; Chavez, Patricia; Nascimento, Francisco; Santana, Orlando; Patel, Rajan; Cavalcante, João L

    2014-11-15

    Randomized control trials (RCTs) have established the use of Coronary Computed Tomography Angiography (CCTA) for the evaluation of low to intermediate risk patients presenting with acute chest pain to the emergency department (ED). However, concerns remain regarding the downstream resource utilization and the clinical impact of such strategy. We performed a meta-analysis of existing studies to compare CCTA to the standard of care (SOC) strategies in the low to intermediate risk chest pain patients. We abstracted the reported incidence of acute coronary syndromes (ACS), the total number of invasive coronary angiography (ICA) and subsequent revascularization procedures, the rates of hospital readmissions and repeat ED visits. We stratified the results according to the type of the studies (randomized or not) and used random effect analysis for the studied outcomes. Four RCTs and 3 case-control studies with 3306 patients undergoing CCTA and 2752 assigned to SOC were included in the analysis. Following the index visit, we observed a significant reduction in the risk of ACS (RR: 0.26, 95% CI, 0.08 to 0.87; p = 0.03) and in the rates of repeat ED visits (RR: 0.58, 95% CI: 0.36 to 0.94; p = 0.03). In addition, a trend toward less hospital readmission (p = 0.07) was noted. There was no difference in ICA (p = 0.99) but an increase in revascularization procedures (RR: 1.46, 95% CI: 1.09 to 1.94; p = 0.01). CCTA use in the ED for the triage of low to intermediate risk patients reduces the risk of future ACS and subsequent ED visits for chest pain. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

  2. A randomized trial comparison of the effects of verbal and pictorial naturalistic communication strategies on spoken language for young children with autism.

    Science.gov (United States)

    Schreibman, Laura; Stahmer, Aubyn C

    2014-05-01

    Presently there is no consensus on the specific behavioral treatment of choice for targeting language in young nonverbal children with autism. This randomized clinical trial compared the effectiveness of a verbally-based intervention, Pivotal Response Training (PRT) to a pictorially-based behavioral intervention, the Picture Exchange Communication System (PECS) on the acquisition of spoken language by young (2-4 years), nonverbal or minimally verbal (≤9 words) children with autism. Thirty-nine children were randomly assigned to either the PRT or PECS condition. Participants received on average 247 h of intervention across 23 weeks. Dependent measures included overall communication, expressive vocabulary, pictorial communication and parent satisfaction. Children in both intervention groups demonstrated increases in spoken language skills, with no significant difference between the two conditions. Seventy-eight percent of all children exited the program with more than 10 functional words. Parents were very satisfied with both programs but indicated PECS was more difficult to implement.

  3. Evidence for a Rad18-independent frameshift mutagenesis pathway in human cell-free extracts.

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    Régine Janel-Bintz

    Full Text Available Bypass of replication blocks by specialized DNA polymerases is crucial for cell survival but may promote mutagenesis and genome instability. To gain insight into mutagenic sub-pathways that coexist in mammalian cells, we examined N-2-acetylaminofluorene (AAF-induced frameshift mutagenesis by means of SV40-based shuttle vectors containing a single adduct. We found that in mammalian cells, as previously observed in E. coli, modification of the third guanine of two target sequences, 5'-GGG-3' (3G and 5'-GGCGCC-3' (NarI site, induces -1 and -2 frameshift mutations, respectively. Using an in vitro assay for translesion synthesis, we investigated the biochemical control of these events. We showed that Pol eta, but neither Pol iota nor Pol zeta, plays a major role in the frameshift bypass of the AAF adduct located in the 3G sequence. By complementing PCNA-depleted extracts with either a wild-type or a non-ubiquitinatable form of PCNA, we found that this Pol eta-mediated pathway requires Rad18 and ubiquitination of PCNA. In contrast, when the AAF adduct is located within the NarI site, TLS is only partially dependent upon Pol eta and Rad18, unravelling the existence of alternative pathways that concurrently bypass this lesion.

  4. Efficient and Heritable Targeted Mutagenesis in Mosses Using the CRISPR/Cas9 System.

    Science.gov (United States)

    Nomura, Toshihisa; Sakurai, Tetsuya; Osakabe, Yuriko; Osakabe, Keishi; Sakakibara, Hitoshi

    2016-12-01

    Targeted genome modification by RNA-guided nucleases derived from the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated nuclease 9 (Cas9) system has seen rapid development in many organisms, including several plant species. In the present study, we succeeded in introducing the CRISPR/Cas9 system into the non-model organism Scopelophila cataractae, a moss that exhibits heavy metal tolerance, and the model organism Physcomitrella patens Utilizing the process by which moss plants regenerate from protoplasts, we conducted targeted mutagenesis by expression of single-chain guide RNA (sgRNA) and Cas9 in protoplasts. Using this method, the acquisition rate of strains exhibiting phenotypic changes associated with the target genes was approximately 45-69%, and strains with phenotypic changes exhibited various insertion and deletion mutations. In addition, we report that our method is capable of multiplex targeted mutagenesis (two independent genes) and also permits the efficient introduction of large deletions (∼3 kbp). These results demonstrate that the CRISPR/Cas9 system can be used to accelerate investigations of bryology and land plant evolution. © The Authors 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

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

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    Sofya A. Medvedeva

    2013-01-01

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

  6. A mouse model of hereditary coproporphyria identified in an ENU mutagenesis screen

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    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.

  7. Caffeine enhanced measurement of mutagenesis by low levels of [gamma]-irradiation in human lymphocytes

    Energy Technology Data Exchange (ETDEWEB)

    Puck, T.P.; Johnson, R.; Waldren, C.A. (Eleanor Roosevelt Institute for Cancer Research, Denver, CO (United States)); Morse, H. (Univ. of Colorado Cancer Center, Denver, CO (United States))

    1993-09-01

    The well-known action of caffeine in synergizing mutagenesis (including chromosome aberrations) of agents like ionizing radiation by inhibition of cellular repair processes has been incorporated into a rapid procedure for detection of mutagenicity with high sensitivity. Effects of 5-10 rads of [gamma]-irradiation, which approximate the human lifetime dose accumulation from background radiation, can be detected in a two-day procedure using an immortalized human WBC culture. Chromosomally visible lesions are scored on cells incubated for 2 h after irradiation in the presence and absence of 1.0 mg/ml of caffeine. An eightfold amplification of scorable lesions is achieved over the action of radiation alone. This approach provides a closer approximation to absolute mutagenicity unmitigated by repair processes, which can vary in different situations. It is proposed that mutagenesis testing of this kind, using caffiene or other repair-inhibitory agents, be employed to identify mutagens in their effective concentrations to which human populations may be exposed; to detect agents such as caffeine that may synergize mutagenic actions and pose epidemiologic threats; and to discover effective anti-mutagens. Information derived from the use of such procedures may help prevent cancer and newly acquired genetic disease.

  8. Identification of 17 hearing impaired mouse strains in the TMGC ENU-mutagenesis screen

    Energy Technology Data Exchange (ETDEWEB)

    Kermany, Mohammad [St. Jude Children' s Research Hospital; Parker, Lisan [St. Jude Children' s Research Hospital; Guo, Yun-Kai [St. Jude Children' s Research Hospital; Miller, Darla R [ORNL; Swanson, Douglas J [ORNL; Yoo, Tai-June [Neuroscience Institute, Memphis, TN; Goldowitz, Daniel [University of Tennessee Health Science Center, Memphis; Zuo, Jian [St. Jude Children' s Research Hospital

    2006-01-01

    The Tennessee Mouse Genome Consortium (TMGC) employed an N-ethyl-N-nitrosourea (ENU)-mutagenesis scheme to identify mouse recessive mutants with hearing phenotypes. We employed auditory brainstem responses (ABR) to click and 8, 16, and 32 kHz stimuli and screened 285 pedigrees (1819 mice of 8-11 weeks old in various mixed genetic backgrounds) each bred to carry a homozygous ENU-induced mutation. To define mutant pedigrees, we measured P12 mice per pedigree in P2 generations and used a criterion where the mean ABR threshold per pedigree was two standard deviations above the mean of all offspring from the same parental strain. We thus identified 17 mutant pedigrees (6%), all exhibiting hearing loss at high frequencies (P16 kHz) with an average threshold elevation of 30-35 dB SPL. Interestingly, four mutants showed sex-biased hearing loss and six mutants displayed wide range frequency hearing loss. Temporal bone histology revealed that six of the first nine mutants displayed cochlear morphological defects: degeneration of spiral ganglia, spiral ligament fibrocytes or inner hair cells (but not outer hair cells) mostly in basal turns. In contrast to other ENU-mutagenesis auditory screens, our screen identified high-frequency, mild and sex-biased hearing defects. Further characterization of these 17 mouse models will advance our understanding of presbycusis and noise-induced hearing loss in humans.

  9. Improving the activity of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation.

    Science.gov (United States)

    Weng, Meizhi; Deng, Xiongwei; Bao, Wei; Zhu, Li; Wu, Jieyuan; Cai, Yongjun; Jia, Yan; Zheng, Zhongliang; Zou, Guolin

    2015-09-25

    Nattokinase (NK), a bacterial serine protease from Bacillus subtilis var. natto, is a potential cardiovascular drug exhibiting strong fibrinolytic activity. To broaden its commercial and medical applications, we constructed a single-mutant (I31L) and two double-mutants (M222A/I31L and T220S/I31L) by site-directed mutagenesis. Active enzymes were expressed in Escherichia coli with periplasmic secretion and were purified to homogeneity. The kinetic parameters of enzymes were examined by spectroscopy assay and isothermal titration calorimetry (ITC), and their fibrinolytic activities were determined by fibrin plate method. The substitution of Leu(31) for Ile(31) resulted in about 2-fold enhancement of catalytic efficiency (Kcat/KM) compared with wild-type NK. The specific activities of both double-mutants (M222A/I31L and T220S/I31L) were significantly increased when compared with the single-mutants (M222A and T220S) and the oxidative stability of M222A/I31L mutant was enhanced with respect to wild-type NK. This study demonstrates the feasibility of improving activity of NK by site-directed mutagenesis and shows successful protein engineering cases to improve the activity of NK as a potent therapeutic agent. Copyright © 2015 Elsevier Inc. All rights reserved.

  10. Lentiviral vector-based insertional mutagenesis identifies genes associated with liver cancer

    Science.gov (United States)

    Ranzani, Marco; Cesana, Daniela; Bartholomae, Cynthia C.; Sanvito, Francesca; Pala, Mauro; Benedicenti, Fabrizio; Gallina, Pierangela; Sergi, Lucia Sergi; Merella, Stefania; Bulfone, Alessandro; Doglioni, Claudio; von Kalle, Christof; Kim, Yoon Jun; Schmidt, Manfred; Tonon, Giovanni; Naldini, Luigi; Montini, Eugenio

    2013-01-01

    Transposons and γ-retroviruses have been efficiently used as insertional mutagens in different tissues to identify molecular culprits of cancer. However, these systems are characterized by recurring integrations that accumulate in tumor cells, hampering the identification of early cancer-driving events amongst bystander and progression-related events. We developed an insertional mutagenesis platform based on lentiviral vectors (LVV) by which we could efficiently induce hepatocellular carcinoma (HCC) in 3 different mouse models. By virtue of LVV’s replication-deficient nature and broad genome-wide integration pattern, LVV-based insertional mutagenesis allowed identification of 4 new liver cancer genes from a limited number of integrations. We validated the oncogenic potential of all the identified genes in vivo, with different levels of penetrance. Our newly identified cancer genes are likely to play a role in human disease, since they are upregulated and/or amplified/deleted in human HCCs and can predict clinical outcome of patients. PMID:23314173

  11. Mechanisms of mutagenesis: DNA replication in the presence of DNA damage.

    Science.gov (United States)

    Liu, Binyan; Xue, Qizhen; Tang, Yong; Cao, Jia; Guengerich, F Peter; Zhang, Huidong

    2016-01-01

    Environmental mutagens cause DNA damage that disturbs replication and produces mutations, leading to cancer and other diseases. We discuss mechanisms of mutagenesis resulting from DNA damage, from the level of DNA replication by a single polymerase to the complex DNA replisome of some typical model organisms (including bacteriophage T7, T4, Sulfolobus solfataricus, Escherichia coli, yeast and human). For a single DNA polymerase, DNA damage can affect replication in three major ways: reducing replication fidelity, causing frameshift mutations, and blocking replication. For the DNA replisome, protein interactions and the functions of accessory proteins can yield rather different results even with a single DNA polymerase. The mechanism of mutation during replication performed by the DNA replisome is a long-standing question. Using new methods and techniques, the replisomes of certain organisms and human cell extracts can now be investigated with regard to the bypass of DNA damage. In this review, we consider the molecular mechanism of mutagenesis resulting from DNA damage in replication at the levels of single DNA polymerases and complex DNA replisomes, including translesion DNA synthesis. Copyright © 2016 Elsevier B.V. All rights reserved.

  12. Laboratory Activity to Promote Student Understanding of UV Mutagenesis and DNA Repair

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    Joshua Ernest Kouassi

    2017-05-01

    Full Text Available Changes in DNA molecules are common, due to the effects of UV light and other external and internal mutagens. Cells have a variety of repair mechanisms which serve to maintain the accuracy of the genetic code. This activity includes a low-cost, safe and technically feasible experiment, which allows students to observe the effects of UV mutagenesis and DNA photorepair in the halophilc archaeon, Haloferax volcanii. An optional extension links this activity to topics of immediate concern to students – how exposure to UVC light contributes to skin cancer risk and the protective effects of sunscreen. Students design and carry out an experiment to test whether SPF 15 sunscreen increases the lethal exposure time for H. volcanii by a factor of 15. Throughout the activity, discussion questions engage students in actively thinking about the biological phenomena and experimental procedures and analysis. This activity is designed for students in college or university genetics, microbiology, or introductory biology courses as well as in high school honors biology courses. Teachers report that this activity was valuable in helping students understand mutagenesis and photorepair and in developing student skills in designing and analyzing experiments.

  13. Increased activity of β-glucuronidase variants produced by site-directed mutagenesis.

    Science.gov (United States)

    Zhang, Xiaolei; Sitasuwan, Pongkwan; Horvath, Gary; Yang, Jia; Nie, Yuzhe; Marinova, Margarita; Lee, L Andrew; Wang, Qian

    2018-02-01

    β-glucuronidase (BGus) is an essential glycosyl hydrolase which has been widely used in biological and biomedical applications. In this paper, we report the construction and screening of nineteen Escherichia coli BGus (EBGus) mutants using site-directed mutagenesis. The mutants G559N, G559S and G559T showed a 3-5 fold increase in enzyme activity in comparison to wild type EBGus. In particular, G559S, with the highest activity, showed 2-6 fold enhanced activity compared to abalone and snail BGus extracts. Moreover, the glycine to serine mutagenesis for the same site in Staphylococcus sp. RLH1 BGus (StBGus) exhibited significantly enhanced activity, which indicated the importance of the G559→S mutation on BGus function. Based on this structural analysis, we postulate that the mutation at G559 plays an important role in the stabilization of the enzyme conformation, and thereby facilitates the effective binding of substrate. Copyright © 2017 Elsevier Inc. All rights reserved.

  14. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants.

    Science.gov (United States)

    Hehle, Verena K; Paul, Matthew J; Roberts, Victoria A; van Dolleweerd, Craig J; Ma, Julian K-C

    2016-04-01

    This study examined the degradation pattern of a murine IgG1κ monoclonal antibody expressed in and extracted from transformedNicotiana tabacum Gel electrophoresis of leaf extracts revealed a consistent pattern of recombinant immunoglobulin bands, including intact and full-length antibody, as well as smaller antibody fragments. N-terminal sequencing revealed these smaller fragments to be proteolytic cleavage products and identified a limited number of protease-sensitive sites in the antibody light and heavy chain sequences. No strictly conserved target sequence was evident, although the peptide bonds that were susceptible to proteolysis were predominantly and consistently located within or near to the interdomain or solvent-exposed regions in the antibody structure. Amino acids surrounding identified cleavage sites were mutated in an attempt to increase resistance. Different Guy's 13 antibody heavy and light chain mutant combinations were expressed transiently inN. tabacumand demonstrated intensity shifts in the fragmentation pattern, resulting in alterations to the full-length antibody-to-fragment ratio. The work strengthens the understanding of proteolytic cleavage of antibodies expressed in plants and presents a novel approach to stabilize full-length antibody by site-directed mutagenesis.-Hehle, V. K., Paul, M. J., Roberts, V. A., van Dolleweerd, C. J., Ma, J. K.-C. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants. © The Author(s).

  15. Randomization tests

    CERN Document Server

    Edgington, Eugene

    2007-01-01

    Statistical Tests That Do Not Require Random Sampling Randomization Tests Numerical Examples Randomization Tests and Nonrandom Samples The Prevalence of Nonrandom Samples in Experiments The Irrelevance of Random Samples for the Typical Experiment Generalizing from Nonrandom Samples Intelligibility Respect for the Validity of Randomization Tests Versatility Practicality Precursors of Randomization Tests Other Applications of Permutation Tests Questions and Exercises Notes References Randomized Experiments Unique Benefits of Experiments Experimentation without Mani

  16. Complex bifurcation lesions: Randomized comparison of a fully bioresorbable modified t stenting strategy versus bifurcation reconstruction with a dedicated self-expanding stent in combination with bioresorbable scaffolds, an OCT study: Rationale and design of the COBRA II trial.

    Science.gov (United States)

    Bennett, J; Adriaenssens, T; Desmet, W; Dubois, C

    2016-11-15

    There is an ongoing controversy regarding the efficacy and safety of different percutaneous stenting techniques for coronary bifurcation lesions needing >1 stent. The promise of safe vessel restoration with bioresorbable scaffolds (BRS) may not be transferable to complex double BRS bifurcation techniques, and permanent metallic scaffolding of the bifurcation core may be needed. We identified modified-T stenting as the most promising fully bioresorbable 2-stent strategy in a preclinical setting. The objective of this study is to assess acute performance and compare long-term vessel healing with this strategy, versus an approach combining BRS with a dedicated metallic drug-eluting bifurcation stent. In a single center, 60 consecutive patients with true and complex coronary bifurcation lesions will be randomly assigned to treatment with the dedicated self-expanding Axxess™ biolimus-eluting bifurcation stent in the proximal main vessel and additional Absorb™ everolimus-eluting BRS in the branches versus a modified T technique using Absorb™ only. Angiography and optical coherence tomography (OCT) will be performed immediately after implantation and at 30 months, and clinical follow-up is foreseen up to 5 years after implantation. The primary endpoint is the change in minimal luminal area assessed with OCT from baseline to 30 months in pre-specified bifurcation segments. To date the use of Absorb™ BRS in complex coronary bifurcations has not been evaluated in a randomized clinical trial setting. The COBRA II study will examine the role and safety of a double BRS strategy in coronary bifurcations, alone or in combination with a metallic dedicated bifurcation device. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  17. Role of Base Excision Repair (BER) in Transcription-associated Mutagenesis of Nutritionally Stressed Nongrowing Bacillus subtilis Cell Subpopulations.

    Science.gov (United States)

    Ambriz-Aviña, Verónica; Yasbin, Ronald E; Robleto, Eduardo A; Pedraza-Reyes, Mario

    2016-11-01

    Compelling evidence points to transcriptional processes as important factors contributing to stationary-phase associated mutagenesis. However, it has not been documented whether or not base excision repair mechanisms play a role in modulating mutagenesis under conditions of transcriptional derepression. Here, we report on a flow cytometry-based methodology that employs a fluorescent reporter system to measure at single-cell level, the occurrence of transcription-associated mutations in nutritionally stressed B. subtilis cultures. Using this approach, we demonstrate that (i) high levels of transcription correlates with augmented mutation frequency, and (ii) mutation frequency is enhanced in nongrowing population cells deficient for deaminated (Ung, YwqL) and oxidized guanine (GO) excision repair, strongly suggesting that accumulation of spontaneous DNA lesions enhance transcription-associated mutagenesis.

  18. 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 soma