WorldWideScience

Sample records for critical target sites

  1. SeedVicious: Analysis of microRNA target and near-target sites.

    Science.gov (United States)

    Marco, Antonio

    2018-01-01

    Here I describe seedVicious, a versatile microRNA target site prediction software that can be easily fitted into annotation pipelines and run over custom datasets. SeedVicious finds microRNA canonical sites plus other, less efficient, target sites. Among other novel features, seedVicious can compute evolutionary gains/losses of target sites using maximum parsimony, and also detect near-target sites, which have one nucleotide different from a canonical site. Near-target sites are important to study population variation in microRNA regulation. Some analyses suggest that near-target sites may also be functional sites, although there is no conclusive evidence for that, and they may actually be target alleles segregating in a population. SeedVicious does not aim to outperform but to complement existing microRNA prediction tools. For instance, the precision of TargetScan is almost doubled (from 11% to ~20%) when we filter predictions by the distance between target sites using this program. Interestingly, two adjacent canonical target sites are more likely to be present in bona fide target transcripts than pairs of target sites at slightly longer distances. The software is written in Perl and runs on 64-bit Unix computers (Linux and MacOS X). Users with no computing experience can also run the program in a dedicated web-server by uploading custom data, or browse pre-computed predictions. SeedVicious and its associated web-server and database (SeedBank) are distributed under the GPL/GNU license.

  2. The concept of target and critical loads

    International Nuclear Information System (INIS)

    Grigal, D.F.

    1991-09-01

    Target and critical loads were initially developed for assessment and control of acidic deposition, but are being considered for other air pollutants such as ozone and air-borne toxic compounds. These loads are based on thresholds, with damage assumed to occur above some defined level of deposition. Many of the historically proposed targets for acidic deposition were based on arbitrary interpretations of data. The concept of critical loads has recently separated from that of target loads. A critical load is the amount of pollutant deposition, determined by technical analysis, above which there is a specific deleterious ecological effect. A target load is the deposition, determined by political agreement, above which unacceptable ecological damage occurs; it may be greater than the critical load because of political or economic considerations, or less to conservatively account for uncertainty in the estimation of the critical load. Recent definitions of critical loads include recognition that each kind of ecosystem and effect may require a different load. Geographic regions contain a mosaic of aquatic and terrestrial resources. If precise knowledge leads to different critical loads for each system, then how is the regional target load established? For better or worse, target and critical loads are likely to be used to regulate air pollutants. The philosophy of their establishment as thresholds, their quantitative validity, and their application in regulation all require careful examination. 36 refs., 3 figs

  3. A Criticality Safety Study on Storing Unirradiated Cintichem-Type Targets at Sandia National Laboratories

    International Nuclear Information System (INIS)

    Romero, D.J.; Parma, E.J.; Busch, R.D.

    1999-01-01

    This criticality safety analysis is performed to determine the effective multiplication factor (k eff ) for a storage cabinet filled with unirradiated Cintichem-type targets. These targets will be used to produce 99 Mo at Sandia National Laboratories and will be stored on-site prior to irradiation in the Annular Core Research Reactor. The analysis consisted of using the Monte Carlo code MCNP (Version 4A) to model and predict the k eff for the proposed dry storage configuration under credible loss of geometry and moderator control. Effects of target pitch, non-uniform loading, and target internal/external flooding are evaluated. Further studies were done with deterministic methods to verify the results obtained from MCNP and to obtain a clearer understanding of the parameters affecting system criticality. The diffusion accelerated neutral particle transport code ONEDANT was used to model the target in a one-dimensional, infinite half-slab geometry and determine the critical slab thickness. Hand calculations were also completed to determine the critical slab thickness with modified one-group, and one-group, two region approximations. Results obtained from ONEDANT and the hand calculations were compared to applicable cases in a commonly used criticality safety analysis handbook. Overall, the critical slab thicknesses obtained in the deterministic analysis were much larger than the dimensions of the cabinet and further support the predictions by MCNP that a critical system cannot be attained for the base case or in conditions where loss of geometry and moderation control occur

  4. Predicting success of oligomerized pool engineering (OPEN for zinc finger target site sequences

    Directory of Open Access Journals (Sweden)

    Goodwin Mathew J

    2010-11-01

    Full Text Available Abstract Background Precise and efficient methods for gene targeting are critical for detailed functional analysis of genomes and regulatory networks and for potentially improving the efficacy and safety of gene therapies. Oligomerized Pool ENgineering (OPEN is a recently developed method for engineering C2H2 zinc finger proteins (ZFPs designed to bind specific DNA sequences with high affinity and specificity in vivo. Because generation of ZFPs using OPEN requires considerable effort, a computational method for identifying the sites in any given gene that are most likely to be successfully targeted by this method is desirable. Results Analysis of the base composition of experimentally validated ZFP target sites identified important constraints on the DNA sequence space that can be effectively targeted using OPEN. Using alternate encodings to represent ZFP target sites, we implemented Naïve Bayes and Support Vector Machine classifiers capable of distinguishing "active" targets, i.e., ZFP binding sites that can be targeted with a high rate of success, from those that are "inactive" or poor targets for ZFPs generated using current OPEN technologies. When evaluated using leave-one-out cross-validation on a dataset of 135 experimentally validated ZFP target sites, the best Naïve Bayes classifier, designated ZiFOpT, achieved overall accuracy of 87% and specificity+ of 90%, with an ROC AUC of 0.89. When challenged with a completely independent test set of 140 newly validated ZFP target sites, ZiFOpT performance was comparable in terms of overall accuracy (88% and specificity+ (92%, but with reduced ROC AUC (0.77. Users can rank potentially active ZFP target sites using a confidence score derived from the posterior probability returned by ZiFOpT. Conclusion ZiFOpT, a machine learning classifier trained to identify DNA sequences amenable for targeting by OPEN-generated zinc finger arrays, can guide users to target sites that are most likely to function

  5. Hiding Critical Targets in Smart Grid Networks

    Energy Technology Data Exchange (ETDEWEB)

    Bao, Wei [Univ. of Arkansas, Fayetteville, AR (United States); Li, Qinghua

    2017-10-23

    With the integration of advanced communication technologies, the power grid is expected to greatly enhance efficiency and reliability of future power systems. However, since most electrical devices in power grid substations are connected via communication networks, cyber security of these communication networks becomes a critical issue. Real-World incidents such as Stuxnet have shown the feasibility of compromising a device in the power grid network to further launch more sophisticated attacks. To deal with security attacks of this spirit, this paper aims to hide critical targets from compromised internal nodes and hence protect them from further attacks launched by those compromised nodes. In particular, we consider substation networks and propose to add carefully-controlled dummy traffic to a substation network to make critical target nodes indistinguishable from other nodes in network traffic patterns. This paper describes the design and evaluation of such a scheme. Evaluations show that the scheme can effectively protect critical nodes with acceptable communication cost.

  6. History of critical experiments at Pajarito Site

    International Nuclear Information System (INIS)

    Paxton, H.C.

    1983-03-01

    This account describes critical and subcritical assemblies operated remotely at the Pajarito Canyon Site at the Los Alamos National Laboratory. Earliest assemblies, directed exclusively toward the nuclear weapons program, were for safety tests. Other weapon-related assemblies provided neutronic information to check detailed weapon calculations. Topsy, the first of these critical assemblies, was followed by Lady Godiva, Jezebel, Flattop, and ultimately Big Ten. As reactor programs came to Los Alamos, design studies and mockups were tested at Pajarito Site. For example, nearly all 16 Rover reactors intended for Nevada tests were preceded by zero-power mockups and proof tests at Pajarito Site. Expanded interest and capability led to fast-pulse assemblies, culminating in Godiva IV and Skua, and to the Kinglet and Sheba solution assemblies

  7. History of critical experiments at Pajarito Site

    Energy Technology Data Exchange (ETDEWEB)

    Paxton, H.C.

    1983-03-01

    This account describes critical and subcritical assemblies operated remotely at the Pajarito Canyon Site at the Los Alamos National Laboratory. Earliest assemblies, directed exclusively toward the nuclear weapons program, were for safety tests. Other weapon-related assemblies provided neutronic information to check detailed weapon calculations. Topsy, the first of these critical assemblies, was followed by Lady Godiva, Jezebel, Flattop, and ultimately Big Ten. As reactor programs came to Los Alamos, design studies and mockups were tested at Pajarito Site. For example, nearly all 16 Rover reactors intended for Nevada tests were preceded by zero-power mockups and proof tests at Pajarito Site. Expanded interest and capability led to fast-pulse assemblies, culminating in Godiva IV and Skua, and to the Kinglet and Sheba solution assemblies.

  8. A new functional site W115 in CdtA is critical for Aggregatibacter actinomycetemcomitans cytolethal distending toxin.

    Directory of Open Access Journals (Sweden)

    Lu Li

    Full Text Available Aggregatibacter actinomycetemcomitans, a specific pathogen of localized aggressive periodontitis, produces a cytolethal distending toxin (CDT that arrests eukaryotic cells irreversibly in G0/G1 or G2/M phase of the cell cycle. Although structural studies show that the aromatic patch region of CdtA plays an important role in its biological activity, the functional sites of CdtA have not been firmly established. In this study, site-specific mutagenesis strategy was employed for cdtA point mutations construction so as to examine the contributions of individual amino acids to receptor binding and the biological activity of holotoxin. The binding ability was reduced in CdtA(Y181ABC holotoxin and the biological function of CDT was not weaken in CdtA(Y105ABC, CdtA(Y125ABC, CdtA(F109ABC and CdtA(S106NBC holotoxin suggesting that these sites were not critical to CDT. But the binding activity and cell cycle arrest ability of holotoxin complexes were inhibited in CdtA(W115GBC. And this site did not affect the holotoxin assembly by size exclusion chromatography. Therefore, W115 might be a critical site of CdtA binding ability. These findings suggest that the functional sites of CdtA are not only in the aromatic patch region. W115, the new functional site is critical for receptor binding and cell cycle arrest, which provides potential targets for pharmacological disruption of CDT activity.

  9. Retention of ferrofluid aggregates at the target site during magnetic drug targeting

    Energy Technology Data Exchange (ETDEWEB)

    Asfer, Mohammed, E-mail: asfer786@gmail.com [School of Engineering and Technology, BML Munjal University, Haryana (India); Saroj, Sunil Kumar [Department of Mechanical Engineering, IIT Kanpur, Kanpur (India); Panigrahi, Pradipta Kumar, E-mail: panig@iitk.ac.in [Department of Mechanical Engineering, IIT Kanpur, Kanpur (India)

    2017-08-15

    Highlights: • The present in vitro work reports the retention dynamics of ferrofluid aggregates at the target site against a bulk flow of DI water inside a micro capillary during magnetic drug targeting. • The recirculation zone at the downstream of the aggregate is found to be a function of aggregate height, Reynolds number and the degree of surface roughness of the outer boundary of the aggregate. • The reported results of the present work can be used as a guideline for the better design of MDT technique for in vivo applications. - Abstract: The present study reports the retention dynamics of a ferrofluid aggregate localized at the target site inside a glass capillary (500 × 500 µm{sup 2} square cross section) against a bulk flow of DI water (Re = 0.16 and 0.016) during the process of magnetic drug targeting (MDT). The dispersion dynamics of iron oxide nanoparticles (IONPs) into bulk flow for different initial size of aggregate at the target site is reported using the brightfield visualization technique. The flow field around the aggregate during the retention is evaluated using the µPIV technique. IONPs at the outer boundary experience a higher shear force as compared to the magnetic force, resulting in dispersion of IONPs into the bulk flow downstream to the aggregate. The blockage effect and the roughness of the outer boundary of the aggregate resulting from chain like clustering of IONPs contribute to the flow recirculation at the downstream region of the aggregate. The entrapment of seeding particles inside the chain like clusters of IONPs at the outer boundary of the aggregate reduces the degree of roughness resulting in a streamlined aggregate at the target site at later time. The effect of blockage, structure of the aggregate, and disturbed flow such as recirculation around the aggregate are the primary factors, which must be investigated for the effectiveness of the MDT process for in vivo applications.

  10. Operating procedures for the Pajarito Site Critical Assembly Facility

    International Nuclear Information System (INIS)

    Malenfant, R.E.

    1983-03-01

    Operating procedures consistent with DOE Order 5480.2, Chapter VI, and the American National Standard Safety Guide for the Performance of Critical Experiments are defined for the Pajarito Site Critical Assembly Facility of the Los Alamos National Laboratory. These operating procedures supersede and update those previously published in 1973 and apply to any criticality experiment performed at the facility

  11. Target-mediated drug disposition model for drugs with two binding sites that bind to a target with one binding site.

    Science.gov (United States)

    Gibiansky, Leonid; Gibiansky, Ekaterina

    2017-10-01

    The paper extended the TMDD model to drugs with two identical binding sites (2-1 TMDD). The quasi-steady-state (2-1 QSS), quasi-equilibrium (2-1 QE), irreversible binding (2-1 IB), and Michaelis-Menten (2-1 MM) approximations of the model were derived. Using simulations, the 2-1 QSS approximation was compared with the full 2-1 TMDD model. As expected and similarly to the standard TMDD for monoclonal antibodies (mAb), 2-1 QSS predictions were nearly identical to 2-1 TMDD predictions, except for times of fast changes following initiation of dosing, when equilibrium has not yet been reached. To illustrate properties of new equations and approximations, several variations of population PK data for mAbs with soluble (slow elimination of the complex) or membrane-bound (fast elimination of the complex) targets were simulated from a full 2-1 TMDD model and fitted to 2-1 TMDD models, to its approximations, and to the standard (1-1) QSS model. For a mAb with a soluble target, it was demonstrated that the 2-1 QSS model provided nearly identical description of the observed (simulated) free drug and total target concentrations, although there was some minor bias in predictions of unobserved free target concentrations. The standard QSS approximation also provided a good description of the observed data, but was not able to distinguish between free drug concentrations (with no target attached and both binding site free) and partially bound drug concentrations (with one of the binding sites occupied by the target). For a mAb with a membrane-bound target, the 2-1 MM approximation adequately described the data. The 2-1 QSS approximation converged 10 times faster than the full 2-1 TMDD, and its run time was comparable with the standard QSS model.

  12. Integrative Analysis of CRISPR/Cas9 Target Sites in the Human HBB Gene

    Directory of Open Access Journals (Sweden)

    Yumei Luo

    2015-01-01

    Full Text Available Recently, the clustered regularly interspaced short palindromic repeats (CRISPR system has emerged as a powerful customizable artificial nuclease to facilitate precise genetic correction for tissue regeneration and isogenic disease modeling. However, previous studies reported substantial off-target activities of CRISPR system in human cells, and the enormous putative off-target sites are labor-intensive to be validated experimentally, thus motivating bioinformatics methods for rational design of CRISPR system and prediction of its potential off-target effects. Here, we describe an integrative analytical process to identify specific CRISPR target sites in the human β-globin gene (HBB and predict their off-target effects. Our method includes off-target analysis in both coding and noncoding regions, which was neglected by previous studies. It was found that the CRISPR target sites in the introns have fewer off-target sites in the coding regions than those in the exons. Remarkably, target sites containing certain transcriptional factor motif have enriched binding sites of relevant transcriptional factor in their off-target sets. We also found that the intron sites have fewer SNPs, which leads to less variation of CRISPR efficiency in different individuals during clinical applications. Our studies provide a standard analytical procedure to select specific CRISPR targets for genetic correction.

  13. Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Raquel S Linheiro

    Full Text Available Transposable elements are mobile DNA sequences that integrate into host genomes using diverse mechanisms with varying degrees of target site specificity. While the target site preferences of some engineered transposable elements are well studied, the natural target preferences of most transposable elements are poorly characterized. Using population genomic resequencing data from 166 strains of Drosophila melanogaster, we identified over 8,000 new insertion sites not present in the reference genome sequence that we used to decode the natural target preferences of 22 families of transposable element in this species. We found that terminal inverted repeat transposon and long terminal repeat retrotransposon families present clade-specific target site duplications and target site sequence motifs. Additionally, we found that the sequence motifs at transposable element target sites are always palindromes that extend beyond the target site duplication. Our results demonstrate the utility of population genomics data for high-throughput inference of transposable element targeting preferences in the wild and establish general rules for terminal inverted repeat transposon and long terminal repeat retrotransposon target site selection in eukaryotic genomes.

  14. On Equivalence between Critical Probabilities of Dynamic Gossip Protocol and Static Site Percolation

    Science.gov (United States)

    Ishikawa, Tetsuya; Hayakawa, Tomohisa

    The relationship between the critical probability of gossip protocol on the square lattice and the critical probability of site percolation on the square lattice is discussed. Specifically, these two critical probabilities are analytically shown to be equal to each other. Furthermore, we present a way of evaluating the critical probability of site percolation by approximating the saturation of gossip protocol. Finally, we provide numerical results which support the theoretical analysis.

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

    Science.gov (United States)

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

    2016-01-01

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

  16. COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites

    Directory of Open Access Journals (Sweden)

    Thomas J Cradick

    2014-01-01

    Full Text Available Precise genome editing using engineered nucleases can significantly facilitate biological studies and disease treatment. In particular, clustered regularly interspaced short palindromic repeats (CRISPR with CRISPR-associated (Cas proteins are a potentially powerful tool for modifying a genome by targeted cleavage of DNA sequences complementary to designed guide strand RNAs. Although CRISPR/Cas systems can have on-target cleavage rates close to the transfection rates, they may also have relatively high off-target cleavage at similar genomic sites that contain one or more base pair mismatches, and insertions or deletions relative to the guide strand. We have developed a bioinformatics-based tool, COSMID (CRISPR Off-target Sites with Mismatches, Insertions, and Deletions that searches genomes for potential off-target sites (http://crispr.bme.gatech.edu. Based on the user-supplied guide strand and input parameters, COSMID identifies potential off-target sites with the specified number of mismatched bases and insertions or deletions when compared with the guide strand. For each site, amplification primers optimal for the chosen application are also given as output. This ranked-list of potential off-target sites assists the choice and evaluation of intended target sites, thus helping the design of CRISPR/Cas systems with minimal off-target effects, as well as the identification and quantification of CRISPR/Cas induced off-target cleavage in cells.

  17. Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies

    NARCIS (Netherlands)

    T. Niu (Tianhua); N. Liu (Ning); M. Zhao (Ming); G. Xie (Guie); L. Zhang (Lei); J. Li (Jian); Y.-F. Pei (Yu-Fang); H. Shen (Hui); X. Fu (Xiaoying); H. He (Hao); S. Lu (Shan); X. Chen (Xiangding); L. Tan (Lijun); T.-L. Yang (Tie-Lin); Y. Guo (Yan); P.J. Leo (Paul); E.L. Duncan (Emma); J. Shen (Jie); Y.-F. Guo (Yan-fang); G.C. Nicholson (Geoffrey); R.L. Prince (Richard L.); J.A. Eisman (John); G. Jones (Graeme); P.N. Sambrook (Philip); X. Hu (Xiang); P.M. Das (Partha M.); Q. Tian (Qing); X.-Z. Zhu (Xue-Zhen); C.J. Papasian (Christopher J.); M.A. Brown (Matthew); A.G. Uitterlinden (André); Y.-P. Wang (Yu-Ping); S. Xiang (Shuanglin); H.-W. Deng

    2015-01-01

    textabstractMicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNAs' Target Sites (poly-miRTS)-centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)-, and femoral neck

  18. Critical Radionuclide and Pathway Analysis for the Savannah River Site, 2016 Update

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, Tim [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL); Hartman, Larry [Savannah River Site (SRS), Aiken, SC (United States). Savannah River National Lab. (SRNL)

    2016-09-08

    During the operational history of Savannah River Site, many different radionuclides have been released from site facilities. However, as shown in this analysis, only a relatively small number of the released radionuclides have been significant contributors to doses to the offsite public. This report is an update to the 2011 analysis, Critical Radionuclide and Pathway Analysis for the Savannah River Site. SRS-based Performance Assessments for E-Area, Saltstone, F-Tank Farm, H-Tank Farm, and a Comprehensive SRS Composite Analysis have been completed. The critical radionuclides and pathways identified in those extensive reports are also detailed and included in this analysis.

  19. Characteristics of Food Industry Web Sites and "Advergames" Targeting Children

    Science.gov (United States)

    Culp, Jennifer; Bell, Robert A.; Cassady, Diana

    2010-01-01

    Objective: To assess the content of food industry Web sites targeting children by describing strategies used to prolong their visits and foster brand loyalty; and to document health-promoting messages on these Web sites. Design: A content analysis was conducted of Web sites advertised on 2 children's networks, Cartoon Network and Nickelodeon. A…

  20. Criticality codes migration to workstations at the Hanford site

    International Nuclear Information System (INIS)

    Miller, E.M.

    1993-01-01

    Westinghouse Hanford Company, Hanford Site Operations contractor, Richland, Washington, currently runs criticality codes on the Cray X-MP EA/232 computer but has recommended that US Department of Energy DOE-Richland replace the Cray with more economical workstations

  1. Computational design of trimeric influenza-neutralizing proteins targeting the hemagglutinin receptor binding site

    Energy Technology Data Exchange (ETDEWEB)

    Strauch, Eva-Maria; Bernard, Steffen M.; La, David; Bohn, Alan J.; Lee, Peter S.; Anderson, Caitlin E.; Nieusma, Travis; Holstein, Carly A.; Garcia, Natalie K.; Hooper, Kathryn A.; Ravichandran, Rashmi; Nelson, Jorgen W.; Sheffler, William; Bloom, Jesse D.; Lee, Kelly K.; Ward, Andrew B.; Yager, Paul; Fuller, Deborah H.; Wilson, Ian A.; Baker , David (UWASH); (Scripps); (FHCRC)

    2017-06-12

    Many viral surface glycoproteins and cell surface receptors are homo-oligomers1, 2, 3, 4, and thus can potentially be targeted by geometrically matched homo-oligomers that engage all subunits simultaneously to attain high avidity and/or lock subunits together. The adaptive immune system cannot generally employ this strategy since the individual antibody binding sites are not arranged with appropriate geometry to simultaneously engage multiple sites in a single target homo-oligomer. We describe a general strategy for the computational design of homo-oligomeric protein assemblies with binding functionality precisely matched to homo-oligomeric target sites5, 6, 7, 8. In the first step, a small protein is designed that binds a single site on the target. In the second step, the designed protein is assembled into a homo-oligomer such that the designed binding sites are aligned with the target sites. We use this approach to design high-avidity trimeric proteins that bind influenza A hemagglutinin (HA) at its conserved receptor binding site. The designed trimers can both capture and detect HA in a paper-based diagnostic format, neutralizes influenza in cell culture, and completely protects mice when given as a single dose 24 h before or after challenge with influenza.

  2. Criticality Safety Evaluation of Hanford Site High Level Waste Storage Tanks

    Energy Technology Data Exchange (ETDEWEB)

    ROGERS, C.A.

    2000-02-17

    This criticality safety evaluation covers operations for waste in underground storage tanks at the high-level waste tank farms on the Hanford site. This evaluation provides the bases for criticality safety limits and controls to govern receipt, transfer, and long-term storage of tank waste. Justification is provided that a nuclear criticality accident cannot occur for tank farms operations, based on current fissile material and operating conditions.

  3. Criticality Safety Evaluation of Hanford Site High-Level Waste Storage Tanks

    International Nuclear Information System (INIS)

    ROGERS, C.A.

    2000-01-01

    This criticality safety evaluation covers operations for waste in underground storage tanks at the high-level waste tank farms on the Hanford site. This evaluation provides the bases for criticality safety limits and controls to govern receipt, transfer, and long-term storage of tank waste. Justification is provided that a nuclear criticality accident cannot occur for tank farms operations, based on current fissile material and operating conditions

  4. Retroviral DNA integration: viral and cellular determinants of target-site selection.

    Directory of Open Access Journals (Sweden)

    Mary K Lewinski

    2006-06-01

    Full Text Available Retroviruses differ in their preferences for sites for viral DNA integration in the chromosomes of infected cells. Human immunodeficiency virus (HIV integrates preferentially within active transcription units, whereas murine leukemia virus (MLV integrates preferentially near transcription start sites and CpG islands. We investigated the viral determinants of integration-site selection using HIV chimeras with MLV genes substituted for their HIV counterparts. We found that transferring the MLV integrase (IN coding region into HIV (to make HIVmIN caused the hybrid to integrate with a specificity close to that of MLV. Addition of MLV gag (to make HIVmGagmIN further increased the similarity of target-site selection to that of MLV. A chimeric virus with MLV Gag only (HIVmGag displayed targeting preferences different from that of both HIV and MLV, further implicating Gag proteins in targeting as well as IN. We also report a genome-wide analysis indicating that MLV, but not HIV, favors integration near DNase I-hypersensitive sites (i.e., +/- 1 kb, and that HIVmIN and HIVmGagmIN also favored integration near these features. These findings reveal that IN is the principal viral determinant of integration specificity; they also reveal a new role for Gag-derived proteins, and strengthen models for integration targeting based on tethering of viral IN proteins to host proteins.

  5. Crops with target-site herbicide resistance for Orobanche and Striga control.

    Science.gov (United States)

    Gressel, Jonathan

    2009-05-01

    It is necessary to control root parasitic weeds before or as they attach to the crop. This can only be easily achieved chemically with herbicides that are systemic, or with herbicides that are active in soil. Long-term control can only be attained if the crops do not metabolise the herbicide, i.e. have target-site resistance. Such target-site resistances have allowed foliar applications of herbicides inhibiting enol-pyruvylshikimate phosphate synthase (EPSPS) (glyphosate), acetolactate synthase (ALS) (e.g. chlorsulfuron, imazapyr) and dihydropteroate synthase (asulam) for Orobanche control in experimental conditions with various crops. Large-scale use of imazapyr as a seed dressing of imidazolinone-resistant maize has been commercialised for Striga control. Crops with two target-site resistances will be more resilient to the evolution of resistance in the parasite, if well managed.

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

    Directory of Open Access Journals (Sweden)

    Voytas Daniel F

    2011-01-01

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

  7. CRITICAL RADIONUCLIDE AND PATHWAY ANALYSIS FOR THE SAVANNAH RIVER SITE

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, T.

    2011-08-30

    This report is an update to the analysis, Assessment of SRS Radiological Liquid and Airborne Contaminants and Pathways, that was performed in 1997. An electronic version of this large original report is included in the attached CD to this report. During the operational history (1954 to the present) of the Savannah River Site (SRS), many different radionuclides have been released to the environment from the various production facilities. However, as will be shown by this updated radiological critical contaminant/critical pathway analysis, only a small number of the released radionuclides have been significant contributors to potential doses and risks to offsite people. The analysis covers radiological releases to the atmosphere and to surface waters, the principal media that carry contaminants offsite. These releases potentially result in exposure to offsite people. The groundwater monitoring performed at the site shows that an estimated 5 to 10% of SRS has been contaminated by radionuclides, no evidence exists from the extensive monitoring performed that groundwater contaminated with these constituents has migrated off the site (SRS 2011). Therefore, with the notable exception of radiological source terms originating from shallow surface water migration into site streams, onsite groundwater was not considered as a potential exposure pathway to offsite people. In addition, in response to the Department of Energy's (DOE) Order 435.1, several Performance Assessments (WSRC 2008; LWO 2009; SRR 2010; SRR 2011) and a Comprehensive SRS Composite Analysis (SRNO 2010) have recently been completed at SRS. The critical radionuclides and pathways identified in these extensive reports are discussed and, where applicable, included in this analysis.

  8. Critical Path Driven Cosynthesis for Heterogeneous Target Architectures

    DEFF Research Database (Denmark)

    Bjørn-Jørgensen, Peter; Madsen, Jan

    1997-01-01

    This paper presents a critical path driven algorithm to produce a static schedule of a single-rate system onto a heterogeneous target architecture. Our algorithm is a list based scheduling algorithm which concurrently assigns tasks to processors and allocates nets to interprocessor communication........ Experimental results show that our algorithm is able to find good results, as compared to other methods, in small amount of CPU time....

  9. Use of a Web Site to Enhance Criticality Safety Training

    International Nuclear Information System (INIS)

    Huang, S T; Morman, J

    2003-01-01

    Currently, a website dedicated to enhancing communication and dissemination of criticality safety information is sponsored by the U.S. Department of Energy (DOE) Nuclear Criticality Safety Program (NCSP). This website was developed as part of the DOE response to the Defense Nuclear Facilities Safety Board (DNFSB) Recommendation 97-2, which reflected the need to make criticality safety information available to a wide audience. The website is the focal point for DOE nuclear criticality safety (NCS) activities, resources and references, including hyperlinks to other sites actively involved in the collection and dissemination of criticality safety information. The website is maintained by the Lawrence Livermore National Laboratory (LLNL) under auspices of the NCSP management. One area of the website contains a series of Nuclear Criticality Safety Engineer Training (NCSET) modules. During the past few years, many users worldwide have accessed the NCSET section of the NCSP website and have downloaded the training modules as an aid for their training programs. This trend was remarkable in that it points out a continuing need of the criticality safety community across the globe. It has long been recognized that training of criticality safety professionals is a continuing process involving both knowledge-based training and experience-based operations floor training. As more of the experienced criticality safety professionals reach retirement age, the opportunities for mentoring programs are reduced. It is essential that some method be provided to assist the training of young criticality safety professionals to replenish this limited human expert resource to support on-going and future nuclear operations. The main objective of this paper is to present the features of the NCSP website, including its mission, contents, and most importantly its use for the dissemination of training modules to the criticality safety community. We will discuss lessons learned and several ideas

  10. Enabling Quantitative Optical Imaging for In-die-capable Critical Dimension Targets

    Science.gov (United States)

    Barnes, B.M.; Henn, M.-A.; Sohn, M. Y.; Zhou, H.; Silver, R. M.

    2017-01-01

    Dimensional scaling trends will eventually bring semiconductor critical dimensions (CDs) down to only a few atoms in width. New optical techniques are required to address the measurement and variability for these CDs using sufficiently small in-die metrology targets. Recently, Qin et al. [Light Sci Appl, 5, e16038 (2016)] demonstrated quantitative model-based measurements of finite sets of lines with features as small as 16 nm using 450 nm wavelength light. This paper uses simulation studies, augmented with experiments at 193 nm wavelength, to adapt and optimize the finite sets of features that work as in-die-capable metrology targets with minimal increases in parametric uncertainty. A finite element based solver for time-harmonic Maxwell's equations yields two- and three-dimensional simulations of the electromagnetic scattering for optimizing the design of such targets as functions of reduced line lengths, fewer number of lines, fewer focal positions, smaller critical dimensions, and shorter illumination wavelength. Metrology targets that exceeded performance requirements are as short as 3 μm for 193 nm light, feature as few as eight lines, and are extensible to sub-10 nm CDs. Target areas measured at 193 nm can be fifteen times smaller in area than current state-of-the-art scatterometry targets described in the literature. This new methodology is demonstrated to be a promising alternative for optical model-based in-die CD metrology. PMID:28757674

  11. A new thermodynamic model for shaftwork targeting on total sites

    Energy Technology Data Exchange (ETDEWEB)

    Sorin, M.; Hammache, A. [CANMET Energy Technology Centre-Varennes, Quebec (Canada)

    2005-05-01

    The purpose of the paper is to introduce a targeting model based on a new thermodynamic insight on cogeneration in general and Rankine cycle in particular. The insight permits to express the ideal shaftwork of a cogeneration unit through the outlet heat load and the difference in Carnot factors between the heat source and heat sink for the given inlet temperature of the heat source. The deviation from the ideal shaftwork to the real one is assessed by using the traditionally turbine isentropic efficiency. Finally the new model allows targeting fuel consumption, cooling requirement and shaftwork production with high accuracy and visualizing then directly as special segments on the T-H diagram. A modified Site Utility Grand Composite Curve (SUGCC) diagram is proposed and compared to the original SUGCC. The shape of the right hand side of the diagram above site pinch is the same, however, below site pinch it is shifted to the left by an amount equal to shaftwork production below site pinch. Above site pinch VHP consumption is also corrected to account for shaftwork production above site pinch that is represented by segments rather than areas on the left hand side of the T-H diagram. (author)

  12. Mathematical description of drug-target interactions: application to biologics that bind to targets with two binding sites.

    Science.gov (United States)

    Gibiansky, Leonid; Gibiansky, Ekaterina

    2018-02-01

    The emerging discipline of mathematical pharmacology occupies the space between advanced pharmacometrics and systems biology. A characteristic feature of the approach is application of advance mathematical methods to study the behavior of biological systems as described by mathematical (most often differential) equations. One of the early application of mathematical pharmacology (that was not called this name at the time) was formulation and investigation of the target-mediated drug disposition (TMDD) model and its approximations. The model was shown to be remarkably successful, not only in describing the observed data for drug-target interactions, but also in advancing the qualitative and quantitative understanding of those interactions and their role in pharmacokinetic and pharmacodynamic properties of biologics. The TMDD model in its original formulation describes the interaction of the drug that has one binding site with the target that also has only one binding site. Following the framework developed earlier for drugs with one-to-one binding, this work aims to describe a rigorous approach for working with similar systems and to apply it to drugs that bind to targets with two binding sites. The quasi-steady-state, quasi-equilibrium, irreversible binding, and Michaelis-Menten approximations of the model are also derived. These equations can be used, in particular, to predict concentrations of the partially bound target (RC). This could be clinically important if RC remains active and has slow internalization rate. In this case, introduction of the drug aimed to suppress target activity may lead to the opposite effect due to RC accumulation.

  13. New emissions targeting strategy for site utility of process industries

    International Nuclear Information System (INIS)

    Manesh, Mohamamd Hasan Khoshgoftar; Amidpour, Majid; Hamedi, Mohammad Hosein; Abadi, Sajad Khamis; Ghalami, Hooman

    2013-01-01

    A new procedure for environmental targeting of co-generation system is presented. The proposed method is based on the concepts of pinch technology for total site targeting of fuel, power, steam, environmental impacts and total annualized cost with considering emissions taxes. This approach provides a consistent, general procedure for determining mass flow rates and efficiencies of the applied turbines. This algorithm utilizes the relationship of entropy with enthalpy and isentropic efficiency. Also, the life cycle assessment (LCA) as a well-known tool for analyzing environmental impacts on a wide perspective with reference to a product system and the related environmental and economic impacts have been applied. In this regard, a damage-oriented impact analysis method based on Eco-indicator 99 and footprints analysis was considered. In addition, the present work demonstrates the effect of including both sensible and latent heating of steam in the extended Site Utility Grand Composite Curve (ESUGCC). It is shown that including sensible heating allows for better thermal matching between the processes. Furthermore, the other representation YSUGCC as the other form of Site Utility Grand Composite has been proposed. Two case studies were used to illustrate the usefulness of the new environmental targeting method

  14. Methods to measure target site penetration of antibiotics in critically ill patients.

    Science.gov (United States)

    Schwameis, Richard; Zeitlinger, Markus

    2013-02-01

    While several tools are necessary to repair a car, the engineer knows exactly which instrument he has to utilize at different parts of the broken machine. Likewise, depending on the information we are interested in, we have to choose different tools to investigate and consecutively understand the multiple aspects that are involved in pharmacokinetics of antimicrobial agents in critically ill patients. Some techniques, like blood sampling, microdialysis or positrons emission tomography (PET) will allow for obtaining continues concentration time profiles while others like bronchoalveolar lavage (BAL), biopsy or surgical tissue samples can only be used a limited number of times per subject. PET and methods based on tissue homogenization will deliver an average of the actual concentrations in intra - and extracellular compartments while investigations in isolated blood cells or microdialysis allow for more distinguished allocation of a concentration to a defined compartment. The present review aims at discussing the advantages and disadvantages of the various methods used for assessing pharmacokinetics in critically ill patients with regard to specific aspects of pharmacokinetic research and further reviews data of selected antibiotics as examples for applications of the individual techniques.

  15. Criticality safety engineering at the Savannah River Site - the 1990s

    International Nuclear Information System (INIS)

    Chandler, J.R.; Apperson, C.E. Jr.

    1996-01-01

    The privatization and downsizing effort that is ongoing within the U.S. Department of Energy (DOE) is requiring a change in the management of criticality safety engineering resources at the Savannah River Site (SRS). Downsizing affects the number of criticality engineers employed by the prime contractor, Westinghouse Savannah River Company (WSRC), and privatization affects the manner in which business is conducted. In the past, criticality engineers at the SRS have been part of the engineering organizations that support each facility handling fissile material. This practice led to different criticality safety engineering organizations dedicated to fuel fabrication activities, reactor loading and unloading activities, separation and waste management operations, and research and development

  16. Evidence from EXAFS for Different Ta/Ti Site Occupancy in High Critical Current Density Nb3Sn Superconductor Wires.

    Science.gov (United States)

    Heald, Steve M; Tarantini, Chiara; Lee, Peter J; Brown, Michael D; Sung, ZuHawn; Ghosh, Arup K; Larbalestier, David C

    2018-03-19

    To meet critical current density, J c , targets for the Future Circular Collider (FCC), the planned replacement for the Large Hadron Collider (LHC), the high field performance of Nb 3 Sn must be improved, but champion J c values have remained static for the last 10 years. Making the A15 phase stoichiometric and enhancing the upper critical field H c2 by Ti or Ta dopants are the standard strategies for enhancing high field performance but detailed recent studies show that even the best modern wires have broad composition ranges. To assess whether further improvement might be possible, we employed Extended X-ray Absorption Fine Structure (EXAFS) to determine the lattice site location of dopants in modern high-performance Nb 3 Sn strands with J c values amongst the best so far achieved. Although Ti and Ta primarily occupy the Nb sites in the A15 structure, we also find significant Ta occupancy on the Sn site. These findings indicate that the best performing Ti-doped stand is strongly sub-stoichiometric in Sn and that antisite disorder likely explains its high average H c2 behavior. These new results suggest an important role for dopant and antisite disorder in minimizing superconducting property distributions and maximizing high field J c properties.

  17. Technical specifications for the Pajarito Site Critical Experiments Facility

    International Nuclear Information System (INIS)

    Malenfant, R.E.; Paxton, H.C.

    1980-12-01

    This document is to satisfy the requirement for technical specifications spelled out in DOE Manual Chapter 0540, Safety of DOE-Owned Reactors. Technical specifications are defined in Sec. 0540-048, and the requirement for them appears in Sec. 0540-015. The following technical specifications update the document, Technical Specifications for the Pajarito Site Critical Experiments Facility

  18. High level radioactive waste siting processes: critical lessons from Canadian siting successes

    International Nuclear Information System (INIS)

    Hardy, D.R.

    1996-01-01

    While not without controversy, Canada's Crown Corporations, municipalities, agencies and private companies have had success in siting and achieving approval for operating: toxic and hazardous waste facilities; dry radioactive materials storage facilities; the Federal low-level radioactive waste disposal facility; and, several large and small domestic landfills. The cumulative experience gained from these siting and approval processes provides valuable advice in support of the siting and approval of high-level radioactive disposal facilities. Among the critical elements for the success of these siting efforts are: 1) the tinting, scope and character of the siting process reflects the cultural and social values of affected people; 2) the siting and approval processes has integrity -- characterized as rational processes in pursuit of the public interest; 3) sufficient time and resources are dedicated to listening carefully and examining issues seen to be important by the public; 4) all information is shared -- even if the information is potentially detrimental to the approval of the facility; 5) proponent has a prioritized multiple focus on 'health, safety and environment issues', on 'insuring that the environmental assessment process is socially acceptable' as well as on the 'approval considerations'; 6) the implementing agency seeks cooperation and win-win solutions with the local community; 7) the community has the option of opting-out of the process and the do-nothing and/or the not here option continues to be considered by the proponent; 8) local emergency response people are well-trained and accepting of the facility; 9) the community has a strong role in determining the terms, conditions and compensation related to the future facility. (author)

  19. Earthquake research for the safer siting of critical facilities

    Energy Technology Data Exchange (ETDEWEB)

    Cluff, J.L. (ed.)

    1980-01-01

    The task of providing the necessities for living, such as adequate electrical power, water, and fuel, is becoming more complicated with time. Some of the facilities that provide these necessities would present potential hazards to the population if serious damage were to occur to them during earthquakes. Other facilities must remain operable immediately after an earthquake to provide life-support services to people who have been affected. The purpose of this report is to recommend research that will improve the information available to those who must decide where to site these critical facilities, and thereby mitigate the effects of the earthquake hazard. The term critical facility is used in this report to describe facilities that could seriously affect the public well-being through loss of life, large financial loss, or degradation of the environment if they were to fail. The term critical facility also is used to refer to facilities that, although they pose a limited hazard to the public, are considered critical because they must continue to function in the event of a disaster so that they can provide vital services.

  20. Characteristics of food industry web sites and "advergames" targeting children.

    Science.gov (United States)

    Culp, Jennifer; Bell, Robert A; Cassady, Diana

    2010-01-01

    To assess the content of food industry Web sites targeting children by describing strategies used to prolong their visits and foster brand loyalty; and to document health-promoting messages on these Web sites. A content analysis was conducted of Web sites advertised on 2 children's networks, Cartoon Network and Nickelodeon. A total of 290 Web pages and 247 unique games on 19 Internet sites were examined. Games, found on 81% of Web sites, were the most predominant promotion strategy used. All games had at least 1 brand identifier, with logos being most frequently used. On average Web sites contained 1 "healthful" message for every 45 exposures to brand identifiers. Food companies use Web sites to extend their television advertising to promote brand loyalty among children. These sites almost exclusively promoted food items high in sugar and fat. Health professionals need to monitor food industry marketing practices used in "new media." Published by Elsevier Inc.

  1. Is there a critical lesion site for unilateral spatial neglect? A meta-analysis using activation likelihood estimation.

    Directory of Open Access Journals (Sweden)

    Pascal eMolenberghs

    2012-04-01

    Full Text Available The critical lesion site responsible for the syndrome of unilateral spatial neglect has been debated for more than a decade. Here we performed an activation likelihood estimation (ALE to provide for the first time an objective quantitative index of the consistency of lesion sites across anatomical group studies of spatial neglect. The analysis revealed several distinct regions in which damage has consistently been associated with spatial neglect symptoms. Lesioned clusters were located in several cortical and subcortical regions of the right hemisphere, including the middle and superior temporal gyrus, inferior parietal lobule, intraparietal sulcus, precuneus, middle occipital gyrus, caudate nucleus and posterior insula, as well as in the white matter pathway corresponding to the posterior part of the superior longitudinal fasciculus. Further analyses suggested that separate lesion sites are associated with impairments in different behavioural tests, such as line bisection and target cancellation. Similarly, specific subcomponents of the heterogeneous neglect syndrome, such as extinction and allocentric and personal neglect, are associated with distinct lesion sites. Future progress in delineating the neuropathological correlates of spatial neglect will depend upon the development of more refined measures of perceptual and cognitive functions than those currently available in the clinical setting.

  2. The SCALE Web site: Resources for the worldwide nuclear criticality safety community

    International Nuclear Information System (INIS)

    Bowman, S.M.

    2000-01-01

    The Standardized Computer Analyses for Licensing Evaluations (SCALE) computer software system developed at Oak Ridge National Laboratory (ORNL) is widely used and accepted around the world for criticality safety analyses. SCALE includes the well-known KENO V.a and KENO VI three-dimensional Monte Carlo criticality computer codes. For several years, the SCALE staff at ORNL has maintained a Web site to provide information and support to sponsors and users in the worldwide criticality safety community. The SCALE WEB site is located at www.cped.ornl.gov/scale and provides information in the following areas: 1. important notices to users; 2. SCALE Users Electronic Notebook; 3. current and past issues of the SCALE Newsletter; 4. verification and validation (V and V) and benchmark reports; 5. download updates, utilities, and V and V input files; 6. SCALE training course information; 7. SCALE Manual on-line; 8. overview of SCALE system; 9. how to install and run SCALE; 10. SCALE quality assurance documents; and 11. nuclear resources on the Internet

  3. Use of a web site to enhance criticality safety training

    International Nuclear Information System (INIS)

    Huang, Song T.; Morman, James A.

    2003-01-01

    Establishment of the NCSP (Nuclear Criticality Safety Program) website represents one attempt by the NCS (Nuclear Criticality Safety) community to meet the need to enhance communication and disseminate NCS information to a wider audience. With the aging work force in this important technical field, there is a common recognition of the need to capture the corporate knowledge of these people and provide an easily accessible, web-based training opportunity to those people just entering the field of criticality safety. A multimedia-based site can provide a wide range of possibilities for criticality safety training. Training modules could range from simple text-based material, similar to the NCSET (Nuclear Criticality Safety Engineer Training) modules, to interactive web-based training classes, to video lecture series. For example, the Los Alamos National Laboratory video series of interviews with pioneers of criticality safety could easily be incorporated into training modules. Obviously, the development of such a program depends largely upon the need and participation of experts who share the same vision and enthusiasm of training the next generation of criticality safety engineers. The NCSP website is just one example of the potential benefits that web-based training can offer. You are encouraged to browse the NCSP website at http://ncsp.llnl.gov. We solicit your ideas in the training of future NCS engineers and welcome your participation with us in developing future multimedia training modules. (author)

  4. Multimedia approach to estimating target cleanup levels for soils at hazardous waste sites

    International Nuclear Information System (INIS)

    Hwang, S.T.

    1990-04-01

    Contaminated soils at hazardous and nuclear waste sites pose a potential threat to human health via transport through environmental media and subsequent human intake. To minimize health risks, it is necessary to identify those risks and ensure that appropriate actions are taken to protect public health. The regulatory process may typically include identification of target cleanup levels and evaluation of the effectiveness of remedial alternatives and the corresponding reduction in risks at a site. The US Environmental Protection Agency (EPA) recommends that exposure assessments be combined with toxicity information to quantify the health risk posed by a specific site. This recommendation then forms the basis for establishing target cleanup levels. An exposure assessment must first identify the chemical concentration in a specific medium (soil, water, air, or food), estimate the exposure potential based on human intake from that media, and then combined with health criteria to estimate the upperbound health risks for noncarcinogens and carcinogens. Estimation of target cleanup levels involves the use of these same principles but can occur in reverse order. The procedure starts from establishing a permissible health effect level and ends with an estimated target cleanup level through an exposure assessment process. 17 refs

  5. Virtual-site correlation mean field approach to criticality in spin systems

    International Nuclear Information System (INIS)

    Sen, Aditi; Sen, Ujjwal

    2013-01-01

    We propose a virtual-site correlation mean field theory for dealing with interacting many-body systems. It involves a coarse-graining technique that terminates a step before the mean field theory: While mean field theory deals with only single-body physical parameters, the virtual-site correlation mean field theory deals with single- as well as two-body ones, and involves a virtual site for every interaction term in the Hamiltonian. We generalize the theory to a cluster virtual-site correlation mean field, that works with a fundamental unit of the lattice of the many-body system. We apply these methods to interacting Ising spin systems in several lattice geometries and dimensions, and show that the predictions of the onset of criticality of these models are generally much better in the proposed theories as compared to the corresponding ones in mean field theories

  6. Radioligand Recognition of Insecticide Targets.

    Science.gov (United States)

    Casida, John E

    2018-04-04

    Insecticide radioligands allow the direct recognition and analysis of the targets and mechanisms of toxic action critical to effective and safe pest control. These radioligands are either the insecticides themselves or analogs that bind at the same or coupled sites. Preferred radioligands and their targets, often in both insects and mammals, are trioxabicyclooctanes for the γ-aminobutyric acid (GABA) receptor, avermectin for the glutamate receptor, imidacloprid for the nicotinic receptor, ryanodine and chlorantraniliprole for the ryanodine receptor, and rotenone or pyridaben for NADH + ubiquinone oxidoreductase. Pyrethroids and other Na + channel modulator insecticides are generally poor radioligands due to lipophilicity and high nonspecific binding. For target site validation, the structure-activity relationships competing with the radioligand in the binding assays should be the same as that for insecticidal activity or toxicity except for rapidly detoxified or proinsecticide analogs. Once the radioligand assay is validated for relevance, it will often help define target site modifications on selection of resistant pest strains, selectivity between insects and mammals, and interaction with antidotes and other chemicals at modulator sites. Binding assays also serve for receptor isolation and photoaffinity labeling to characterize the interactions involved.

  7. An integrated CRISPR Bombyx mori genome editing system with improved efficiency and expanded target sites.

    Science.gov (United States)

    Ma, Sanyuan; Liu, Yue; Liu, Yuanyuan; Chang, Jiasong; Zhang, Tong; Wang, Xiaogang; Shi, Run; Lu, Wei; Xia, Xiaojuan; Zhao, Ping; Xia, Qingyou

    2017-04-01

    Genome editing enabled unprecedented new opportunities for targeted genomic engineering of a wide variety of organisms ranging from microbes, plants, animals and even human embryos. The serial establishing and rapid applications of genome editing tools significantly accelerated Bombyx mori (B. mori) research during the past years. However, the only CRISPR system in B. mori was the commonly used SpCas9, which only recognize target sites containing NGG PAM sequence. In the present study, we first improve the efficiency of our previous established SpCas9 system by 3.5 folds. The improved high efficiency was also observed at several loci in both BmNs cells and B. mori embryos. Then to expand the target sites, we showed that two newly discovered CRISPR system, SaCas9 and AsCpf1, could also induce highly efficient site-specific genome editing in BmNs cells, and constructed an integrated CRISPR system. Genome-wide analysis of targetable sites was further conducted and showed that the integrated system cover 69,144,399 sites in B. mori genome, and one site could be found in every 6.5 bp. The efficiency and resolution of this CRISPR platform will probably accelerate both fundamental researches and applicable studies in B. mori, and perhaps other insects. Copyright © 2017 Elsevier Ltd. All rights reserved.

  8. Novel and viable acetylcholinesterase target site for developing effective and environmentally safe insecticides.

    Science.gov (United States)

    Pang, Yuan-Ping; Brimijoin, Stephen; Ragsdale, David W; Zhu, Kun Yan; Suranyi, Robert

    2012-04-01

    Insect pests are responsible for human suffering and financial losses worldwide. New and environmentally safe insecticides are urgently needed to cope with these serious problems. Resistance to current insecticides has resulted in a resurgence of insect pests, and growing concerns about insecticide toxicity to humans discourage the use of insecticides for pest control. The small market for insecticides has hampered insecticide development; however, advances in genomics and structural genomics offer new opportunities to develop insecticides that are less dependent on the insecticide market. This review summarizes the literature data that support the hypothesis that an insect-specific cysteine residue located at the opening of the acetylcholinesterase active site is a promising target site for developing new insecticides with reduced off-target toxicity and low propensity for insect resistance. These data are used to discuss the differences between targeting the insect-specific cysteine residue and targeting the ubiquitous catalytic serine residue of acetylcholinesterase from the perspective of reducing off-target toxicity and insect resistance. Also discussed is the prospect of developing cysteine-targeting anticholinesterases as effective and environmentally safe insecticides for control of disease vectors, crop damage, and residential insect pests within the financial confines of the present insecticide market.

  9. Criticality of the random-site Ising model: Metropolis, Swendsen-Wang and Wolff Monte Carlo algorithms

    Directory of Open Access Journals (Sweden)

    D.Ivaneyko

    2005-01-01

    Full Text Available We apply numerical simulations to study of the criticality of the 3D Ising model with random site quenched dilution. The emphasis is given to the issues not being discussed in detail before. In particular, we attempt a comparison of different Monte Carlo techniques, discussing regions of their applicability and advantages/disadvantages depending on the aim of a particular simulation set. Moreover, besides evaluation of the critical indices we estimate the universal ratio Γ+/Γ- for the magnetic susceptibility critical amplitudes. Our estimate Γ+/Γ- = 1.67 ± 0.15 is in a good agreement with the recent MC analysis of the random-bond Ising model giving further support that both random-site and random-bond dilutions lead to the same universality class.

  10. Renton's Quendall Terminals on List of EPA Superfund Sites Targeted for Immediate, Intense Attention

    Science.gov (United States)

    EPA released the list of Superfund sites that Administrator Pruitt has targeted for intense and immediate attention, including the Quendall Terminals Site, a former creosote facility on the shore of Lake Washington in Renton, Washington.

  11. INR targets and site-level anticoagulation control: results from the Veterans AffaiRs Study to Improve Anticoagulation (VARIA).

    Science.gov (United States)

    Rose, A J; Berlowitz, D R; Miller, D R; Hylek, E M; Ozonoff, A; Zhao, S; Reisman, J I; Ash, A S

    2012-04-01

    Not all clinicians target the same International Normalized Ratio (INR) for patients with a guideline-recommended target range of 2-3. A patient's mean INR value suggests the INR that was actually targeted. We hypothesized that sites would vary by mean INR, and that sites of care with mean values nearest to 2.5 would achieve better anticoagulation control, as measured by per cent time in therapeutic range (TTR). To examine variations among sites in mean INR and the relationship with anticoagulation control in an integrated system of care. We studied 103,897 patients receiving oral anticoagulation with an expected INR target between 2 and 3 at 100 Veterans Health Administration (VA) sites from 1 October 2006 to 30 September 2008. Key site-level variables were: proportion near 2.5 (that is, percentage of patients with mean INR between 2.3 and 2.7) and mean risk-adjusted TTR. Site mean INR ranged from 2.22 to 2.89; proportion near 2.5, from 30 to 64%. Sites' proportions of patients near 2.5, below 2.3 and above 2.7 were consistent from year to year. A 10 percentage point increase in the proportion near 2.5 predicted a 3.8 percentage point increase in risk-adjusted TTR (P < 0.001). Proportion of patients with mean INR near 2.5 is a site-level 'signature' of care and an implicit measure of targeted INR. This proportion varies by site and is strongly associated with site-level TTR. Our study suggests that sites wishing to improve TTR, and thereby improve patient outcomes, should avoid the explicit or implicit pursuit of non-standard INR targets. © 2012 International Society on Thrombosis and Haemostasis.

  12. Nuclear incident monitor criticality alarm instrument for the Savannah River Site: Technical manual

    International Nuclear Information System (INIS)

    Jenkins, J.B.

    1996-01-01

    The Savannah River Site is a Department of Energy facility. The facility stores, processes, and works with fissionable material at a number of locations. Technical standards and US Department of Energy orders, require these locations to be monitored by criticality alarm systems under certain circumstances. The Savannah River Site calls such instruments Nuclear Incident Monitors or NIMs. The Sole purpose of the Nuclear Incident Monitor is to provide an immediate evacuation signal in the case of an accidental criticality in order to minimize personnel exposure to radiation. The new unit is the third generation Nuclear Incident Monitor at the Savannah River Site. The second generation unit was developed in 1979. It was designed to eliminate vacuum-tube circuits, and was the first solid state NIM at SRS. The major design objectives of the second generation NIM were to improve reliability and reduce maintenance costs. Ten prototype units have been built and tested. This report describes the design of the new NIM and the testing that took place to verify its acceptability

  13. Retroviral DNA integration: ASLV, HIV, and MLV show distinct target site preferences.

    Directory of Open Access Journals (Sweden)

    Rick S Mitchell

    2004-08-01

    Full Text Available The completion of the human genome sequence has made possible genome-wide studies of retroviral DNA integration. Here we report an analysis of 3,127 integration site sequences from human cells. We compared retroviral vectors derived from human immunodeficiency virus (HIV, avian sarcoma-leukosis virus (ASLV, and murine leukemia virus (MLV. Effects of gene activity on integration targeting were assessed by transcriptional profiling of infected cells. Integration by HIV vectors, analyzed in two primary cell types and several cell lines, strongly favored active genes. An analysis of the effects of tissue-specific transcription showed that it resulted in tissue-specific integration targeting by HIV, though the effect was quantitatively modest. Chromosomal regions rich in expressed genes were favored for HIV integration, but these regions were found to be interleaved with unfavorable regions at CpG islands. MLV vectors showed a strong bias in favor of integration near transcription start sites, as reported previously. ASLV vectors showed only a weak preference for active genes and no preference for transcription start regions. Thus, each of the three retroviruses studied showed unique integration site preferences, suggesting that virus-specific binding of integration complexes to chromatin features likely guides site selection.

  14. Novel acetylcholinesterase target site for malaria mosquito control.

    Directory of Open Access Journals (Sweden)

    Yuan-Ping Pang

    2006-12-01

    Full Text Available Current anticholinesterase pesticides were developed during World War II and are toxic to mammals because they target a catalytic serine residue of acetylcholinesterases (AChEs in insects and in mammals. A sequence analysis of AChEs from 73 species and a three-dimensional model of a malaria-carrying mosquito (Anopheles gambiae AChE (AgAChE reported here show that C286 and R339 of AgAChE are conserved at the opening of the active site of AChEs in 17 invertebrate and four insect species, respectively. Both residues are absent in the active site of AChEs of human, monkey, dog, cat, cattle, rabbit, rat, and mouse. The 17 invertebrates include house mosquito, Japanese encephalitis mosquito, African malaria mosquito, German cockroach, Florida lancelet, rice leaf beetle, African bollworm, beet armyworm, codling moth, diamondback moth, domestic silkworm, honey bee, oat or wheat aphid, the greenbug, melon or cotton aphid, green peach aphid, and English grain aphid. The four insects are house mosquito, Japanese encephalitis mosquito, African malaria mosquito, and German cockroach. The discovery of the two invertebrate-specific residues enables the development of effective and safer pesticides that target the residues present only in mosquito AChEs rather than the ubiquitous serine residue, thus potentially offering an effective control of mosquito-borne malaria. Anti-AgAChE pesticides can be designed to interact with R339 and subsequently covalently bond to C286. Such pesticides would be toxic to mosquitoes but not to mammals.

  15. Targeting Alternative Sites on the Androgen Receptor to Treat Castration-Resistant Prostate Cancer

    Directory of Open Access Journals (Sweden)

    Paul S. Rennie

    2013-06-01

    Full Text Available Recurrent, metastatic prostate cancer continues to be a leading cause of cancer-death in men. The androgen receptor (AR is a modular, ligand-inducible transcription factor that regulates the expression of genes that can drive the progression of this disease, and as a consequence, this receptor is a key therapeutic target for controlling prostate cancer. The current drugs designed to directly inhibit the AR are called anti-androgens, and all act by competing with androgens for binding to the androgen/ligand binding site. Unfortunately, with the inevitable progression of the cancer to castration resistance, many of these drugs become ineffective. However, there are numerous other regulatory sites on this protein that have not been exploited therapeutically. The regulation of AR activity involves a cascade of complex interactions with numerous chaperones, co-factors and co-regulatory proteins, leading ultimately to direct binding of AR dimers to specific DNA androgen response elements within the promoter and enhancers of androgen-regulated genes. As part of the family of nuclear receptors, the AR is organized into modular structural and functional domains with specialized roles in facilitating their inter-molecular interactions. These regions of the AR present attractive, yet largely unexploited, drug target sites for reducing or eliminating androgen signaling in prostate cancers. The design of small molecule inhibitors targeting these specific AR domains is only now being realized and is the culmination of decades of work, including crystallographic and biochemistry approaches to map the shape and accessibility of the AR surfaces and cavities. Here, we review the structure of the AR protein and describe recent advancements in inhibiting its activity with small molecules specifically designed to target areas distinct from the receptor’s androgen binding site. It is anticipated that these new classes of anti-AR drugs will provide an additional

  16. A mathematical model of single target site location by Brownian movement in subcellular compartments.

    Science.gov (United States)

    Kuthan, Hartmut

    2003-03-07

    The location of distinct sites is mandatory for many cellular processes. In the subcompartments of the cell nucleus, only very small numbers of diffusing macromolecules and specific target sites of some types may be present. In this case, we are faced with the Brownian movement of individual macromolecules and their "random search" for single/few specific target sites, rather than bulk-averaged diffusion and multiple sites. In this article, I consider the location of a distant central target site, e.g. a globular protein, by individual macromolecules executing unbiased (i.e. drift-free) random walks in a spherical compartment. For this walk-and-capture model, the closed-form analytic solution of the first passage time probability density function (p.d.f.) has been obtained as well as the first and second moment. In the limit of a large ratio of the radii of the spherical diffusion space and central target, well-known relations for the variance and the first two moments for the exponential p.d.f. were found to hold with high accuracy. These calculations reinforce earlier numerical results and Monte Carlo simulations. A major implication derivable from the model is that non-directed random movement is an effective means for locating single sites in submicron-sized compartments, even when the diffusion coefficients are comparatively small and the diffusing species are present in one copy only. These theoretical conclusions are underscored numerically for effective diffusion constants ranging from 0.5 to 10.0 microm(2) s(-1), which have been reported for a couple of nuclear proteins in their physiological environment. Spherical compartments of submicron size are, for example, the Cajal bodies (size: 0.1-1.0 microm), which are present in 1-5 copies in the cell nucleus. Within a small Cajal body of radius 0.1 microm a single diffusing protein molecule (with D=0.5 microm(2) s(-1)) would encounter a medium-sized protein of radius 2.5 nm within 1 s with a probability near

  17. Engineered Proteins Program Mammalian Cells to Target Inflammatory Disease Sites.

    Science.gov (United States)

    Qudrat, Anam; Mosabbir, Abdullah Al; Truong, Kevin

    2017-06-22

    Disease sites in atherosclerosis and cancer feature cell masses (e.g., plaques/tumors), a low pH extracellular microenvironment, and various pro-inflammatory cytokines such as tumor necrosis factor α (TNFα). The ability to engineer a cell to seek TNFα sources allows for targeted therapeutic delivery. To accomplish this, here we introduced a system of proteins: an engineered TNFα chimeric receptor (named TNFR1chi), a previously engineered Ca 2+ -activated RhoA (named CaRQ), vesicular stomatitis virus glycoprotein G (VSVG), and thymidine kinase. Upon binding TNFα, TNFR1chi generates a Ca 2+ signal that in turn activates CaRQ-mediated non-apoptotic blebs that allow migration toward the TNFα source. Next, the addition of VSVG, upon low pH induction, causes membrane fusion of the engineered and TNFα source cells. Finally, after ganciclovir treatment cells undergo death via the thymidine kinase suicide mechanism. Hence, we assembled a system of proteins that forms the basis of engineering a cell to target inflammatory disease sites characterized by TNFα secretion and a low-pH microenvironment. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Centredale Manor Superfund Site in Rhode Island included on EPA List of Targeted for Immediate Attention

    Science.gov (United States)

    Today, the U.S. Environmental Protection Agency released the list of Superfund sites that Administrator Pruitt has targeted for immediate and intense attention. The Centredale Manor Restoration Project superfund site is one of the 21 sites on the list.

  19. Some problems of neutron source multiplication method for site measurement technology in nuclear critical safety

    International Nuclear Information System (INIS)

    Shi Yongqian; Zhu Qingfu; Hu Dingsheng; He Tao; Yao Shigui; Lin Shenghuo

    2004-01-01

    The paper gives experiment theory and experiment method of neutron source multiplication method for site measurement technology in the nuclear critical safety. The measured parameter by source multiplication method actually is a sub-critical with source neutron effective multiplication factor k s , but not the neutron effective multiplication factor k eff . The experiment research has been done on the uranium solution nuclear critical safety experiment assembly. The k s of different sub-criticality is measured by neutron source multiplication experiment method, and k eff of different sub-criticality, the reactivity coefficient of unit solution level, is first measured by period method, and then multiplied by difference of critical solution level and sub-critical solution level and obtained the reactivity of sub-critical solution level. The k eff finally can be extracted from reactivity formula. The effect on the nuclear critical safety and different between k eff and k s are discussed

  20. Nuclear criticality safety calculations for a K-25 site vacuum cleaner

    International Nuclear Information System (INIS)

    Shor, J.T.; Haire, M.J.

    1997-02-01

    A modified Nilfisk model GSJ dry vacuum cleaner is used throughout the K-25 Site to collect dry forms of highly enriched uranium (HEU). When vacuuming, solids are collected in a cyclone-type separator vacuum cleaner body. Calculations were done with the SCALE (KENO V.a) computer code to establish conditions at which a nuclear criticality event might occur if the vacuum cleaner was filled with fissile solution. Conditions evaluated included full (12-in. water) reflection and nominal (1-in. water) reflection, and full (100%) and 20% 235 U enrichment. Validation analyses of SCALE/KENO and the SCALE 27-group cross sections for nuclear criticality safety applications indicate that a calculated k eff + 2σ eff + 2σ ≥ 0.9605 is considered unsafe and may be critical. Critical conditions were calculated to be 70 g U/L for 100% 235 U and full 12-in. water reflection. This corresponds to a minimum critical mass of approximately 1,400 g 235 U for the approximate 20.0-L volume of the vacuum cleaner. The actual volume of the vacuum cleaner is smaller than the modeled volume because some internal materials of construction were assumed to be fissile solution. The model was an overestimate, for conservatism, of fissile solution occupancy. At nominal reflection conditions, the critical concentration in a vacuum cleaner full of UO 2 F 2 solution was calculated to be 100 g 235 U/L, or 2,000 g mass of 100% 235 U. At 20% 235 U for the 20.0-L volume of the vacuum cleaner. At 15% 235 U enrichment and full reflection, critical conditions were not reached at any possible concentration of uranium as a uranyl fluoride solution. At 17.5% 235 U enrichment, criticality was reached at approximately 1,300 g U/L which is beyond saturation at 25 C

  1. Slp-76 is a critical determinant of NK cell-mediated recognition of missing-self targets

    Science.gov (United States)

    Lampe, Kristin; Endale, Mehari; Cashman, Siobhan; Fang, Hao; Mattner, Jochen; Hildeman, David; Hoebe, Kasper

    2015-01-01

    Absence of MHC class I expression is an important mechanism by which NK cells recognize a variety of target cells, yet the pathways underlying “missing-self” recognition, including the involvement of activating receptors, remain poorly understood. Using ENU mutagenesis in mice, we identified a germline mutant, designated Ace, with a marked defect in NK cell-mediated recognition and elimination of “missing-self” targets. The causative mutation was linked to chromosome 11 and identified as a missense mutation [Thr428Ile] in the SH2 domain of Slp-76—a critical adapter molecule downstream of ITAM-containing surface receptors. The Slp-76 Ace mutation behaved as a hypomorphic allele—while no major defects were observed in conventional T cell development/function, a marked defect in NK cell-mediated elimination of β2-Microglobulin (β2M)-deficient target cells was observed. Further studies revealed Slp-76 to control NK cell receptor expression and maturation, however, activation of Slp-76ace/ace NK cells through ITAM-containing NK cell receptors or allogeneic/tumor target cells appeared largely unaffected. Imagestream analysis of the NK-β2M−/− target cell synapse, revealed a specific defect in actin recruitment to the conjugate synapse in Slp-76ace/ace NK cells. Overall these studies establish Slp-76 as a critical determinant of NK cell development and NK cell-mediated elimination of missing-self target cells. PMID:25929249

  2. Slp-76 is a critical determinant of NK-cell mediated recognition of missing-self targets.

    Science.gov (United States)

    Lampe, Kristin; Endale, Mehari; Cashman, Siobhan; Fang, Hao; Mattner, Jochen; Hildeman, David; Hoebe, Kasper

    2015-07-01

    Absence of MHC class I expression is an important mechanism by which NK cells recognize a variety of target cells, yet the pathways underlying "missing-self" recognition, including the involvement of activating receptors, remain poorly understood. Using ethyl-N-nitrosourea mutagenesis in mice, we identified a germline mutant, designated Ace, with a marked defect in NK cell mediated recognition and elimination of "missing-self" targets. The causative mutation was linked to chromosome 11 and identified as a missense mutation (Thr428Ile) in the SH2 domain of Slp-76-a critical adapter molecule downstream of ITAM-containing surface receptors. The Slp-76 Ace mutation behaved as a hypomorphic allele-while no major defects were observed in conventional T-cell development/function, a marked defect in NK cell mediated elimination of β2-microglobulin (β2M) deficient target cells was observed. Further studies revealed Slp-76 to control NK-cell receptor expression and maturation; however, activation of Slp-76(ace/ace) NK cells through ITAM-containing NK-cell receptors or allogeneic/tumor target cells appeared largely unaffected. Imagestream analysis of the NK-β2M(-/-) target cell synapse revealed a specific defect in actin recruitment to the conjugate synapse in Slp-76(ace/ace) NK cells. Overall these studies establish Slp-76 as a critical determinant of NK-cell development and NK cell mediated elimination of missing-self target cells in mice. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Targets for high-resolution studies with heavy-ion reactions

    International Nuclear Information System (INIS)

    Erskine, J.R.

    1975-01-01

    Target problems in heavy ion reaction studies are discussed, including non-uniformity in thickness effects and the inability to fully compensate for reaction-site effects, both problems becoming more serious the heavier the ion. For the non-uniformity effects, the flatness of the target is very critical. Other problems not yet solved are beam-spot heating and the buildup of carbon

  4. Directional R-Loop Formation by the CRISPR-Cas Surveillance Complex Cascade Provides Efficient Off-Target Site Rejection

    Directory of Open Access Journals (Sweden)

    Marius Rutkauskas

    2015-03-01

    Full Text Available CRISPR-Cas systems provide bacteria and archaea with adaptive immunity against foreign nucleic acids. In type I CRISPR-Cas systems, invading DNA is detected by a large ribonucleoprotein surveillance complex called Cascade. The crRNA component of Cascade is used to recognize target sites in foreign DNA (protospacers by formation of an R-loop driven by base-pairing complementarity. Using single-molecule supercoiling experiments with near base-pair resolution, we probe here the mechanism of R-loop formation and detect short-lived R-loop intermediates on off-target sites bearing single mismatches. We show that R-loops propagate directionally starting from the protospacer-adjacent motif (PAM. Upon reaching a mismatch, R-loop propagation stalls and collapses in a length-dependent manner. This unambiguously demonstrates that directional zipping of the R-loop accomplishes efficient target recognition by rapidly rejecting binding to off-target sites with PAM-proximal mutations. R-loops that reach the protospacer end become locked to license DNA degradation by the auxiliary Cas3 nuclease/helicase without further target verification.

  5. Immunological Reactivity Using Monoclonal and Polyclonal Antibodies of Autoimmune Thyroid Target Sites with Dietary Proteins

    Directory of Open Access Journals (Sweden)

    Datis Kharrazian

    2017-01-01

    Full Text Available Many hypothyroid and autoimmune thyroid patients experience reactions with specific foods. Additionally, food interactions may play a role in a subset of individuals who have difficulty finding a suitable thyroid hormone dosage. Our study was designed to investigate the potential role of dietary protein immune reactivity with thyroid hormones and thyroid axis target sites. We identified immune reactivity between dietary proteins and target sites on the thyroid axis that includes thyroid hormones, thyroid receptors, enzymes, and transport proteins. We also measured immune reactivity of either target specific monoclonal or polyclonal antibodies for thyroid-stimulating hormone (TSH receptor, 5′deiodinase, thyroid peroxidase, thyroglobulin, thyroxine-binding globulin, thyroxine, and triiodothyronine against 204 purified dietary proteins commonly consumed in cooked and raw forms. Dietary protein determinants included unmodified (raw and modified (cooked and roasted foods, herbs, spices, food gums, brewed beverages, and additives. There were no dietary protein immune reactions with TSH receptor, thyroid peroxidase, and thyroxine-binding globulin. However, specific antigen-antibody immune reactivity was identified with several purified food proteins with triiodothyronine, thyroxine, thyroglobulin, and 5′deiodinase. Laboratory analysis of immunological cross-reactivity between thyroid target sites and dietary proteins is the initial step necessary in determining whether dietary proteins may play a potential immunoreactive role in autoimmune thyroid disease.

  6. Health Activism Targeting Corporations: A Critical Health Communication Perspective.

    Science.gov (United States)

    Zoller, Heather M

    2017-02-01

    Health activists and health social movements have transformed medical treatment, promoted public health policies, and extended civil rights for people with illness and disability. This essay explores health activism that targets corporate-generated illness and risk in order to understand the unique communicative challenges involved in this area of contention. Arguing for greater critical engagement with policy, the article integrates policy research with social movements, subpolitics, and issue management literature. Drawing from activist discourse and multidisciplinary research, the article describes how a wide array of groups groups build visibility for corporate health effects, create the potential for networking and collaboration, and politicize health by attributing illness to corporate behaviors. The discussion articulates the implications of this activism for health communication theory, research, and practice.

  7. Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

    Energy Technology Data Exchange (ETDEWEB)

    Lewis-Ballester, Ariel; Pham, Khoa N.; Batabyal, Dipanwita; Karkashon, Shay; Bonanno, Jeffrey B.; Poulos, Thomas L.; Yeh, Syun-Ru (Einstein); (UCI)

    2017-11-22

    Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

  8. Protecting important sites for biodiversity contributes to meeting global conservation targets.

    Directory of Open Access Journals (Sweden)

    Stuart H M Butchart

    Full Text Available Protected areas (PAs are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs (referred to collectively hereafter as 'important sites'. Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites. Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs. While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45-1.14% annually since 1950 for IBAs and 0.79-1.49% annually for AZEs. Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends.

  9. A Conserved Target Site in HIV-1 Gag RNA is Accessible to Inhibition by Both an HDV Ribozyme and a Short Hairpin RNA

    Directory of Open Access Journals (Sweden)

    Robert J Scarborough

    2014-01-01

    Full Text Available Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies.

  10. Numerical modeling of laser-driven ion acceleration from near-critical gas targets

    Science.gov (United States)

    Tatomirescu, Dragos; Vizman, Daniel; d’Humières, Emmanuel

    2018-06-01

    In the past two decades, laser-accelerated ion sources and their applications have been intensely researched. Recently, it has been shown through experiments that proton beams with characteristics comparable to those obtained with solid targets can be obtained from gaseous targets. By means of particle-in-cell simulations, this paper studies in detail the effects of a near-critical density gradient on ion and electron acceleration after the interaction with ultra high intensity lasers. We can observe that the peak density of the gas jet has a significant influence on the spectrum features. As the gas jet density increases, so does the peak energy of the central quasi-monoenergetic ion bunch due to the increase in laser absorption while at the same time having a broadening effect on the electron angular distribution.

  11. Protecting Important Sites for Biodiversity Contributes to Meeting Global Conservation Targets

    Science.gov (United States)

    Butchart, Stuart H. M.; Scharlemann, Jörn P. W.; Evans, Mike I.; Quader, Suhel; Aricò, Salvatore; Arinaitwe, Julius; Balman, Mark; Bennun, Leon A.; Bertzky, Bastian; Besançon, Charles; Boucher, Timothy M.; Brooks, Thomas M.; Burfield, Ian J.; Burgess, Neil D.; Chan, Simba; Clay, Rob P.; Crosby, Mike J.; Davidson, Nicholas C.; De Silva, Naamal; Devenish, Christian; Dutson, Guy C. L.; Fernández, David F. Día z; Fishpool, Lincoln D. C.; Fitzgerald, Claire; Foster, Matt; Heath, Melanie F.; Hockings, Marc; Hoffmann, Michael; Knox, David; Larsen, Frank W.; Lamoreux, John F.; Loucks, Colby; May, Ian; Millett, James; Molloy, Dominic; Morling, Paul; Parr, Mike; Ricketts, Taylor H.; Seddon, Nathalie; Skolnik, Benjamin; Stuart, Simon N.; Upgren, Amy; Woodley, Stephen

    2012-01-01

    Protected areas (PAs) are a cornerstone of conservation efforts and now cover nearly 13% of the world's land surface, with the world's governments committed to expand this to 17%. However, as biodiversity continues to decline, the effectiveness of PAs in reducing the extinction risk of species remains largely untested. We analyzed PA coverage and trends in species' extinction risk at globally significant sites for conserving birds (10,993 Important Bird Areas, IBAs) and highly threatened vertebrates and conifers (588 Alliance for Zero Extinction sites, AZEs) (referred to collectively hereafter as ‘important sites’). Species occurring in important sites with greater PA coverage experienced smaller increases in extinction risk over recent decades: the increase was half as large for bird species with>50% of the IBAs at which they occur completely covered by PAs, and a third lower for birds, mammals and amphibians restricted to protected AZEs (compared with unprotected or partially protected sites). Globally, half of the important sites for biodiversity conservation remain unprotected (49% of IBAs, 51% of AZEs). While PA coverage of important sites has increased over time, the proportion of PA area covering important sites, as opposed to less important land, has declined (by 0.45–1.14% annually since 1950 for IBAs and 0.79–1.49% annually for AZEs). Thus, while appropriately located PAs may slow the rate at which species are driven towards extinction, recent PA network expansion has under-represented important sites. We conclude that better targeted expansion of PA networks would help to improve biodiversity trends. PMID:22457717

  12. Insight into PreImplantation Factor (PIF* mechanism for embryo protection and development: target oxidative stress and protein misfolding (PDI and HSP through essential RIKP [corrected] binding site.

    Directory of Open Access Journals (Sweden)

    Eytan R Barnea

    Full Text Available Endogenous PIF, upon which embryo development is dependent, is secreted only by viable mammalian embryos, and absent in non-viable ones. Synthetic PIF (sPIF administration promotes singly cultured embryos development and protects against their demise caused by embryo-toxic serum. To identify and characterize critical sPIF-embryo protein interactions novel biochemical and bio-analytical methods were specifically devised.FITC-PIF uptake/binding by cultured murine and equine embryos was examined and compared with scrambled FITC-PIF (control. Murine embryo (d10 lysates were fractionated by reversed-phase HPLC, fractions printed onto microarray slides and probed with Biotin-PIF, IDE and Kv1.3 antibodies, using fluorescence detection. sPIF-based affinity column was developed to extract and identify PIF-protein interactions from lysates using peptide mass spectrometry (LC/MS/MS. In silico evaluation examined binding of PIF to critical targets, using mutation analysis.PIF directly targets viable cultured embryos as compared with control peptide, which failed to bind. Multistep Biotin-PIF targets were confirmed by single-step PIF-affinity column based isolation. PIF binds protein disulfide isomerases a prolyl-4-hydroxylase β-subunit, (PDI, PDIA4, PDIA6-like containing the antioxidant thioredoxin domain. PIF also binds protective heat shock proteins (70&90, co-chaperone, BAG-3. Remarkably, PIF targets a common RIKP [corrected] site in PDI and HSP proteins. Further, single PIF amino acid mutation significantly reduced peptide-protein target bonding. PIF binds promiscuous tubulins, neuron backbones and ACTA-1,2 visceral proteins. Significant anti-IDE, while limited anti-Kv1.3b antibody-binding to Biotin-PIF positive lysates HPLC fractions were documented.Collectively, data identifies PIF shared targets on PDI and HSP in the embryo. Such are known to play a critical role in protecting against oxidative stress and protein misfolding. PIF-affinity-column is a

  13. Remaining Sites Verification Package for the 600-111, P-11 Critical Mass Laboratory Crib, and UPR-600-16, Fire and Contamination Spread Waste Sites. Attachment to Waste Site Reclassification Form 2004-065

    International Nuclear Information System (INIS)

    Capron, J.M.

    2008-01-01

    The 600-111, P-11 Critical Mass Laboratory Crib waste site, also referred to as the P-11 Facility, included the 120 Experimental Building, the 123 Control Building, and the P-11 Crib. The facility was constructed in 1949 and was used as a laboratory for plutonium criticality studies. In accordance with this evaluation, the confirmatory and verification sampling results support a reclassification of this site to Interim Closed Out. The results of confirmatory and verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River

  14. Impact of MicroRNA Levels, Target-Site Complementarity, and Cooperativity on Competing Endogenous RNA-Regulated Gene Expression.

    Science.gov (United States)

    Denzler, Rémy; McGeary, Sean E; Title, Alexandra C; Agarwal, Vikram; Bartel, David P; Stoffel, Markus

    2016-11-03

    Expression changes of competing endogenous RNAs (ceRNAs) have been proposed to influence microRNA (miRNA) activity and thereby regulate other transcripts containing miRNA-binding sites. Here, we find that although miRNA levels define the extent of repression, they have little effect on the magnitude of the ceRNA expression change required to observe derepression. Canonical 6-nt sites, which typically mediate modest repression, can nonetheless compete for miRNA binding, with potency ∼20% of that observed for canonical 8-nt sites. In aggregate, low-affinity/background sites also contribute to competition. Sites with extensive additional complementarity can appear as more potent, but only because they induce miRNA degradation. Cooperative binding of proximal sites for the same or different miRNAs does increase potency. These results provide quantitative insights into the stoichiometric relationship between miRNAs and target abundance, target-site spacing, and affinity requirements for ceRNA-mediated gene regulation, and the unusual circumstances in which ceRNA-mediated gene regulation might be observed. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

  15. Outreach for Outreach: Targeting social media audiences to promote a NASA kids’ web site

    Science.gov (United States)

    Pham, C. C.

    2009-12-01

    The Space Place is a successful NASA web site that benefits upper elementary school students and educators by providing games, activities, and resources to stimulate interest in science, technology, engineering, and mathematics, as well as to inform the audience of NASA’s contributions. As online social networking grows to be a central component of modern communication, The Space Place has explored the benefits of integrating social networks with the web site to increase awareness of materials the web site offers. This study analyzes the capabilities of social networks, and specifically the demographics of Twitter and Facebook. It then compares these results with the content, audience, and perceived demographics of The Space Place web site. Based upon the demographic results, we identified a target constituency that would benefit from the integration of social networks into The Space Place web site. As a result of this study, a Twitter feed has been established that releases a daily tweet from The Space Place. In addition, a Facebook page has been created to showcase new content and prompt interaction among fans of The Space Place. Currently, plans are under way to populate the Space Place Facebook page. Each social network has been utilized in an effort to spark excitement about the content on The Space Place, as well as to attract followers to the main NASA Space Place web site. To pursue this idea further, a plan has been developed to promote NASA Space Place’s social media tools among the target audience.

  16. Molecular characterization of monoclonal antibodies that inhibit acetylcholinesterase by targeting the peripheral site and backdoor region.

    Directory of Open Access Journals (Sweden)

    Yves Bourne

    Full Text Available The inhibition properties and target sites of monoclonal antibodies (mAbs Elec403, Elec408 and Elec410, generated against Electrophorus electricus acetylcholinesterase (AChE, have been defined previously using biochemical and mutagenesis approaches. Elec403 and Elec410, which bind competitively with each other and with the peptidic toxin inhibitor fasciculin, are directed toward distinctive albeit overlapping epitopes located at the AChE peripheral anionic site, which surrounds the entrance of the active site gorge. Elec408, which is not competitive with the other two mAbs nor fasciculin, targets a second epitope located in the backdoor region, distant from the gorge entrance. To characterize the molecular determinants dictating their binding site specificity, we cloned and sequenced the mAbs; generated antigen-binding fragments (Fab retaining the parental inhibition properties; and explored their structure-function relationships using complementary x-ray crystallography, homology modeling and flexible docking approaches. Hypermutation of one Elec403 complementarity-determining region suggests occurrence of antigen-driven selection towards recognition of the AChE peripheral site. Comparative analysis of the 1.9Å-resolution structure of Fab408 and of theoretical models of its Fab403 and Fab410 congeners evidences distinctive surface topographies and anisotropic repartitions of charges, consistent with their respective target sites and inhibition properties. Finally, a validated, data-driven docking model of the Fab403-AChE complex suggests a mode of binding at the PAS that fully correlates with the functional data. This comprehensive study documents the molecular peculiarities of Fab403 and Fab410, as the largest peptidic inhibitors directed towards the peripheral site, and those of Fab408, as the first inhibitor directed toward the backdoor region of an AChE and a unique template for the design of new, specific modulators of AChE catalysis.

  17. Identification of the heart as the critical site of adenosine mediated embryo protection

    Directory of Open Access Journals (Sweden)

    Greene Robert W

    2010-05-01

    Full Text Available Abstract Background Our understanding of the mechanisms that protect the developing embryo from intrauterine stress is limited. Recently, adenosine has been demonstrated to play a critical role in protecting the embryo against hypoxia via adenosine A1 receptors (A1ARs, which are expressed in the heart, nervous system, and other sites during development. However, the sites of A1AR action that mediate embryo protection are not known. To determine if the heart is a key site of adenosine-mediated embryo protection, A1ARs were selectively deleted in the embryonic heart using a Cre-LoxP system in which the alpha-myosin heavy chain promoter drives Cre-recombinase expression and excision of the A1AR gene from cardiomyocytes. Results With increasing exposure of maternal hypoxia (10% O2 from 48-96 hours beginning at embryonic day (E 8.5, embryo viability decreased in the cardiac-A1AR deleted embryos. 48 hours of hypoxia reduced embryonic viability by 49% in embryos exposed from E10.5-12.5 but no effect on viability was observed in younger embryos exposed to hypoxia from E8.5-10.5. After 72 hours of hypoxia, 57.8% of the cardiac-A1AR deleted embryos were either dead or re-absorbed compared to 13.7% of control littermates and after 96 hours 81.6% of cardiac-A1AR deleted embryos were dead or re-absorbed. After 72 hours of hypoxia, cardiac size was reduced significantly more in the cardiac-A1AR deleted hearts compared to controls. Gene expression analysis revealed clusters of genes that are regulated by both hypoxia and A1AR expression. Conclusions These data identify the embryonic heart as the critical site where adenosine acts to protect the embryo against hypoxia. As such these studies identify a previously unrecognized mechanism of embryo protection.

  18. A genome-wide analysis of lentivector integration sites using targeted sequence capture and next generation sequencing technology.

    Science.gov (United States)

    Ustek, Duran; Sirma, Sema; Gumus, Ergun; Arikan, Muzaffer; Cakiris, Aris; Abaci, Neslihan; Mathew, Jaicy; Emrence, Zeliha; Azakli, Hulya; Cosan, Fulya; Cakar, Atilla; Parlak, Mahmut; Kursun, Olcay

    2012-10-01

    One application of next-generation sequencing (NGS) is the targeted resequencing of interested genes which has not been used in viral integration site analysis of gene therapy applications. Here, we combined targeted sequence capture array and next generation sequencing to address the whole genome profiling of viral integration sites. Human 293T and K562 cells were transduced with a HIV-1 derived vector. A custom made DNA probe sets targeted pLVTHM vector used to capture lentiviral vector/human genome junctions. The captured DNA was sequenced using GS FLX platform. Seven thousand four hundred and eighty four human genome sequences flanking the long terminal repeats (LTR) of pLVTHM fragment sequences matched with an identity of at least 98% and minimum 50 bp criteria in both cells. In total, 203 unique integration sites were identified. The integrations in both cell lines were totally distant from the CpG islands and from the transcription start sites and preferentially located in introns. A comparison between the two cell lines showed that the lentiviral-transduced DNA does not have the same preferred regions in the two different cell lines. Copyright © 2012 Elsevier B.V. All rights reserved.

  19. Determining Antifungal Target Sites in the Sterol Pathway of the Yeast Candida and Saccharomyces

    National Research Council Canada - National Science Library

    Bard, Martin

    1998-01-01

    ... as in topical infections which lead to significant losses in work-place productivity. The work reported here seeks to identify new target sites in the sterol biosynthetic pathway against which new antifungal compounds might be developed...

  20. Multi-criteria analysis for the detection of the most critical European UNESCO Heritage sites

    Science.gov (United States)

    Valagussa, Andrea; Frattini, Paolo; Berta, Nadia; Spizzichino, Daniele; Leoni, Gabriele; Margottini, Claudio; Battista Crosta, Giovanni

    2017-04-01

    A GIS-based multi-criteria analysis has been implemented to identify and to rank the most critical UNESCO Heritage sites at the European scale in the context of PROTHEGO JPI-Project. Two multi-criteria methods have been tested and applied to more than 300 European UNESCO Sites. First, the Analytic Hierarchy Procedure (AHP) was applied to the data of the UNESCO Periodic Report, in relation to 13 natural hazards that have affected or can potentially affect the Heritage sites. According to these reports, 22% of sites are without any documented hazard and 70% of the sites have at least one hazard affecting the site. The most important hazards on the European country are: fire (wildfire), storm, flooding, earthquake and erosion. For each UNESCO site, the potential risk was calculated as a weighed sum of the hazards that affect the site. The weighs of the 13 hazards were obtained by AHP procedure, which is a technique for multi-attribute decision making that enables the decomposition of a problem into hierarchy, based on the opinion of different experts about the dominance of risks. The weights are obtained by rescaling between 0 and 1 the eigenvectors relative to the maximum eigenvalue for the matrix of the coefficients. The internal coherence of the expert's attributions is defined through the calculation of the consistency ratio (Saaty, 1990). The result of the AHP method consists in a map of the UNESCO sites ranked according to the potential risk, where the site most at risk results to be the Geirangerfjord and Nærøyfjord in Norway. However, the quality of these results lies in the reliability of the Period Reports, which are produced by different experts with unknown level of scientific background. To test the reliability of these results, a comparison of the information of the periodic reports with available high-quality datasets (earthquake, volcano and landslide) at the Italian scale has been performed. Sites properly classified by the Period Reports range from

  1. Real-time WAMI streaming target tracking in fog

    Science.gov (United States)

    Chen, Yu; Blasch, Erik; Chen, Ning; Deng, Anna; Ling, Haibin; Chen, Genshe

    2016-05-01

    Real-time information fusion based on WAMI (Wide-Area Motion Imagery), FMV (Full Motion Video), and Text data is highly desired for many mission critical emergency or security applications. Cloud Computing has been considered promising to achieve big data integration from multi-modal sources. In many mission critical tasks, however, powerful Cloud technology cannot satisfy the tight latency tolerance as the servers are allocated far from the sensing platform, actually there is no guaranteed connection in the emergency situations. Therefore, data processing, information fusion, and decision making are required to be executed on-site (i.e., near the data collection). Fog Computing, a recently proposed extension and complement for Cloud Computing, enables computing on-site without outsourcing jobs to a remote Cloud. In this work, we have investigated the feasibility of processing streaming WAMI in the Fog for real-time, online, uninterrupted target tracking. Using a single target tracking algorithm, we studied the performance of a Fog Computing prototype. The experimental results are very encouraging that validated the effectiveness of our Fog approach to achieve real-time frame rates.

  2. Occurrence Prospect of HDR and Target Site Selection Study in Southeastern of China

    Science.gov (United States)

    Lin, W.; Gan, H.

    2017-12-01

    Hot dry rock (HDR) geothermal resource is one of the most important clean energy in future. Site selection a HDR resource is a fundamental work to explore the HDR resources. This paper compiled all the HDR development projects domestic and abroad, and summarized the location of HDR geothermal geological index. After comparing the geological background of HDR in the southeast coastal area of China, Yangjiang Xinzhou in Guangdong province, Leizhou Peninsula area, Lingshui in Hainan province and Huangshadong in Guangzhou were selected from some key potential target area along the southeast coast of China. Deep geothermal field model of the study area is established based on the comprehensive analysis of the target area of deep geothermal geological background and deep thermal anomalies. This paper also compared the hot dry rock resources target locations, and proposed suggestions for the priority exploration target area and exploration scheme.

  3. Braking wind in Australia. A critical evaluation of the renewable energy target

    International Nuclear Information System (INIS)

    Valentine, Scott

    2010-01-01

    This paper provides a critical evaluation of Australia's new Renewable Energy Target (RET) program with respect to its capacity to support wind power development. Four structural flaws associated with the RET which undermine its effectiveness as a catalyst for technological change in the electricity sector are discussed: (1) the inclusion of waste coal mine gas (WCMG) as an eligible fuel source which acts as an indirect coal industry subsidy, (2) program duration which is too short and ill-structured, (3) a multiplier that is well-intended to support small-scale renewable technologies but which creates 'phantom capacity', and (4) the capped target of 45,000 GWh which will stymie long-term wind power market investment. The paper concludes with recommendations which stress the importance of passing effective Carbon Pollution Renewable Scheme (CPRS) legislation to offset the weaknesses associated with the RET. If an effective CPRS cannot be implemented, the paper recommends that amendments be made to the RET to (1) remove WCMG from the list of approved alternative energy sources, and (2) extend the RET targets to reach 120,000 GWh by 2030. (author)

  4. Mohawk Tannery Hazardous Waste Site in New Hampshire included on EPA List of Targeted for Immediate Attention

    Science.gov (United States)

    Today, the U.S. Environmental Protection Agency released the list of Superfund sites that Administrator Pruitt has targeted for immediate and intense attention. The former Mohawk Tannery facility (a.k.a. Granite State Leathers) is one of the 21 sites on th

  5. Contribution of non-target-site resistance in imidazolinone-resistant Imisun sunflower

    Directory of Open Access Journals (Sweden)

    Gabriela Breccia

    2017-08-01

    Full Text Available ABSTRACT The first commercial herbicide-resistant trait in sunflower (Helianthus annuus L. is known as ‘Imisun’. Imidazolinone resistance in Imisun cultivars has been reported to be genetically controlled by a major gene (known as Imr1 or Ahasl1-1 and modifier genes. Imr1 is an allelic variant of the Ahasl1 locus that codes for the acetohydroxyacid synthase, which is the target site of these herbicides. The mechanism of resistance endowed by modifier genes has not been characterized and it could be related to non-target-site resistance. The objective of this study was to evaluate the role of cytochrome P450 monooxygenases (P450s in Imisun resistance. The response to imazapyr herbicide in combination with P450s inhibitor malathion was evaluated in 2 Imisun lines, IMI-1 and RHA426. Malathion reduced herbicide efficacy in both lines, but IMI-1 was affected in a greater extent. A significant reduction in plant growth in response to P450s inhibitors 1-aminobenzotriazole and piperonyl butoxide treatment was detected in the Imisun line HA425. The increased susceptibility to imazapyr after P450s-inhibitor treatment indicates that herbicide metabolism by P450s is a mechanism involved in Imisun resistance. These results also suggest the involvement of different P450s isozymes in endowing resistance to imazapyr in Imisun cultivars.

  6. Target based drug design - a reality in virtual sphere.

    Science.gov (United States)

    Verma, Saroj; Prabhakar, Yenamandra S

    2015-01-01

    The target based drug design approaches are a series of computational procedures, including visualization tools, to support the decision systems of drug design/discovery process. In the essence of biological targets shaping the potential lead/drug molecules, this review presents a comprehensive position of different components of target based drug design which include target identification, protein modeling, molecular dynamics simulations, binding/catalytic sites identification, docking, virtual screening, fragment based strategies, substructure treatment of targets in tackling drug resistance, in silico ADMET, structural vaccinology, etc along with the key issues involved therein and some well investigated case studies. The concepts and working of these procedures are critically discussed to arouse interest and to advance the drug research.

  7. Remaining Sites Verification Package for the 600-111, P-11 Critical Mass Laboratory Crib, and UPR-600-16, Fire and Contamination Spread Waste Sites. Attachment to Waste Site Reclassification Form 2004-065 and 2008-045

    International Nuclear Information System (INIS)

    Capron, J.M.

    2008-01-01

    The UPR-600-16, Fire and Contamination Spread waste site is an unplanned release that occurred on December 4, 1951, when plutonium contamination was spread by a fire that ignited inside the 120 Experimental Building. The 120 Experimental Building was a laboratory building that was constructed in 1949 and used for plutonium criticality studies as part of the P-11 Project. In November 1951, a criticality occurred in the 120 Experimental Building that resulted in extensive plutonium contamination inside the building. The confirmatory evaluation supports a reclassification of this site to Interim Closed Out. The current site conditions achieve the remedial action objectives and the corresponding remedial action goals established in the Remaining Sites ROD. The results of the extensive radiological survey of the surface soil and the confirmatory and verification sampling show that residual contaminant concentrations do not preclude any future uses and allow for unrestricted use of shallow zone soils. The results also demonstrate that residual contaminant concentrations are protective of groundwater and the Columbia River

  8. The National Criticality Experiments Research Center at the Device Assembly Facility, Nevada National Security Site: Status and Capabilities, Summary Report

    International Nuclear Information System (INIS)

    Bragg-Sitton, S.; Bess, J.; Werner, J.

    2011-01-01

    The National Criticality Experiments Research Center (NCERC) was officially opened on August 29, 2011. Located within the Device Assembly Facility (DAF) at the Nevada National Security Site (NNSS), the NCERC has become a consolidation facility within the United States for critical configuration testing, particularly those involving highly enriched uranium (HEU). The DAF is a Department of Energy (DOE) owned facility that is operated by the National Nuclear Security Agency/Nevada Site Office (NNSA/NSO). User laboratories include the Lawrence Livermore National Laboratory (LLNL) and Los Alamos National Laboratory (LANL). Personnel bring their home lab qualifications and procedures with them to the DAF, such that non-site specific training need not be repeated to conduct work at DAF. The NNSS Management and Operating contractor is National Security Technologies, LLC (NSTec) and the NNSS Safeguards and Security contractor is Wackenhut Services. The complete report provides an overview and status of the available laboratories and test bays at NCERC, available test materials and test support configurations, and test requirements and limitations for performing sub-critical and critical tests. The current summary provides a brief summary of the facility status and the method by which experiments may be introduced to NCERC.

  9. Glyphosate-Resistant Parthenium hysterophorus in the Caribbean Islands: Non Target Site Resistance and Target Site Resistance in Relation to Resistance Levels.

    Directory of Open Access Journals (Sweden)

    Enzo Bracamonte

    2016-12-01

    of a proline to serine change in Cu-R1, Do-R1 Do-R2. The above-mentioned results indicate that high resistance values are determined by the number of defense mechanisms (target-site and non-target-site resistance possessed by the different P. hysterophorus accessions, concurrently.

  10. Visualizing multiple inter-organelle contact sites using the organelle-targeted split-GFP system.

    Science.gov (United States)

    Kakimoto, Yuriko; Tashiro, Shinya; Kojima, Rieko; Morozumi, Yuki; Endo, Toshiya; Tamura, Yasushi

    2018-04-18

    Functional integrity of eukaryotic organelles relies on direct physical contacts between distinct organelles. However, the entity of organelle-tethering factors is not well understood due to lack of means to analyze inter-organelle interactions in living cells. Here we evaluate the split-GFP system for visualizing organelle contact sites in vivo and show its advantages and disadvantages. We observed punctate GFP signals from the split-GFP fragments targeted to any pairs of organelles among the ER, mitochondria, peroxisomes, vacuole and lipid droplets in yeast cells, which suggests that these organelles form contact sites with multiple organelles simultaneously although it is difficult to rule out the possibilities that these organelle contacts sites are artificially formed by the irreversible associations of the split-GFP probes. Importantly, split-GFP signals in the overlapped regions of the ER and mitochondria were mainly co-localized with ERMES, an authentic ER-mitochondria tethering structure, suggesting that split-GFP assembly depends on the preexisting inter-organelle contact sites. We also confirmed that the split-GFP system can be applied to detection of the ER-mitochondria contact sites in HeLa cells. We thus propose that the split-GFP system is a potential tool to observe and analyze inter-organelle contact sites in living yeast and mammalian cells.

  11. Structure of an N276-Dependent HIV-1 Neutralizing Antibody Targeting a Rare V5 Glycan Hole Adjacent to the CD4 Binding Site

    Energy Technology Data Exchange (ETDEWEB)

    Wibmer, Constantinos Kurt; Gorman, Jason; Anthony, Colin S.; Mkhize, Nonhlanhla N.; Druz, Aliaksandr; York, Talita; Schmidt, Stephen D.; Labuschagne, Phillip; Louder, Mark K.; Bailer, Robert T.; Karim, Salim S. Abdool; Mascola, John R.; Williamson, Carolyn; Moore, Penny L.; Kwong, Peter D.; Morris, Lynn (NHLS-South Africa); (NIH); (Witwatersrand); (KwaZulu-Natal)

    2016-08-31

    ABSTRACT

    All HIV-1-infected individuals develop strain-specific neutralizing antibodies to their infecting virus, which in some cases mature into broadly neutralizing antibodies. Defining the epitopes of strain-specific antibodies that overlap conserved sites of vulnerability might provide mechanistic insights into how broadly neutralizing antibodies arise. We previously described an HIV-1 clade C-infected donor, CAP257, who developed broadly neutralizing plasma antibodies targeting an N276 glycan-dependent epitope in the CD4 binding site. The initial CD4 binding site response potently neutralized the heterologous tier 2 clade B viral strain RHPA, which was used to design resurfaced gp120 antigens for single-B-cell sorting. Here we report the isolation and structural characterization of CAP257-RH1, an N276 glycan-dependent CD4 binding site antibody representative of the early CD4 binding site plasma response in donor CAP257. The cocrystal structure of CAP257-RH1 bound to RHPA gp120 revealed critical interactions with the N276 glycan, loop D, and V5, but not with aspartic acid 368, similarly to HJ16 and 179NC75. The CAP257-RH1 monoclonal antibody was derived from the immunoglobulin-variable IGHV3-33 and IGLV3-10 genes and neutralized RHPA but not the transmitted/founder virus from donor CAP257. Its narrow neutralization breadth was attributed to a binding angle that was incompatible with glycosylated V5 loops present in almost all HIV-1 strains, including the CAP257 transmitted/founder virus. Deep sequencing of autologous CAP257 viruses, however, revealed minority variants early in infection that lacked V5 glycans. These glycan-free V5 loops are unusual holes in the glycan shield that may have been necessary for initiating this N276 glycan-dependent CD4 binding site B-cell lineage.

    IMPORTANCEThe conserved CD4 binding site on gp120 is a major target for HIV-1 vaccine design, but key events in the elicitation and maturation of

  12. Examination of CRISPR/Cas9 design tools and the effect of target site accessibility on Cas9 activity.

    Science.gov (United States)

    Lee, Ciaran M; Davis, Timothy H; Bao, Gang

    2018-04-01

    What is the topic of this review? In this review, we analyse the performance of recently described tools for CRISPR/Cas9 guide RNA design, in particular, design tools that predict CRISPR/Cas9 activity. What advances does it highlight? Recently, many tools designed to predict CRISPR/Cas9 activity have been reported. However, the majority of these tools lack experimental validation. Our analyses indicate that these tools have poor predictive power. Our preliminary results suggest that target site accessibility should be considered in order to develop better guide RNA design tools with improved predictive power. The recent adaptation of the clustered regulatory interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system for targeted genome engineering has led to its widespread application in many fields worldwide. In order to gain a better understanding of the design rules of CRISPR/Cas9 systems, several groups have carried out large library-based screens leading to some insight into sequence preferences among highly active target sites. To facilitate CRISPR/Cas9 design, these studies have spawned a plethora of guide RNA (gRNA) design tools with algorithms based solely on direct or indirect sequence features. Here, we demonstrate that the predictive power of these tools is poor, suggesting that sequence features alone cannot accurately inform the cutting efficiency of a particular CRISPR/Cas9 gRNA design. Furthermore, we demonstrate that DNA target site accessibility influences the activity of CRISPR/Cas9. With further optimization, we hypothesize that it will be possible to increase the predictive power of gRNA design tools by including both sequence and target site accessibility metrics. © 2017 The Authors. Experimental Physiology © 2017 The Physiological Society.

  13. mRNA-engineered mesenchymal stem cells for targeted delivery of interleukin-10 to sites of inflammation.

    Science.gov (United States)

    Levy, Oren; Zhao, Weian; Mortensen, Luke J; Leblanc, Sarah; Tsang, Kyle; Fu, Moyu; Phillips, Joseph A; Sagar, Vinay; Anandakumaran, Priya; Ngai, Jessica; Cui, Cheryl H; Eimon, Peter; Angel, Matthew; Lin, Charles P; Yanik, Mehmet Fatih; Karp, Jeffrey M

    2013-10-03

    Mesenchymal stem cells (MSCs) are promising candidates for cell-based therapy to treat several diseases and are compelling to consider as vehicles for delivery of biological agents. However, MSCs appear to act through a seemingly limited "hit-and-run" mode to quickly exert their therapeutic impact, mediated by several mechanisms, including a potent immunomodulatory secretome. Furthermore, MSC immunomodulatory properties are highly variable and the secretome composition following infusion is uncertain. To determine whether a transiently controlled antiinflammatory MSC secretome could be achieved at target sites of inflammation, we harnessed mRNA transfection to generate MSCs that simultaneously express functional rolling machinery (P-selectin glycoprotein ligand-1 [PSGL-1] and Sialyl-Lewis(x) [SLeX]) to rapidly target inflamed tissues and that express the potent immunosuppressive cytokine interleukin-10 (IL-10), which is not inherently produced by MSCs. Indeed, triple-transfected PSGL-1/SLeX/IL-10 MSCs transiently increased levels of IL-10 in the inflamed ear and showed a superior antiinflammatory effect in vivo, significantly reducing local inflammation following systemic administration. This was dependent on rapid localization of MSCs to the inflamed site. Overall, this study demonstrates that despite the rapid clearance of MSCs in vivo, engineered MSCs can be harnessed via a "hit-and-run" action for the targeted delivery of potent immunomodulatory factors to treat distant sites of inflammation.

  14. siRNAs targeted to certain polyadenylation sites promote specific, RISC-independent degradation of messenger RNAs.

    Science.gov (United States)

    Vickers, Timothy A; Crooke, Stanley T

    2012-07-01

    While most siRNAs induce sequence-specific target mRNA cleavage and degradation in a process mediated by Ago2/RNA-induced silencing complex (RISC), certain siRNAs have also been demonstrated to direct target RNA reduction through deadenylation and subsequent degradation of target transcripts in a process which involves Ago1/RISC and P-bodies. In the current study, we present data suggesting that a third class of siRNA exist, which are capable of promoting target RNA reduction that is independent of both Ago and RISC. These siRNAs bind the target messenger RNA at the polyA signal and are capable of redirecting a small amount of polyadenylation to downstream polyA sites when present, however, the majority of the activity appears to be due to inhibition of polyadenylation or deadenylation of the transcript, followed by exosomal degradation of the immature mRNA.

  15. Assessment of mycorrhizal colonisation and soil nutrients in unmanaged fire-impacted soils from two target restoration sites

    Energy Technology Data Exchange (ETDEWEB)

    Dias, J. M.; Oliveira, R. S.; Franco, A. R.; Ritz, K.; Nunan, N.; Castro, P. M. L.

    2010-07-01

    The mycorrhizal colonisation of plants grown in unmanaged soils from two restoration sites with a fire history in Northern Portugal was evaluated from the perspective of supporting restoration programmes. To promote restoration of original tree stands, Quercus ilex L. and Pinus pinaster Ait. were used as target species on two sites, denoted Site 1 and 2 respectively. The aim of the study was to assess whether mycorrhizal propagules that survived fire episodes could serve as in situ inoculum sources, and to analyse the spatial distribution of soil nutrients and mycorrhizal parameters. In a laboratory bioassay, P. pinaster and Q. ilex seedlings were grown on soils from the target sites and root colonisation by ectomycorrhizal (ECM) and arbuscular mycorrhizal (AM) fungi was determined. The ECM root colonisation levels found indicated that soil from Site 2 contained sufficient ECM propagules to serve as a primary source of inoculum for P. pinaster. The low levels of ECM and AM colonisation obtained on the roots of plants grown in soil from Site 1 indicated that the existing mycorrhizal propagules might be insufficient for effective root colonisation of Q. ilex. Different ECM morphotypes were found in plants grown in soil from the two sites. At Site 2 mycorrhizal parameters were found to be spatially structured, with significant differences in ECM colonisation and soil P concentrations between regions of either side of an existing watercourse. The spatial distribution of mycorrhizal propagules was related to edaphic parameters (total C and extractable P), and correlations between soil nutrients and mycorrhizal parameters were found. (Author) 31 refs.

  16. Targeted Delivery of LXR Agonist Using a Site-Specific Antibody-Drug Conjugate.

    Science.gov (United States)

    Lim, Reyna K V; Yu, Shan; Cheng, Bo; Li, Sijia; Kim, Nam-Jung; Cao, Yu; Chi, Victor; Kim, Ji Young; Chatterjee, Arnab K; Schultz, Peter G; Tremblay, Matthew S; Kazane, Stephanie A

    2015-11-18

    Liver X receptor (LXR) agonists have been explored as potential treatments for atherosclerosis and other diseases based on their ability to induce reverse cholesterol transport and suppress inflammation. However, this therapeutic potential has been hindered by on-target adverse effects in the liver mediated by excessive lipogenesis. Herein, we report a novel site-specific antibody-drug conjugate (ADC) that selectively delivers a LXR agonist to monocytes/macrophages while sparing hepatocytes. The unnatural amino acid para-acetylphenylalanine (pAcF) was site-specifically incorporated into anti-CD11a IgG, which binds the α-chain component of the lymphocyte function-associated antigen 1 (LFA-1) expressed on nearly all monocytes and macrophages. An aminooxy-modified LXR agonist was conjugated to anti-CD11a IgG through a stable, cathepsin B cleavable oxime linkage to afford a chemically defined ADC. The anti-CD11a IgG-LXR agonist ADC induced LXR activation specifically in human THP-1 monocyte/macrophage cells in vitro (EC50-27 nM), but had no significant effect in hepatocytes, indicating that payload delivery is CD11a-mediated. Moreover, the ADC exhibited higher-fold activation compared to a conventional synthetic LXR agonist T0901317 (Tularik) (3-fold). This novel ADC represents a fundamentally different strategy that uses tissue targeting to overcome the limitations of LXR agonists for potential use in treating atherosclerosis.

  17. Crystal structure of ryanodine receptor N-terminal domain from Plutella xylostella reveals two potential species-specific insecticide-targeting sites.

    Science.gov (United States)

    Lin, Lianyun; Liu, Chen; Qin, Juan; Wang, Jie; Dong, Shengjie; Chen, Wei; He, Weiyi; Gao, Qingzhi; You, Minsheng; Yuchi, Zhiguang

    2018-01-01

    Ryanodine receptors (RyRs) are large calcium-release channels located in sarcoplasmic reticulum membrane. They play a central role in excitation-contraction coupling of muscle cells. Three commercialized insecticides targeting pest RyRs generate worldwide sales over 2 billion U.S. dollars annually, but the structure of insect RyRs remains elusive, hindering our understanding of the mode of action of RyR-targeting insecticides and the development of insecticide resistance in pests. Here we present the crystal structure of RyR N-terminal domain (NTD) (residue 1-205) at 2.84 Å resolution from the diamondback moth (DBM), Plutella xylostella, a destructive pest devouring cruciferous crops all over the world. Similar to its mammalian homolog, DBM RyR NTD consists of a beta-trefoil folding motif and a flanking alpha helix. Interestingly, two regions in NTD interacting with neighboring domains showed distinguished conformations in DBM relative to mammalian RyRs. Using homology modeling and molecular dynamics simulation, we created a structural model of the N-terminal three domains, showing two unique binding pockets that could be targeted by potential species-specific insecticides. Thermal melt experiment showed that the stability of DBM RyR NTD was higher than mammalian RyRs, probably due to a stable intra-domain disulfide bond observed in the crystal structure. Previously DBM NTD was shown to be one of the two critical regions to interact with insecticide flubendiamide, but isothermal titration calorimetry experiments negated DBM NTD alone as a major binding site for flubendiamide. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. Chamber wall response to target implosion in inertial fusion reactors: new and critical assessments

    International Nuclear Information System (INIS)

    Hassanein, A.; Morozov, V.

    2002-01-01

    The chamber walls in inertial fusion energy (IFE) reactors are exposed to harsh conditions following each target implosion. Key issues of the cyclic IFE operation include intense photon and ion deposition, wall thermal and hydrodynamic evolution, wall erosion and fatigue lifetime, and chamber clearing and evacuation to ensure desirable conditions prior to next target implosion. Several methods for wall protection have been proposed in the past, each having its own advantages and disadvantages. These methods include use of solid bare walls, gas-filled cavities, and liquid walls/jets. Detailed models have been developed for reflected laser light, emitted photons, and target debris deposition and interaction with chamber components and have been implemented in the comprehensive HEIGHTS software package. The focus of this study is to critically assess the reliability and the dynamic response of chamber walls in IFE systems. Of particular concern is the effect on wall erosion lifetime due to various erosion mechanisms, such as vaporization, chemical and physical sputtering, melt/liquid splashing and explosive erosion, and fragmentation of liquid walls

  19. Transportable criticality alarm system

    International Nuclear Information System (INIS)

    Clem, W.E.

    1988-09-01

    The Transportable Criticality Alarm System was developed at the Hanford Site in 1982 to comply with the requirements of US Department of Energy Order DOE 5480.1, 12/18/80, and ANSI/ANS-8.3- 1979. The portable unit that it replaced failed to comply with the new requirements in that it did not provide the necessary warning of malfunctions, nor did it provide the Hanford Site standard criticality alarm signal. Modern technology allowed the Transportable Criticality Alarm System to comply with the criticality requirements cited and to incorporate other features that make it more usable, maintainable, and reliable. The Transportable Criticality Alarm System (TCAS) provides temporary criticality coverage in manned areas where the facility criticality alarm system is not operable. This gamma radiation-sensitive system has been in use for the past 6 yr at the Hanford Site. 2 refs., 4 figs., 1 tab

  20. TargetM6A: Identifying N6-Methyladenosine Sites From RNA Sequences via Position-Specific Nucleotide Propensities and a Support Vector Machine.

    Science.gov (United States)

    Li, Guang-Qing; Liu, Zi; Shen, Hong-Bin; Yu, Dong-Jun

    2016-10-01

    As one of the most ubiquitous post-transcriptional modifications of RNA, N 6 -methyladenosine ( [Formula: see text]) plays an essential role in many vital biological processes. The identification of [Formula: see text] sites in RNAs is significantly important for both basic biomedical research and practical drug development. In this study, we designed a computational-based method, called TargetM6A, to rapidly and accurately target [Formula: see text] sites solely from the primary RNA sequences. Two new features, i.e., position-specific nucleotide/dinucleotide propensities (PSNP/PSDP), are introduced and combined with the traditional nucleotide composition (NC) feature to formulate RNA sequences. The extracted features are further optimized to obtain a much more compact and discriminative feature subset by applying an incremental feature selection (IFS) procedure. Based on the optimized feature subset, we trained TargetM6A on the training dataset with a support vector machine (SVM) as the prediction engine. We compared the proposed TargetM6A method with existing methods for predicting [Formula: see text] sites by performing stringent jackknife tests and independent validation tests on benchmark datasets. The experimental results show that the proposed TargetM6A method outperformed the existing methods for predicting [Formula: see text] sites and remarkably improved the prediction performances, with MCC = 0.526 and AUC = 0.818. We also provided a user-friendly web server for TargetM6A, which is publicly accessible for academic use at http://csbio.njust.edu.cn/bioinf/TargetM6A.

  1. Decaleside: a new class of natural insecticide targeting tarsal gustatory sites

    Science.gov (United States)

    Rajashekar, Yallappa; Rao, Lingamallu J. M.; Shivanandappa, Thimmappa

    2012-10-01

    Natural sources for novel insecticide molecules hold promise in view of their eco-friendly nature, selectivity, and mammalian safety. Recent progress in understanding the biology of insect olfaction and taste offers new strategies for developing selective pest control agents. We have isolated two natural insecticidal molecules from edible roots of Decalepis hamiltonii named Decalesides I and II, which are novel trisaccharides, highly toxic to household insect pests and stored-product insects. We have experimentally shown that insecticidal activity requires contact with tarsi on the legs but is not toxic orally. The insecticidal activity of molecules is lost by hydrolysis, and various sugars modify toxic response, showing that the insecticidal activity is via gustatory sites on the tarsi. Selective toxicity to insects by virtue of their gustatory site of action and the mammalian safety of the new insecticides is inherent in their chemical structure with 1-4 or 1-1 α linkage that is easily hydrolyzed by digestive enzymes of mammals. Decalesides represent a new chemical class of natural insecticides with a unique mode of action targeting tarsal chemosensory/gustatory system of insects.

  2. Experience with performance based training of nuclear criticality safety engineers

    International Nuclear Information System (INIS)

    Taylor, R.G.

    1993-01-01

    For non-reactor nuclear facilities, the U.S. Department of Energy (DOE) does not require that nuclear criticality safety engineers demonstrate qualification for their job. It is likely, however, that more formalism will be required in the future. Current DOE requirements for those positions which do have to demonstrate qualification indicate that qualification should be achieved by using a systematic approach such as performance based training (PBT). Assuming that PBT would be an acceptable mechanism for nuclear criticality safety engineer training in a more formal environment, a site-specific analysis of the nuclear criticality safety engineer job was performed. Based on this analysis, classes are being developed and delivered to a target audience of newer nuclear criticality safety engineers. Because current interest is in developing training for selected aspects of the nuclear criticality safety engineer job, the analysis is incompletely developed in some areas

  3. Fidelity of target site duplication and sequence preference during integration of xenotropic murine leukemia virus-related virus.

    Directory of Open Access Journals (Sweden)

    Sanggu Kim

    Full Text Available Xenotropic murine leukemia virus (MLV-related virus (XMRV is a new human retrovirus associated with prostate cancer and chronic fatigue syndrome. The causal relationship of XMRV infection to human disease and the mechanism of pathogenicity have not been established. During retrovirus replication, integration of the cDNA copy of the viral RNA genome into the host cell chromosome is an essential step and involves coordinated joining of the two ends of the linear viral DNA into staggered sites on target DNA. Correct integration produces proviruses that are flanked by a short direct repeat, which varies from 4 to 6 bp among the retroviruses but is invariant for each particular retrovirus. Uncoordinated joining of the two viral DNA ends into target DNA can cause insertions, deletions, or other genomic alterations at the integration site. To determine the fidelity of XMRV integration, cells infected with XMRV were clonally expanded and DNA sequences at the viral-host DNA junctions were determined and analyzed. We found that a majority of the provirus ends were correctly processed and flanked by a 4-bp direct repeat of host DNA. A weak consensus sequence was also detected at the XMRV integration sites. We conclude that integration of XMRV DNA involves a coordinated joining of two viral DNA ends that are spaced 4 bp apart on the target DNA and proceeds with high fidelity.

  4. Role of renal function in risk assessment of target non-attainment after standard dosing of meropenem in critically ill patients: a prospective observational study.

    Science.gov (United States)

    Ehmann, Lisa; Zoller, Michael; Minichmayr, Iris K; Scharf, Christina; Maier, Barbara; Schmitt, Maximilian V; Hartung, Niklas; Huisinga, Wilhelm; Vogeser, Michael; Frey, Lorenz; Zander, Johannes; Kloft, Charlotte

    2017-10-21

    Severe bacterial infections remain a major challenge in intensive care units because of their high prevalence and mortality. Adequate antibiotic exposure has been associated with clinical success in critically ill patients. The objective of this study was to investigate the target attainment of standard meropenem dosing in a heterogeneous critically ill population, to quantify the impact of the full renal function spectrum on meropenem exposure and target attainment, and ultimately to translate the findings into a tool for practical application. A prospective observational single-centre study was performed with critically ill patients with severe infections receiving standard dosing of meropenem. Serial blood samples were drawn over 4 study days to determine meropenem serum concentrations. Renal function was assessed by creatinine clearance according to the Cockcroft and Gault equation (CLCR CG ). Variability in meropenem serum concentrations was quantified at the middle and end of each monitored dosing interval. The attainment of two pharmacokinetic/pharmacodynamic targets (100%T >MIC , 50%T >4×MIC ) was evaluated for minimum inhibitory concentration (MIC) values of 2 mg/L and 8 mg/L and standard meropenem dosing (1000 mg, 30-minute infusion, every 8 h). Furthermore, we assessed the impact of CLCR CG on meropenem concentrations and target attainment and developed a tool for risk assessment of target non-attainment. Large inter- and intra-patient variability in meropenem concentrations was observed in the critically ill population (n = 48). Attainment of the target 100%T >MIC was merely 48.4% and 20.6%, given MIC values of 2 mg/L and 8 mg/L, respectively, and similar for the target 50%T >4×MIC . A hyperbolic relationship between CLCR CG (25-255 ml/minute) and meropenem serum concentrations at the end of the dosing interval (C 8h ) was derived. For infections with pathogens of MIC 2 mg/L, mild renal impairment up to augmented renal function was

  5. Target molecular weights for red cell band 3 stilbene and mercurial binding sites

    International Nuclear Information System (INIS)

    Verkman, A.S.; Skorecki, K.L.; Jung, C.Y.; Ausiello, D.A.

    1986-01-01

    Radiation inactivation was used to measure the target sizes for binding of disulfonic stilbene anion transport inhibitor 4,4'-dibenzamido-2,2'-disulfonic stilbene (DBDS) and mercurial water transport inhibitor p-chloromercuribenzene sulfonate (pCMBS) to human erythrocytes. The measured target size for erythrocyte ghost acetylcholinesterase was 78 +/- 3 kDa. DBDS binding to ghost membranes was measured by a fluorescence enhancement technique. Radiation (0-26 Mrad) had no effect on total membrane protein and DBDS binding affinity, whereas DBDS binding stoichiometry decreased exponentially with radiation dose, giving a target size of 59 +/- 4 kDa. H2-4,4'-diisothiocyano-2,2'-disulfonic stilbene (H2-DIDS, 5 microM) blocked greater than 95% of DBDS binding at all radiation doses. pCMBS binding was measured from the time course of tryptophan fluorescence quenching in ghosts treated with the sulfhydryl reagent N-ethylmaleimide (NEM). Radiation did not affect the kinetics of tryptophan quenching, whereas the total amplitude of the fluorescence signal inactivated with radiation with a target size of 31 +/- 6 kDa. These results support the notion that DBDS and pCMBS bind to the transmembrane domain of erythrocyte band 3 in NEM-treated ghosts and demonstrate that radiation inactivation may probe a target significantly smaller than a covalently linked protein subunit. The small target size for the band 3 stilbene binding site may correspond to the intramembrane domain of the band 3 monomer (52 kDa), which is physically distinct from the cytoplasmic domain (42 kDa)

  6. Chemoproteomic profiling of targets of lipid-derived electrophiles by bioorthogonal aminooxy probe

    Directory of Open Access Journals (Sweden)

    Ying Chen

    2017-08-01

    Full Text Available Redox imbalance in cells induces lipid peroxidation and generates a class of highly reactive metabolites known as lipid-derived electrophiles (LDEs that can modify proteins and affects their functions. Identifying targets of LDEs is critical to understand how such modifications are functionally implicated in oxidative-stress associated diseases. Here we report a quantitative chemoproteomic method to globally profile protein targets and sites modified by LDEs. In this strategy, we designed and synthesized an alkyne-functionalized aminooxy probe to react with LDE-modified proteins for imaging and proteomic profiling. Using this probe, we successfully quantified >4000 proteins modified by 4-hydroxy-2-nonenal (HNE of high confidence in mammalian cell lysate and combined with a tandem-orthogonal proteolysis activity-based protein profiling (TOP-ABPP strategy, we identified ~400 residue sites targeted by HNE including reactive cysteines in peroxiredoxins, an important family of enzymes with anti-oxidant roles. Our method expands the toolbox to quantitatively profile protein targets of endogenous electrophiles and the enlarged inventory of LDE-modified proteins and sites will contribute to functional elucidation of cellular pathways affected by oxidative stress. Keywords: Lipid-derived electrophile, 4-hydroxy-2-nonenal, Chemoproteomics, Aminooxy probe, Activity-based protein profiling

  7. The SPOR Domain, a Widely Conserved Peptidoglycan Binding Domain That Targets Proteins to the Site of Cell Division.

    Science.gov (United States)

    Yahashiri, Atsushi; Jorgenson, Matthew A; Weiss, David S

    2017-07-15

    Sporulation-related repeat (SPOR) domains are small peptidoglycan (PG) binding domains found in thousands of bacterial proteins. The name "SPOR domain" stems from the fact that several early examples came from proteins involved in sporulation, but SPOR domain proteins are quite diverse and contribute to a variety of processes that involve remodeling of the PG sacculus, especially with respect to cell division. SPOR domains target proteins to the division site by binding to regions of PG devoid of stem peptides ("denuded" glycans), which in turn are enriched in septal PG by the intense, localized activity of cell wall amidases involved in daughter cell separation. This targeting mechanism sets SPOR domain proteins apart from most other septal ring proteins, which localize via protein-protein interactions. In addition to SPOR domains, bacteria contain several other PG-binding domains that can exploit features of the cell wall to target proteins to specific subcellular sites. Copyright © 2017 American Society for Microbiology.

  8. A Queer Theorist's Critique of Online Domestic Violence Advocacy: Critically Responding to the National Coalition Against Domestic Violence Web Site.

    Science.gov (United States)

    Shelton, Samuel Z

    2018-01-01

    Since the foundations of the contemporary anti-violence movement in the 1960s and 1970s, advocates have sought to establish a critical understanding of domestic violence that we can use to direct our efforts for social change. Yet many advocates and advocacy organizations continue to rely on a problematic narrative of sameness that marginalizes and erases diverse victims' experiences and needs. In this article, I conduct a critical discourse analysis of the National Coalition Against Domestic Violence Web site to identify outcomes of this narrative for the inclusivity of advocacy efforts. I argue that despite the organization's numerous claims to represent diverse victims' experiences, Web site content reveals that its purportedly general account of domestic violence normalizes the experiences of a small group of victims-namely, heterosexual, cisgender women. Further, the Web site's content greatly limits the potential for thinking about and discussing violence across difference. I conclude with recommendations for changes in advocacy practices.

  9. Mitochondrial targets of photodynamic therapy and their contribution to cell death

    Science.gov (United States)

    Oleinick, Nancy L.; Usuda, Jitsuo; Xue, Liang-yan; Azizuddin, Kashif; Chiu, Song-mao; Lam, Minh C.; Morris, Rachel L.; Nieminen, Anna-Liisa

    2002-06-01

    In response to photodynamic therapy (PDT), many cells in culture or within experimental tumors are eliminated by apoptosis. PDT with photosensitizers that localize in or target mitochondria, such as the phthalocyanine Pc 4, causes prompt release of cytochrome c into the cytoplasm and activation of caspases-9 and -3, among other caspases, that are responsible for initiating cell degradation. Some cells appear resistant to apoptosis after PDT; however, if they have sustained sufficient damage, they will die by a necrotic process or through a different apoptotic pathway. In the case of PDT, the distinction between apoptosis and necrosis may be less important than the mechanism that triggers both processes, since critical lethal damage appears to occur during treatment and does not require the major steps in apoptosis to be expressed. We earlier showed, for example, that human breast cancer MCF-7 cells that lack caspase-3 are resistant to the induction of apoptosis by PDT, but are just as sensitive to the loss of clonogenicity as MCF-7 cells stably expressing transfected procaspase-3. Many photosensitizers that target mitochondria specifically attack the anti-apoptotic protein Bcl-2, generating a variety of crosslinked and cleaved photoproducts. Recent evidence suggests that the closely related protein Bcl-xL is also a target of Pc 4-PDT. Transient transfection of an expression vector encoding deletion mutants of Bcl-2 have identified the critical sensitive site in the protein that is required for photodamage. This region contains two alpha helices that form a secondary membrane anchorage site and are thought to be responsible for pore formation by Bcl-2. As specific protein targets are identified, we are becoming better able to model the critical events in PDT-induced cell death.

  10. The effect of simulation courseware on critical thinking in undergraduate nursing students: multi-site pre-post study.

    Science.gov (United States)

    Shin, Hyunsook; Ma, Hyunhee; Park, Jiyoung; Ji, Eun Sun; Kim, Dong Hee

    2015-04-01

    The use of simulations has been considered as opportunities for students to enhance their critical thinking (CT), but previous studies were limited because they did not provide in-depth information on the working dynamics of simulation or on the effects of the number of simulation exposures on CT. This study examined the effect of an integrated pediatric nursing simulation used in a nursing practicum on students' CT abilities and identified the effects of differing numbers of simulation exposures on CT in a multi-site environment. The study used a multi-site, pre-test, post-test design. A total of 237 nursing students at three universities enrolled in a pediatric practicum participated in this study from February to December 2013. All three schools used the same simulation courseware, including the same simulation scenarios, evaluation tools, and simulation equipment. The courseware incorporated high-fidelity simulators and standardized patients. Students at school A completed one simulation session, whereas students at schools B and C completed two and three simulation sessions, respectively. Yoon's Critical Thinking Disposition tool (2008) was used to measure students' CT abilities. The gains in students' CT scores varied according to their numbers of exposures to the simulation courseware. With a single exposure, there were no statistically significant gains in CT, whereas three exposures to the courseware produced significant gains in CT. In seven subcategories of critical thinking, three exposures to the simulation courseware produced CT gains in the prudence and intellectual eagerness subcategories, and the overall simulation experience produced CT gains in the prudence, systematicity, healthy skepticism, and intellectual eagerness subcategories. Simulation courseware may produce positive learning outcomes for prudence in nursing education. In addition, the findings from the multi-site comparative study may contribute to greater understanding of how patient

  11. Organelle targeting: third level of drug targeting

    Directory of Open Access Journals (Sweden)

    Sakhrani NM

    2013-07-01

    Full Text Available Niraj M Sakhrani, Harish PadhDepartment of Cell and Molecular Biology, BV Patel Pharmaceutical Education and Research Development (PERD Centre, Gujarat, IndiaAbstract: Drug discovery and drug delivery are two main aspects for treatment of a variety of disorders. However, the real bottleneck associated with systemic drug administration is the lack of target-specific affinity toward a pathological site, resulting in systemic toxicity and innumerable other side effects as well as higher dosage requirement for efficacy. An attractive strategy to increase the therapeutic index of a drug is to specifically deliver the therapeutic molecule in its active form, not only into target tissue, nor even to target cells, but more importantly, into the targeted organelle, ie, to its intracellular therapeutic active site. This would ensure improved efficacy and minimize toxicity. Cancer chemotherapy today faces the major challenge of delivering chemotherapeutic drugs exclusively to tumor cells, while sparing normal proliferating cells. Nanoparticles play a crucial role by acting as a vehicle for delivery of drugs to target sites inside tumor cells. In this review, we spotlight active and passive targeting, followed by discussion of the importance of targeting to specific cell organelles and the potential role of cell-penetrating peptides. Finally, the discussion will address the strategies for drug/DNA targeting to lysosomes, mitochondria, nuclei and Golgi/endoplasmic reticulum.Keywords: intracellular drug delivery, cancer chemotherapy, therapeutic index, cell penetrating peptides

  12. The intensity of non-target site mechanisms influences the level of resistance of sourgrass to glyphosate

    Directory of Open Access Journals (Sweden)

    Flávia Regina da Costa

    2014-02-01

    Full Text Available Non-target site mechanisms are involved in the resistance of sourgrass (Digitaria insularis to glyphosate. Studies on the 14C-glyphosate absorption and translocation as well as the detection of glyphosate and its metabolites in sourgrass plants were carried out under controlled conditions to investigate if the differential response of resistant sourgrass biotypes (R1 and R2 is derived from the intensity of non-target site mechanisms involved in the resistance to glyphosate. Different pattern of absorption was observed between S (susceptible and R2 from 12 up to 48 hours after treatment with glyphosate (HAT, and between S and R1 just at 12 HAT. The initial difference in glyphosate absorption among the biotypes did not maintained at 96 HAT and afterwards. Smaller amount of herbicide left the treated leaf into the rest of shoot and roots in R2 (25% than in S (58% and R1 (52%. In addition, slight difference in glyphosate translocation was observed between S and R1. We found high percentage (81% of glyphosate in the S biotype up to 168 HAT, while just 44% and 2% of glyphosate was recovered from R1 and R2 plant tissues. In addition, high percentage of glyphosate metabolites was found in R2 (98% and R1 (56% biotypes, while a very low percentage (11% was found in the S biotype. As previous studies indicated resistant factors of 3.5 and 5.6 for R1 and R2, respectively, we conclude that the differential response of sourgrass biotypes is derived from the intensity of the non-target site mechanisms involved in the resistance to glyphosate.

  13. International critical perspectives

    NARCIS (Netherlands)

    Sambrook, S.A.; Poell, R.F.

    2014-01-01

    The Problem Critical perspectives on human resource development (HRD) have emerged, across Europe and America, hailed as the future of the field. However, we note the paucity of critical perspectives globally, the problematic dominance of critical HRD activities in Western sites of theory and

  14. First record of target-site-resistance of poverty brome (Bromus sterilis to ACCase inhibitors

    Directory of Open Access Journals (Sweden)

    Dicke, Dominik

    2014-02-01

    Full Text Available In 2011 reduced efficacy of grass weed herbicides to poverty brome (Bromus sterilis was observed in oilseed rape on a site in East Hessen. The field was cultivated by using the ploughless tillage system more than 25 years. The site showed high densities of poverty brome (>1000 plants/m² prior to herbicide treatment. Poverty brome seeds were collected in 2012 in the hessian oilseed rape field and from a site in East Westphalia, where poverty brome appeared at low densities (10 plants/m² and was not suspected to resistance. The seeds were sown in to pots and plants cultivated. The plants were treated with two application rates (normal dose, double dose with herbicides of different HRAC-classes. The time of treatment was adjusted to the best expectable treatment/efficiency conditions of the individual herbicides (see chapter 3. Clear differences in efficacy that were caused by herbicide, the origins of poverty brome and the dosages were recorded via visual rating eight weeks after spraying. The herbicides Agil and Focus Ultra were able to control about 90% of the poverty brome plants of the East Westphalia site origin. However, only 20-30% of the Hessian plants could be knocked out by the same herbicides. The ACCase-gene of single powerty brome leaf samples from the hessian site was analyzed after resistance assessment. A molecular genetic analysis on 7 variable positions identified target site resistance: Isoleucine (Ile was replaced by asparagine (Asn at position 2041.

  15. Analysis of Critical Issues in Biosphere Assessment Modelling and Site Investigation

    Energy Technology Data Exchange (ETDEWEB)

    Egan, M.J.; Thorne, M.C.; Little, R.H.; Pasco, R.F. [Quintessa Limited, Henley-on-Thames (United Kingdom)

    2003-07-01

    The aim of this document is to present a critical review of issues concerned with the treatment of the biosphere and geosphere-biosphere interface in long-term performance assessment studies for nuclear waste disposal in Sweden. The review covers three main areas of investigation: a review of SKB's plans for undertaking site investigations at candidate locations for the development of a deep geological repository for spent fuel; identification of critical uncertainties associated with SKB's treatment of the geosphere-biosphere interface in recent performance assessments; and a preliminary modelling investigation of the significance of features, events and processes in the near-surface environment in terms of their effect on the accumulation and redistribution of radionuclides at the geosphere-biosphere interface. Overall, SKB's proposals for site investigations are considered to be comprehensive and, if they can be carried out to the specification presented, will constitute a benchmark that other waste management organisations will have to work hard to emulate. The main concern is that expertise for undertaking the investigations and reporting the results could be stretched very thin. The authors have also identified weaknesses in the documentation concerning the collection of evidence for environmental change and on developing scenarios for future environmental change. A fundamental assumption adopted in the renewed assessment of the SFR 1 repository, which is not discussed or justified in any of the documentation that has been reviewed, is that radionuclides enter the water column of the coastal and lake models directly, without passing first through the bed sediments. The modelling study reported herein suggests that SKB's models are robust to range of alternative conceptual descriptions relating to the geosphere-biosphere interface. There are however situations, in which contaminated groundwater is released via sediment rather than directly

  16. Analysis of Critical Issues in Biosphere Assessment Modelling and Site Investigation

    International Nuclear Information System (INIS)

    Egan, M.J.; Thorne, M.C.; Little, R.H.; Pasco, R.F.

    2003-07-01

    The aim of this document is to present a critical review of issues concerned with the treatment of the biosphere and geosphere-biosphere interface in long-term performance assessment studies for nuclear waste disposal in Sweden. The review covers three main areas of investigation: a review of SKB's plans for undertaking site investigations at candidate locations for the development of a deep geological repository for spent fuel; identification of critical uncertainties associated with SKB's treatment of the geosphere-biosphere interface in recent performance assessments; and a preliminary modelling investigation of the significance of features, events and processes in the near-surface environment in terms of their effect on the accumulation and redistribution of radionuclides at the geosphere-biosphere interface. Overall, SKB's proposals for site investigations are considered to be comprehensive and, if they can be carried out to the specification presented, will constitute a benchmark that other waste management organisations will have to work hard to emulate. The main concern is that expertise for undertaking the investigations and reporting the results could be stretched very thin. The authors have also identified weaknesses in the documentation concerning the collection of evidence for environmental change and on developing scenarios for future environmental change. A fundamental assumption adopted in the renewed assessment of the SFR 1 repository, which is not discussed or justified in any of the documentation that has been reviewed, is that radionuclides enter the water column of the coastal and lake models directly, without passing first through the bed sediments. The modelling study reported herein suggests that SKB's models are robust to range of alternative conceptual descriptions relating to the geosphere-biosphere interface. There are however situations, in which contaminated groundwater is released via sediment rather than directly to the water column

  17. A criticism of applications with multi-criteria decision analysis that are used for the site selection for the disposal of municipal solid wastes

    International Nuclear Information System (INIS)

    Kemal Korucu, M.; Erdagi, Bora

    2012-01-01

    Highlights: ► The existing structure of the multi-criteria decision analysis for site selection is criticized. ► Fundamental problematic points based on the critics are defined. ► Some modifications are suggested in order to provide solutions to these problematical points. ► A new structure for the decision making mechanism is proposed. ► The feasibility of the new method is subjected to an evaluation process. - Abstract: The main aim of this study is to criticize the process of selecting the most appropriate site for the disposal of municipal solid wastes which is one of the problematic issues of waste management operations. These kinds of problems are pathological symptoms of existing problematical human–nature relationship which is related to the syndrome called ecological crisis. In this regard, solving the site selection problem, which is just a small part of a larger entity, for the good of ecological rationality and social justice is only possible by founding a new and extensive type of human–nature relationship. In this study, as a problematic point regarding the discussions on ecological problems, the existing structure of the applications using multi-criteria decision analysis in the process of site selection with three main criteria is criticized. Based on this critique, fundamental problematic points (to which applications are insufficient to find solutions) will be defined. Later, some modifications will be suggested in order to provide solutions to these problematical points. Finally, the criticism addressed to the structure of the method with three main criteria and the feasibility of the new method with four main criteria is subjected to an evaluation process. As a result, it is emphasized that the new structure with four main criteria may be effective in solution of the fundamental problematic points.

  18. A criticism of applications with multi-criteria decision analysis that are used for the site selection for the disposal of municipal solid wastes

    Energy Technology Data Exchange (ETDEWEB)

    Kemal Korucu, M., E-mail: kemal.korucu@kocaeli.edu.tr [University of Kocaeli, Department of Environmental Engineering, 41380 Kocaeli (Turkey); Erdagi, Bora [University of Kocaeli, Department of Philosophy, 41380 Kocaeli (Turkey)

    2012-12-15

    Highlights: Black-Right-Pointing-Pointer The existing structure of the multi-criteria decision analysis for site selection is criticized. Black-Right-Pointing-Pointer Fundamental problematic points based on the critics are defined. Black-Right-Pointing-Pointer Some modifications are suggested in order to provide solutions to these problematical points. Black-Right-Pointing-Pointer A new structure for the decision making mechanism is proposed. Black-Right-Pointing-Pointer The feasibility of the new method is subjected to an evaluation process. - Abstract: The main aim of this study is to criticize the process of selecting the most appropriate site for the disposal of municipal solid wastes which is one of the problematic issues of waste management operations. These kinds of problems are pathological symptoms of existing problematical human-nature relationship which is related to the syndrome called ecological crisis. In this regard, solving the site selection problem, which is just a small part of a larger entity, for the good of ecological rationality and social justice is only possible by founding a new and extensive type of human-nature relationship. In this study, as a problematic point regarding the discussions on ecological problems, the existing structure of the applications using multi-criteria decision analysis in the process of site selection with three main criteria is criticized. Based on this critique, fundamental problematic points (to which applications are insufficient to find solutions) will be defined. Later, some modifications will be suggested in order to provide solutions to these problematical points. Finally, the criticism addressed to the structure of the method with three main criteria and the feasibility of the new method with four main criteria is subjected to an evaluation process. As a result, it is emphasized that the new structure with four main criteria may be effective in solution of the fundamental problematic points.

  19. Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells.

    Science.gov (United States)

    Byrne, Susan M; Ortiz, Luis; Mali, Prashant; Aach, John; Church, George M

    2015-02-18

    Sequence-specific nucleases such as TALEN and the CRISPR/Cas9 system have so far been used to disrupt, correct or insert transgenes at precise locations in mammalian genomes. We demonstrate efficient 'knock-in' targeted replacement of multi-kilobase genes in human induced pluripotent stem cells (iPSC). Using a model system replacing endogenous human genes with their mouse counterpart, we performed a comprehensive study of targeting vector design parameters for homologous recombination. A 2.7 kilobase (kb) homozygous gene replacement was achieved in up to 11% of iPSC without selection. The optimal homology arm length was around 2 kb, with homology length being especially critical on the arm not adjacent to the cut site. Homologous sequence inside the cut sites was detrimental to targeting efficiency, consistent with a synthesis-dependent strand annealing (SDSA) mechanism. Using two nuclease sites, we observed a high degree of gene excisions and inversions, which sometimes occurred more frequently than indel mutations. While homozygous deletions of 86 kb were achieved with up to 8% frequency, deletion frequencies were not solely a function of nuclease activity and deletion size. Our results analyzing the optimal parameters for targeting vector design will inform future gene targeting efforts involving multi-kilobase gene segments, particularly in human iPSC. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  20. Simultaneous quantification of protein phosphorylation sites using liquid chromatography-tandem mass spectrometry-based targeted proteomics: a linear algebra approach for isobaric phosphopeptides.

    Science.gov (United States)

    Xu, Feifei; Yang, Ting; Sheng, Yuan; Zhong, Ting; Yang, Mi; Chen, Yun

    2014-12-05

    As one of the most studied post-translational modifications (PTM), protein phosphorylation plays an essential role in almost all cellular processes. Current methods are able to predict and determine thousands of phosphorylation sites, whereas stoichiometric quantification of these sites is still challenging. Liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS)-based targeted proteomics is emerging as a promising technique for site-specific quantification of protein phosphorylation using proteolytic peptides as surrogates of proteins. However, several issues may limit its application, one of which relates to the phosphopeptides with different phosphorylation sites and the same mass (i.e., isobaric phosphopeptides). While employment of site-specific product ions allows for these isobaric phosphopeptides to be distinguished and quantified, site-specific product ions are often absent or weak in tandem mass spectra. In this study, linear algebra algorithms were employed as an add-on to targeted proteomics to retrieve information on individual phosphopeptides from their common spectra. To achieve this simultaneous quantification, a LC-MS/MS-based targeted proteomics assay was first developed and validated for each phosphopeptide. Given the slope and intercept of calibration curves of phosphopeptides in each transition, linear algebraic equations were developed. Using a series of mock mixtures prepared with varying concentrations of each phosphopeptide, the reliability of the approach to quantify isobaric phosphopeptides containing multiple phosphorylation sites (≥ 2) was discussed. Finally, we applied this approach to determine the phosphorylation stoichiometry of heat shock protein 27 (HSP27) at Ser78 and Ser82 in breast cancer cells and tissue samples.

  1. Epitope-based peptide vaccine design and target site depiction against Ebola viruses: an immunoinformatics study.

    Science.gov (United States)

    Khan, M A; Hossain, M U; Rakib-Uz-Zaman, S M; Morshed, M N

    2015-07-01

    Ebola viruses (EBOVs) have been identified as an emerging threat in recent year as it causes severe haemorrhagic fever in human. Epitope-based vaccine design for EBOVs remains a top priority because a mere progress has been made in this regard. Another reason is the lack of antiviral drug and licensed vaccine although there is a severe outbreak in Central Africa. In this study, we aimed to design an epitope-based vaccine that can trigger a significant immune response as well as to prognosticate inhibitor that can bind with potential drug target sites using various immunoinformatics and docking simulation tools. The capacity to induce both humoral and cell-mediated immunity by T cell and B cell was checked for the selected protein. The peptide region spanning 9 amino acids from 42 to 50 and the sequence TLASIGTAF were found as the most potential B and T cell epitopes, respectively. This peptide could interact with 12 HLAs and showed high population coverage up to 80.99%. Using molecular docking, the epitope was further appraised for binding against HLA molecules to verify the binding cleft interaction. In addition with this, the allergenicity of the epitopes was also evaluated. In the post-therapeutic strategy, docking study of predicted 3D structure identified suitable therapeutic inhibitor against targeted protein. However, this computational epitope-based peptide vaccine designing and target site prediction against EBOVs open up a new horizon which may be the prospective way in Ebola viruses research; the results require validation by in vitro and in vivo experiments. © 2015 John Wiley & Sons Ltd.

  2. Structural Insights into the Mechanisms of Action of Short-Peptide HIV-1 Fusion Inhibitors Targeting the Gp41 Pocket

    Directory of Open Access Journals (Sweden)

    Xiujuan Zhang

    2018-02-01

    Full Text Available The deep hydrophobic pocket of HIV-1 gp41 has been considered a drug target, but short-peptides targeting this site usually lack potent antiviral activity. By applying the M-T hook structure, we previously generated highly potent short-peptide fusion inhibitors that specifically targeted the pocket site, such as MT-SC22EK, HP23L, and LP-11. Here, the crystal structures of HP23L and LP-11 bound to the target mimic peptide N36 demonstrated the critical intrahelical and interhelical interactions, especially verifying that the hook-like conformation was finely adopted while the methionine residue was replaced by the oxidation-less prone residue leucine, and that addition of an extra glutamic acid significantly enhanced the binding and inhibitory activities. The structure of HP23L bound to N36 with two mutations (E49K and L57R revealed the critical residues and motifs mediating drug resistance and provided new insights into the mechanism of action of inhibitors. Therefore, the present data help our understanding for the structure-activity relationship (SAR of HIV-1 fusion inhibitors and facilitate the development of novel antiviral drugs.

  3. Activity dependent protein degradation is critical for the formation and stability of fear memory in the amygdala.

    Directory of Open Access Journals (Sweden)

    Timothy J Jarome

    Full Text Available Protein degradation through the ubiquitin-proteasome system [UPS] plays a critical role in some forms of synaptic plasticity. However, its role in memory formation in the amygdala, a site critical for the formation of fear memories, currently remains unknown. Here we provide the first evidence that protein degradation through the UPS is critically engaged at amygdala synapses during memory formation and retrieval. Fear conditioning results in NMDA-dependent increases in degradation-specific polyubiquitination in the amygdala, targeting proteins involved in translational control and synaptic structure and blocking the degradation of these proteins significantly impairs long-term memory. Furthermore, retrieval of fear memory results in a second wave of NMDA-dependent polyubiquitination that targets proteins involved in translational silencing and synaptic structure and is critical for memory updating following recall. These results indicate that UPS-mediated protein degradation is a major regulator of synaptic plasticity necessary for the formation and stability of long-term memories at amygdala synapses.

  4. Chamber wall response to target implosion in inertial fusion reactors : new and critical assessments

    International Nuclear Information System (INIS)

    Hassanein, A.; Morozov, V.

    2002-01-01

    The chamber walls in inertial fusion energy (IFE) reactors are exposed to harsh conditions following each target implosion. Key issues of the cyclic IFE operation include intense photon and ion deposition, wall thermal and hydrodynamic evolution, wall erosion and fatigue lifetime, and chamber clearing and evacuation to ensure desirable conditions prior to target implosion. Several methods for wall protection have been proposed in the past, each having its own advantages and disadvantages. These methods include use of solid bare walls, gas-filled cavities, and liquid walls/jets. Detailed models have been developed for reflected laser light, emitted photons, and target debris deposition and interaction with chamber components and have been implemented in the comprehensive HEIGHTS software package. The hydrodynamic response of gas filled cavities and photon radiation transport of the deposited energy has been calculated by means of new and advanced numerical techniques. Fragmentation models of liquid jets as a result of the deposited energy have also been developed, and the impact on chamber clearing dynamics has been evaluated. Th focus of this study is to critically assess the reliability and the dynamic response of chamber walls in various proposed protection methods for IFE systems. Of particular concern is the effect on wall erosion lifetime of various erosion mechanisms, such as vaporization, chemical and physical sputtering, melt/liquid splashing and explosive erosion, and fragmentation of liquid walls

  5. TargetSpy: a supervised machine learning approach for microRNA target prediction.

    Science.gov (United States)

    Sturm, Martin; Hackenberg, Michael; Langenberger, David; Frishman, Dmitrij

    2010-05-28

    Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved) seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences.In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I) no seed match requirement, II) seed match requirement, and III) conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed) predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on mouse and performs well in human and drosophila

  6. TargetSpy: a supervised machine learning approach for microRNA target prediction

    Directory of Open Access Journals (Sweden)

    Langenberger David

    2010-05-01

    Full Text Available Abstract Background Virtually all currently available microRNA target site prediction algorithms require the presence of a (conserved seed match to the 5' end of the microRNA. Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites. Results We developed TargetSpy, a novel computational approach for predicting target sites regardless of the presence of a seed match. It is based on machine learning and automatic feature selection using a wide spectrum of compositional, structural, and base pairing features covering current biological knowledge. Our model does not rely on evolutionary conservation, which allows the detection of species-specific interactions and makes TargetSpy suitable for analyzing unconserved genomic sequences. In order to allow for an unbiased comparison of TargetSpy to other methods, we classified all algorithms into three groups: I no seed match requirement, II seed match requirement, and III conserved seed match requirement. TargetSpy predictions for classes II and III are generated by appropriate postfiltering. On a human dataset revealing fold-change in protein production for five selected microRNAs our method shows superior performance in all classes. In Drosophila melanogaster not only our class II and III predictions are on par with other algorithms, but notably the class I (no-seed predictions are just marginally less accurate. We estimate that TargetSpy predicts between 26 and 112 functional target sites without a seed match per microRNA that are missed by all other currently available algorithms. Conclusion Only a few algorithms can predict target sites without demanding a seed match and TargetSpy demonstrates a substantial improvement in prediction accuracy in that class. Furthermore, when conservation and the presence of a seed match are required, the performance is comparable with state-of-the-art algorithms. TargetSpy was trained on

  7. Economic evaluation of targeted cancer interventions: critical review and recommendations.

    Science.gov (United States)

    Elkin, Elena B; Marshall, Deborah A; Kulin, Nathalie A; Ferrusi, Ilia L; Hassett, Michael J; Ladabaum, Uri; Phillips, Kathryn A

    2011-10-01

    Scientific advances have improved our ability to target cancer interventions to individuals who will benefit most and spare the risks and costs to those who will derive little benefit or even be harmed. Several approaches are currently used for targeting interventions for cancer risk reduction, screening, and treatment, including risk prediction algorithms for identifying high-risk subgroups and diagnostic tests for tumor markers and germline genetic mutations. Economic evaluation can inform decisions about the use of targeted interventions, which may be more costly than traditional strategies. However, assessing the impact of a targeted intervention on costs and health outcomes requires explicit consideration of the method of targeting. In this study, we describe the importance of this principle by reviewing published cost-effectiveness analyses of targeted interventions in breast cancer. Few studies we identified explicitly evaluated the relationships among the method of targeting, the accuracy of the targeting test, and outcomes of the targeted intervention. Those that did found that characteristics of targeting tests had a substantial impact on outcomes. We posit that the method of targeting and the outcomes of a targeted intervention are inextricably linked and recommend that cost-effectiveness analyses of targeted interventions explicitly consider costs and outcomes of the method of targeting.

  8. Experimental study on neutronics in bombardment of thick targets by high energy proton beams for accelerator-driven sub-critical system

    CERN Document Server

    Guo Shi Lun; Shi Yong Qian; Shen Qing Biao; Wan Jun Sheng; Brandt, R; Vater, P; Kulakov, B A; Krivopustov, M I; Sosnin, A N

    2002-01-01

    The experimental study on neutronics in the target region of accelerator-driven sub-critical system is carried out by using the high energy accelerator in Joint Institute for Nuclear Research, Dubna, Russia. The experiments with targets U(Pb), Pb and Hg bombarded by 0.533, 1.0, 3.7 and 7.4 GeV proton beams show that the neutron yield ratio of U(Pb) to Hg and Pb to Hg targets is (2.10 +- 0.10) and (1.76 +- 0.33), respectively. Hg target is disadvantageous to U(Pb) and Pb targets to get more neutrons. Neutron yield drops along 20 cm thick targets as the thickness penetrated by protons increases. The lower the energy of protons, the steeper the neutron yield drops. In order to get more uniform field of neutrons in the targets, the energy of protons from accelerators should not be lower than 1 GeV. The spectra of secondary neutrons produced by different energies of protons are similar, but the proportion of neutrons with higher energy gradually increases as the proton energy increases

  9. JCO criticality accident termination operation

    International Nuclear Information System (INIS)

    Kanamori, Masashi

    2001-12-01

    On September 30 at around 10:35 AM, criticality accident occurred at the JCO's conversion building in Tokai-mura. Since criticality accident had not been anticipated, neither devices for termination of criticality accident nor neutron detectors were available. Immediately after the information of the accident, our emergency staff (Japan Nuclear Cycle development institute staff) went to JCO site, to measure the intensity of neutrons and gammas. There were four main tasks, first one was to measure the radiation intensity, second one was to terminate the criticality accident, third one is to alert the residents surrounding the JCO site, fourth one is to evacuate the employees in the site. These tasks were successfully performed until October 1. This paper describes about how these operations were performed by the relevant staffs. (author)

  10. Use of critical pathway models and log-normal frequency distributions for siting nuclear facilities

    International Nuclear Information System (INIS)

    Waite, D.A.; Denham, D.H.

    1975-01-01

    The advantages and disadvantages of potential sites for nuclear facilities are evaluated through the use of environmental pathway and log-normal distribution analysis. Environmental considerations of nuclear facility siting are necessarily geared to the identification of media believed to be sifnificant in terms of dose to man or to be potential centres for long-term accumulation of contaminants. To aid in meeting the scope and purpose of this identification, an exposure pathway diagram must be developed. This type of diagram helps to locate pertinent environmental media, points of expected long-term contaminant accumulation, and points of population/contaminant interface for both radioactive and non-radioactive contaminants. Confirmation of facility siting conclusions drawn from pathway considerations must usually be derived from an investigatory environmental surveillance programme. Battelle's experience with environmental surveillance data interpretation using log-normal techniques indicates that this distribution has much to offer in the planning, execution and analysis phases of such a programme. How these basic principles apply to the actual siting of a nuclear facility is demonstrated for a centrifuge-type uranium enrichment facility as an example. A model facility is examined to the extent of available data in terms of potential contaminants and facility general environmental needs. A critical exposure pathway diagram is developed to the point of prescribing the characteristics of an optimum site for such a facility. Possible necessary deviations from climatic constraints are reviewed and reconciled with conclusions drawn from the exposure pathway analysis. Details of log-normal distribution analysis techniques are presented, with examples of environmental surveillance data to illustrate data manipulation techniques and interpretation procedures as they affect the investigatory environmental surveillance programme. Appropriate consideration is given these

  11. The critical role of the industrial sector in reaching long-term emission reduction, energy efficiency and renewable targets

    International Nuclear Information System (INIS)

    Fais, Birgit; Sabio, Nagore; Strachan, Neil

    2016-01-01

    Highlights: • A new industrial modelling approach in a whole energy systems model is developed. • The contribution of UK industry to long-term energy policy targets is analysed. • Emission reductions of up to 77% can be achieved in the UK industry until 2050. • The UK industry sector is essential for achieving the overall efficiency commitments. • UK industry can make a moderate contribution to the expansion of renewable energies. - Abstract: This paper evaluates the critical contribution of the industry sector to long-term decarbonisation, efficiency and renewable energy policy targets. Its methodological novelty is the incorporation of a process-oriented modelling approach based on a comprehensive technology database for the industry sector in a national energy system model for the UK (UKTM), allowing quantification of the role of both decarbonisation of upstream energy vectors and of mitigation options in the industrial sub-categories. This enhanced model is then applied in a comparative policy scenario analysis that explores various target dimensions on emission mitigation, renewable energy and energy efficiency at both a national and European level. The results show that ambitious emission cuts in the industry sector of up to 77% until 2050 compared to 2010 can be achieved. Moreover, with a reduction in industrial energy demand of up to 31% between 2010 and 2050, the sector is essential for achieving the overall efficiency commitments. The industry sector also makes a moderate contribution to the expansion of renewable energies mostly through the use of biomass for low-temperature heating services. However, additional sub-targets on renewable sources and energy efficiency need to be assessed critically, as they can significantly distort the cost-efficiency of the long-term mitigation pathway.

  12. Rectal cancer: The radiation basis of radiotherapy, target volume

    International Nuclear Information System (INIS)

    Bosset, J.F.; Servagi-Vernat, S.; Crehange, G.; Azria, D.; Gerard, J.P.; Hennequin, C.

    2011-01-01

    Since the implementation of preoperative chemo-radiotherapy and meso-rectal excision, the 5-year rates of locoregional failures in T3-T4 N0-N1M0 rectal cancer fell from 25-30% thirty years ago to 5-8% nowadays. A critical analysis of the locoregional failures sites and mechanisms, as well as the identification of nodal extension, helps the radiation oncologist to optimize the radiotherapy target definition. The upper limit of the clinical target volume is usually set at the top of the third sacral vertebra. The lateral pelvic nodes should be included when the tumor is located in the distal part of the rectum. The anal sphincter and the levator muscles should be spared when a conservative surgery is planned. In case of abdomino-perineal excision, the ischio-rectal fossa and the sphincters should be included in the clinical target volume. A confrontation with radiologist and surgeon is mandatory to improve the definition of the target volumes to be treated. (authors)

  13. Experience with performance based training of nuclear criticality safety engineers

    International Nuclear Information System (INIS)

    Taylor, R.G.

    1993-01-01

    Historically, new entrants to the practice of nuclear criticality safety have learned their job primarily by on-the-job training (OJT) often by association with an experienced nuclear criticality safety engineer who probably also learned their job by OJT. Typically, the new entrant learned what he/she needed to know to solve a particular problem and accumulated experience as more problems were solved. It is likely that more formalism will be required in the future. Current US Department of Energy requirements for those positions which have to demonstrate qualification indicate that it should be achieved by using a systematic approach such as performance based training (PBT). Assuming that PBT would be an acceptable mechanism for nuclear criticality safety engineer training in a more formal environment, a site-specific analysis of the nuclear criticality safety engineer job was performed. Based on this analysis, classes are being developed and delivered to a target audience of newer nuclear criticality safety engineers. Because current interest is in developing training for selected aspects of the nuclear criticality safety engineer job, the analysis i's incompletely developed in some areas. Details of this analysis are provided in this report

  14. Cell survival following alpha particle irradiation: critical sites and implications for carcinogenesis

    International Nuclear Information System (INIS)

    Lloyd, E.L.; Gemmell, M.A.; Henning, C.B.; Gemmell, D.S.; Zabransky, B.J.

    1976-01-01

    In experiments in which mammalian cells were irradiated with 5.6 MeV alpha particles from a Tandem Van de Graaff machine we have confirmed the finding of others that the mean lethal dose (D 0 ) is about 100 rad, but by measurements of the area of the cell nuclei as irradiated we found that this mean lethal dose corresponds not to 1, as expected, but to about 27 alpha particles per cell nucleus. (The exact number appears to change slightly with cell passage number.) This allows for the possibility that the direct action of alpha particles on the nucleus may be the important event in carcinogenesis, a theory which was previously difficult to accept if a single particle hitting the nucleus anywhere was considered to be lethal. Evidence is presented to implicate the nucleolus as a possible critical site for the inhibition of reproductive integrity of the cell

  15. Targeting Policy for Obesity Prevention: Identifying the Critical Age for Weight Gain in Women

    Directory of Open Access Journals (Sweden)

    Trevor J. B. Dummer

    2012-01-01

    Full Text Available The obesity epidemic requires the development of prevention policy targeting individuals most likely to benefit. We used self-reported prepregnancy body weight of all women giving birth in Nova Scotia between 1988 and 2006 to define obesity and evaluated socioeconomic, demographic, and temporal trends in obesity using linear regression. There were 172,373 deliveries in this cohort of 110,743 women. Maternal body weight increased significantly by 0.5 kg per year from 1988, and lower income and rural residence were both associated significantly with increasing obesity. We estimated an additional 82,000 overweight or obese women in Nova Scotia in 2010, compared to the number that would be expected from obesity rates of just two decades ago. The critical age for weight gain was identified as being between 20 and 24 years. This age group is an important transition age between adolescence and adulthood when individuals first begin to accept responsibility for food planning, purchasing, and preparation. Policy and public health interventions must target those most at risk, namely, younger women and the socially deprived, whilst tackling the marketing of low-cost energy-dense foods at the expense of healthier options.

  16. Random Tagging Genotyping by Sequencing (rtGBS, an Unbiased Approach to Locate Restriction Enzyme Sites across the Target Genome.

    Directory of Open Access Journals (Sweden)

    Elena Hilario

    Full Text Available Genotyping by sequencing (GBS is a restriction enzyme based targeted approach developed to reduce the genome complexity and discover genetic markers when a priori sequence information is unavailable. Sufficient coverage at each locus is essential to distinguish heterozygous from homozygous sites accurately. The number of GBS samples able to be pooled in one sequencing lane is limited by the number of restriction sites present in the genome and the read depth required at each site per sample for accurate calling of single-nucleotide polymorphisms. Loci bias was observed using a slight modification of the Elshire et al.some restriction enzyme sites were represented in higher proportions while others were poorly represented or absent. This bias could be due to the quality of genomic DNA, the endonuclease and ligase reaction efficiency, the distance between restriction sites, the preferential amplification of small library restriction fragments, or bias towards cluster formation of small amplicons during the sequencing process. To overcome these issues, we have developed a GBS method based on randomly tagging genomic DNA (rtGBS. By randomly landing on the genome, we can, with less bias, find restriction sites that are far apart, and undetected by the standard GBS (stdGBS method. The study comprises two types of biological replicates: six different kiwifruit plants and two independent DNA extractions per plant; and three types of technical replicates: four samples of each DNA extraction, stdGBS vs. rtGBS methods, and two independent library amplifications, each sequenced in separate lanes. A statistically significant unbiased distribution of restriction fragment size by rtGBS showed that this method targeted 49% (39,145 of BamH I sites shared with the reference genome, compared to only 14% (11,513 by stdGBS.

  17. Abundant off-target edits from site-directed RNA editing can be reduced by nuclear localization of the editing enzyme.

    Science.gov (United States)

    Vallecillo-Viejo, Isabel C; Liscovitch-Brauer, Noa; Montiel-Gonzalez, Maria Fernanda; Eisenberg, Eli; Rosenthal, Joshua J C

    2018-01-02

    Site-directed RNA editing (SDRE) is a general strategy for making targeted base changes in RNA molecules. Although the approach is relatively new, several groups, including our own, have been working on its development. The basic strategy has been to couple the catalytic domain of an adenosine (A) to inosine (I) RNA editing enzyme to a guide RNA that is used for targeting. Although highly efficient on-target editing has been reported, off-target events have not been rigorously quantified. In this report we target premature termination codons (PTCs) in messages encoding both a fluorescent reporter protein and the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein transiently transfected into human epithelial cells. We demonstrate that while on-target editing is efficient, off-target editing is extensive, both within the targeted message and across the entire transcriptome of the transfected cells. By redirecting the editing enzymes from the cytoplasm to the nucleus, off-target editing is reduced without compromising the on-target editing efficiency. The addition of the E488Q mutation to the editing enzymes, a common strategy for increasing on-target editing efficiency, causes a tremendous increase in off-target editing. These results underscore the need to reduce promiscuity in current approaches to SDRE.

  18. Target and identify: triazene linker helps identify azidation sites of labelled proteins via click and cleave strategy.

    Science.gov (United States)

    Lohse, Jonas; Schindl, Alexandra; Danda, Natasha; Williams, Chris P; Kramer, Karl; Kuster, Bernhard; Witte, Martin D; Médard, Guillaume

    2017-10-31

    A method for identifying probe modification of proteins via tandem mass spectrometry was developed. Azide bearing molecules are immobilized on functionalised sepharose beads via copper catalysed Huisgen-type click chemistry and selectively released under acidic conditions by chemical cleavage of the triazene linkage. We applied this method to identify the modification site of targeted-diazotransfer on BirA.

  19. CasA mediates Cas3-catalyzed target degradation during CRISPR RNA-guided interference.

    Science.gov (United States)

    Hochstrasser, Megan L; Taylor, David W; Bhat, Prashant; Guegler, Chantal K; Sternberg, Samuel H; Nogales, Eva; Doudna, Jennifer A

    2014-05-06

    In bacteria, the clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) DNA-targeting complex Cascade (CRISPR-associated complex for antiviral defense) uses CRISPR RNA (crRNA) guides to bind complementary DNA targets at sites adjacent to a trinucleotide signature sequence called the protospacer adjacent motif (PAM). The Cascade complex then recruits Cas3, a nuclease-helicase that catalyzes unwinding and cleavage of foreign double-stranded DNA (dsDNA) bearing a sequence matching that of the crRNA. Cascade comprises the CasA-E proteins and one crRNA, forming a structure that binds and unwinds dsDNA to form an R loop in which the target strand of the DNA base pairs with the 32-nt RNA guide sequence. Single-particle electron microscopy reconstructions of dsDNA-bound Cascade with and without Cas3 reveal that Cascade positions the PAM-proximal end of the DNA duplex at the CasA subunit and near the site of Cas3 association. The finding that the DNA target and Cas3 colocalize with CasA implicates this subunit in a key target-validation step during DNA interference. We show biochemically that base pairing of the PAM region is unnecessary for target binding but critical for Cas3-mediated degradation. In addition, the L1 loop of CasA, previously implicated in PAM recognition, is essential for Cas3 activation following target binding by Cascade. Together, these data show that the CasA subunit of Cascade functions as an essential partner of Cas3 by recognizing DNA target sites and positioning Cas3 adjacent to the PAM to ensure cleavage.

  20. How to target inter-regional phase synchronization with dual-site Transcranial Alternating Current Stimulation

    DEFF Research Database (Denmark)

    Saturnino, Guilherme Bicalho; Madsen, Kristoffer Hougaard; Siebner, Hartwig Roman

    2017-01-01

    oscillations in two connected cortical areas. While the frequency of ds-TACS is matched, the phase of stimulation is either identical (in-phase stimulation) or opposite (anti-phase stimulation) in the two cortical target areas. In-phase stimulation is thought to synchronize the endogenous oscillations...... and hereby to improve behavioral performance. Conversely, anti-phase stimulation is thought to desynchronize neural oscillations in the two areas, which is expected to decrease performance. Critically, in- and anti-phase ds-TACS should only differ with respect to temporal phase, while all other stimulation...... unambiguously the causal contribution of phase coupling to specific cognitive processes in the human brain....

  1. The potential role of nano- and micro-technology in the management of critical illnesses.

    Science.gov (United States)

    Sadikot, Ruxana T

    2014-11-20

    In recent years nanomedicine has become an attractive concept for the targeted delivery of therapeutic and diagnostic compounds to injured or inflamed organs. Nanoscale drug delivery systems have the ability to improve the pharmacokinetics and increase the biodistribution of therapeutic agents to target organs, thereby resulting in improved efficacy and reduced drug toxicity. These systems are exploited for therapeutic purposes to carry the drug in the body in a controlled manner from the site of administration to the therapeutic target. The mortality in many of the critical illnesses such as sepsis and acute respiratory distress syndrome continues to remain high despite of an increased understanding of the molecular pathogenesis of these diseases. Several promising targets that have been identified as potential therapies for these devastating diseases have been limited because of difficulty with delivery systems. In particular, delivery of peptides, proteins, and miRNAs to the lung is an ongoing challenge. Hence, it is an attractive strategy to test potential targets by employing nanotechnology. Here some of the novel nanomedicine approaches that have been proposed and studied in recent years to facilitate the delivery of therapeutic agents in the setting of critical illnesses such as acute respiratory distress syndrome, sepsis and ventilator associated pneumonia are reviewed. Published by Elsevier B.V.

  2. Critical/non-critical system methodology report

    International Nuclear Information System (INIS)

    1989-01-01

    The method used to determine how the waste Isolation Pilot Plant (WIPP) facilities/systems were classified as critical or non-critical to the receipt of CH waste is described within this report. All WIPP critical facilities/systems are listed in the Operational Readiness Review Dictionary. Using the Final Safety Analysis Report (FSAR) as a guide to define the boundaries of the facilities/systems, a direct correlation of the ORR Dictionary to the FSAR can be obtained. The critical facilities/systems are those which are directly related to or have a critical support role in the receipt of CH waste. The facility/systems must meet one of the following requirements to be considered critical: (a) confinement or measure of the release of radioactive materials; (b) continued receipt and/or storage of transuranic waste (TRU) without an interruption greater than one month according to the shipping plan schedule; (c) the environmental and occupational safety of personnel meets the established site programs; and (d) the physical security of the WIPP facilities

  3. Morphometry for alpha particle hits of critical targets in the lungs. Final technical report

    International Nuclear Information System (INIS)

    Mercer, R.R.

    1998-01-01

    The objective of this study is to provide detailed data on the number, location and type of critical target cells in the airspaces and to use these data in order to make risk assessments of the health effects of radon and radon progeny in the lungs. This will be done by quantitative morphometric study of the distribution of the various cell types and mucous lining layers in the lungs. The results provide anatomically correct models for dosimetry in the rate and human airways which significantly improve the ability to do risk assessment for radon exposures by providing quantitative data for specific cell types and provide a basis for mechanism based comparison between data available in animal exposures and human epidemiology

  4. Young drivers' engagement with social interactive technology on their smartphone: Critical beliefs to target in public education messages.

    Science.gov (United States)

    Gauld, Cassandra S; Lewis, Ioni M; White, Katherine M; Watson, Barry

    2016-11-01

    The current study forms part of a larger study based on the Step Approach to Message Design and Testing (SatMDT), a new and innovative framework designed to guide the development and evaluation of health communication messages, including road safety messages. This four step framework is based on several theories, including the Theory of Planned Behaviour. The current study followed steps one and two of the SatMDT framework and utilised a quantitative survey to validate salient beliefs (behavioural, normative, and control) about initiating, monitoring/reading, and responding to social interactive technology on smartphones by N=114 (88F, 26M) young drivers aged 17-25 years. These beliefs had been elicited in a prior in-depth qualitative study. A subsequent critical beliefs analysis identified seven beliefs as potential targets for public education messages, including, 'slow-moving traffic' (control belief - facilitator) for both monitoring/reading and responding behaviours; 'feeling at ease that you had received an expected communication' (behavioural belief -advantage) for monitoring/reading behaviour; and 'friends/peers more likely to approve' (normative belief) for responding behaviour. Potential message content targeting these seven critical beliefs is discussed in accordance with the SatMDT. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. The behavior of the critical current density below and above the first matching field in superconductors with periodic square arrays of pinning sites

    International Nuclear Information System (INIS)

    Obaidat, I.M.; Al Khawaja, U.; Benkraouda, M.; Salmeen, N.

    2006-01-01

    We have studied the effect of the applied magnetic field on critical depinning force at zero and finite temperatures and for several values of pinning strength. This was achieved by conducting extensive series of molecular dynamic simulations on driven vortex lattices interacting with periodic square arrays of pinning sites. We have found that the critical depinning force decreases as the applied magnetic field is increased. We have also observed two distinct behaviors of dependence of the critical depinning force on the applied magnetic field below and above the first matching filed

  6. Analysis of Properties of Reflectance Reference Targets for Permanent Radiometric Test Sites of High Resolution Airborne Imaging Systems

    Directory of Open Access Journals (Sweden)

    Eero Ahokas

    2010-08-01

    Full Text Available Reliable and optimal exploitation of rapidly developing airborne imaging methods requires geometric and radiometric quality assurance of production systems in operational conditions. Permanent test sites are the most promising approach for cost-efficient performance assessment. Optimal construction of permanent radiometric test sites for high resolution airborne imaging systems is an unresolved issue. The objective of this study was to assess the performance of commercially available gravels and painted and unpainted concrete targets for permanent, open-air radiometric test sites under sub-optimal climate conditions in Southern Finland. The reflectance spectrum and reflectance anisotropy and their stability were characterized during the summer of 2009. The management of reflectance anisotropy and stability were shown to be the key issues for better than 5% reflectance accuracy.

  7. Liposome as nanocarrier: Site targeted delivery in lung cancer

    Directory of Open Access Journals (Sweden)

    Najeeb Ullah

    2017-08-01

    Full Text Available Lung cancer is fatal and spreading rapidly worldwide. Different clinical strategies are applied to stop this cancer. As the lung is a delicate organ, special clinical applications must be used and nanodrugs delivery systems are the most important applications of all. This review discusses the lung problems such as lung cancer, lung inflammation and bronchi constrictions followed by repetitive intake of some drugs. The objective of this review is to study how nanodrug delivery systems were synthesized and used in lung disorder treatment especially in lung cancer. The authors studied some articles from 1989 to 2015. Liposome encapsulation was done in various ways for the delivery of different drugs such as metaproterenol into liposomes caused bronchodilation, immunoliposomes bearing antibodies for doxorubicin reduced 50% inhibitory effects, radioliposomes with high penetrating ability to peripheral airways, aerosol delivery systems with deep pulmonary deposition, polymeric drug delivery having potential to improve beneficial index of drug, solid lipid liposomes, liposomal gentamicin with altered different clinical susceptibilities of resistance, transferrin conjugated liposomes to deliver cytostatic drugs to site of lungs, anti-inflammatory drugs with mannosylated liposomes, liposomal suspensions with single stranded RNAs and peptide encapsulation of liposomes. This review indicates that many animals perished with intravenous administration of drugs but survived in liposomal targeting groups.

  8. Metabolic and Target-Site Mechanisms Combine to Confer Strong DDT Resistance in Anopheles gambiae

    Science.gov (United States)

    Mitchell, Sara N.; Rigden, Daniel J.; Dowd, Andrew J.; Lu, Fang; Wilding, Craig S.; Weetman, David; Dadzie, Samuel; Jenkins, Adam M.; Regna, Kimberly; Boko, Pelagie; Djogbenou, Luc; Muskavitch, Marc A. T.; Ranson, Hilary; Paine, Mark J. I.; Mayans, Olga; Donnelly, Martin J.

    2014-01-01

    The development of resistance to insecticides has become a classic exemplar of evolution occurring within human time scales. In this study we demonstrate how resistance to DDT in the major African malaria vector Anopheles gambiae is a result of both target-site resistance mechanisms that have introgressed between incipient species (the M- and S-molecular forms) and allelic variants in a DDT-detoxifying enzyme. Sequencing of the detoxification enzyme, Gste2, from DDT resistant and susceptible strains of An. gambiae, revealed a non-synonymous polymorphism (I114T), proximal to the DDT binding domain, which segregated with strain phenotype. Recombinant protein expression and DDT metabolism analysis revealed that the proteins from the susceptible strain lost activity at higher DDT concentrations, characteristic of substrate inhibition. The effect of I114T on GSTE2 protein structure was explored through X-ray crystallography. The amino acid exchange in the DDT-resistant strain introduced a hydroxyl group nearby the hydrophobic DDT-binding region. The exchange does not result in structural alterations but is predicted to facilitate local dynamics and enzyme activity. Expression of both wild-type and 114T alleles the allele in Drosophila conferred an increase in DDT tolerance. The 114T mutation was significantly associated with DDT resistance in wild caught M-form populations and acts in concert with target-site mutations in the voltage gated sodium channel (Vgsc-1575Y and Vgsc-1014F) to confer extreme levels of DDT resistance in wild caught An. gambiae. PMID:24675797

  9. Mission Critical Occupation (MCO) Charts

    Data.gov (United States)

    Office of Personnel Management — Agencies report resource data and targets for government-wide mission critical occupations and agency specific mission critical and/or high risk occupations. These...

  10. A Generic Multi-Compartmental CNS Distribution Model Structure for 9 Drugs Allows Prediction of Human Brain Target Site Concentrations

    NARCIS (Netherlands)

    Yamamoto, Yumi; Valitalo, Pyry A.; van den Berg, Dirk-Jan; Hartman, Robin; van den Brink, Willem; Wong, Yin Cheong; Huntjens, Dymphy R.; Proost, Johannes H.; Vermeulen, An; Krauwinkel, Walter; Bakshi, Suruchi; Aranzana-Climent, Vincent; Marchand, Sandrine; Dahyot-Fizelier, Claire; Couet, William; Danhof, Meindert; van Hasselt, Johan G. C.; de lange, Elizabeth C. M.

    Purpose Predicting target site drug concentration in the brain is of key importance for the successful development of drugs acting on the central nervous system. We propose a generic mathematical model to describe the pharmacokinetics in brain compartments, and apply this model to predict human

  11. Criticality accident:

    International Nuclear Information System (INIS)

    Canavese, Susana I.

    2000-01-01

    A criticality accident occurred at 10:35 on September 30, 1999. It occurred in a precipitation tank in a Conversion Test Building at the JCO Tokai Works site in Tokaimura (Tokai Village) in the Ibaraki Prefecture of Japan. STA provisionally rated this accident a 4 on the seven-level, logarithmic International Nuclear Event Scale (INES). The September 30, 1999 criticality accident at the JCO Tokai Works Site in Tokaimura, Japan in described in preliminary, technical detail. Information is based on preliminary presentations to technical groups by Japanese scientists and spokespersons, translations by technical and non-technical persons of technical web postings by various nuclear authorities, and English-language non-technical reports from various news media and nuclear-interest groups. (author)

  12. Barriers to Liposomal Gene Delivery: from Application Site to the Target.

    Science.gov (United States)

    Saffari, Mostafa; Moghimi, Hamid Reza; Dass, Crispin R

    2016-01-01

    Gene therapy is a therapeutic approach to deliver genetic material into cells to alter their function in entire organism. One promising form of gene delivery system (DDS) is liposomes. The success of liposome-mediated gene delivery is a multifactorial issue and well-designed liposomal systems might lead to optimized gene transfection particularly in vivo. Liposomal gene delivery systems face different barriers from their site of application to their target, which is inside the cells. These barriers include presystemic obstacles (epithelial barriers), systemic barriers in blood circulation and cellular barriers. Epithelial barriers differ depending on the route of administration. Systemic barriers include enzymatic degradation, binding and opsonisation. Both of these barriers can act as limiting hurdles that genetic material and their vector should overcome before reaching the cells. Finally liposomes should overcome cellular barriers that include cell entrance, endosomal escape and nuclear uptake. These barriers and their impact on liposomal gene delivery will be discussed in this review.

  13. Imaging the PCP site of the NMDA ion channel

    Energy Technology Data Exchange (ETDEWEB)

    Waterhouse, Rikki N. E-mail: rnw7@columbia.edu

    2003-11-01

    The N-methyl-D-aspartate (NMDA) ion channel plays a role in neuroprotection, neurodegeneration, long-term potentiation, memory, and cognition. It is implicated in the pathophysiology of several neurological and neuropsychiatric disorders including Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. The development of effective radiotracers for the study of NMDA receptors is critical for our understanding of their function, and their modulation by endogenousr substances or therapeutic drugs. Since the NMDA/PCP receptor lies within the channel, it is a unique target and is theoretically accessible only when the channel is in the active and 'open' state, but not when it is in the inactive or 'closed' state. The physical location of the NMDA/PCP receptor not only makes it an important imaging target but also complicates the development of suitable PET and SPECT radiotracers for this site. An intimate understanding of the biochemical, pharmacological, physiological and behavioral processes associated with the NMDA ion channel is essential to develop improved imaging agents. This review outlines progress made towards the development of radiolabeled agents for PCP sites of the NMDA ion channel. In addition, the animal and pharmacological models used for in vitro and in vivo assessment of NMDA receptor targeted agents are discussed.

  14. Imaging the PCP site of the NMDA ion channel

    International Nuclear Information System (INIS)

    Waterhouse, Rikki N.

    2003-01-01

    The N-methyl-D-aspartate (NMDA) ion channel plays a role in neuroprotection, neurodegeneration, long-term potentiation, memory, and cognition. It is implicated in the pathophysiology of several neurological and neuropsychiatric disorders including Parkinson's Disease, Huntington's Chorea, schizophrenia, alcoholism and stroke. The development of effective radiotracers for the study of NMDA receptors is critical for our understanding of their function, and their modulation by endogenousr substances or therapeutic drugs. Since the NMDA/PCP receptor lies within the channel, it is a unique target and is theoretically accessible only when the channel is in the active and 'open' state, but not when it is in the inactive or 'closed' state. The physical location of the NMDA/PCP receptor not only makes it an important imaging target but also complicates the development of suitable PET and SPECT radiotracers for this site. An intimate understanding of the biochemical, pharmacological, physiological and behavioral processes associated with the NMDA ion channel is essential to develop improved imaging agents. This review outlines progress made towards the development of radiolabeled agents for PCP sites of the NMDA ion channel. In addition, the animal and pharmacological models used for in vitro and in vivo assessment of NMDA receptor targeted agents are discussed

  15. Critical heat flux performance of hypervapotrons proposed for use in the ITER divertor vertical target

    International Nuclear Information System (INIS)

    Youchison, D.L.; Marshall, T.D.; McDonald, J.M.; Lutz, T.J.; Watson, R.D.; Driemeyer, D.E.; Kubik, D.L.; Slattery, K.T.; Hellwig, T.H.

    1997-09-01

    Task T-222 of the International Thermonuclear Experimental Reactor (ITER) program addresses the manufacturing and testing of permanent components for use in the ITER divertor. Thermalhydraulic and critical heat flux performance of the heat sinks proposed for use in the divertor vertical target are part of subtask T-222.4. As part of this effort, two single channel, medium scale, bare copper alloy, hypervapotron mockups were designed, fabricated, and tested using the EB-1200 electron beam system. The objectives of the effort were to develop the design and manufacturing procedures required for construction of robust high heat flux (HHF) components, verify thermalhydraulic, thermomechanical and critical heat flux (CHF) performance under ITER relevant conditions, and perform analyses of HHF data to identify design guidelines and failure criteria and possibly modify any applicable CHF correlations. The design, fabrication, and finite element modeling of two types of hypervapotrons are described; a common version already in use at the Joint European Torus (JET) and a new attached fin design. HHF test data on the attached fin hypervapotron will be used to compare the CHF performance under uniform heating profiles on long heated lengths with that of localized, highly peaked, off nominal profiles

  16. Critical heat flux performance of hypervapotrons proposed for use in the ITER divertor vertical target

    Energy Technology Data Exchange (ETDEWEB)

    Youchison, D.L.; Marshall, T.D.; McDonald, J.M.; Lutz, T.J.; Watson, R.D. [Sandia National Labs., Albuquerque, NM (United States); Driemeyer, D.E. Kubik, D.L.; Slattery, K.T.; Hellwig, T.H. [McDonnell Douglas Aerospace, St. Louis, MO (United States)

    1997-09-01

    Task T-222 of the International Thermonuclear Experimental Reactor (ITER) program addresses the manufacturing and testing of permanent components for use in the ITER divertor. Thermalhydraulic and critical heat flux performance of the heat sinks proposed for use in the divertor vertical target are part of subtask T-222.4. As part of this effort, two single channel, medium scale, bare copper alloy, hypervapotron mockups were designed, fabricated, and tested using the EB-1200 electron beam system. The objectives of the effort were to develop the design and manufacturing procedures required for construction of robust high heat flux (HHF) components, verify thermalhydraulic, thermomechanical and critical heat flux (CHF) performance under ITER relevant conditions, and perform analyses of HHF data to identify design guidelines and failure criteria and possibly modify any applicable CHF correlations. The design, fabrication, and finite element modeling of two types of hypervapotrons are described; a common version already in use at the Joint European Torus (JET) and a new attached fin design. HHF test data on the attached fin hypervapotron will be used to compare the CHF performance under uniform heating profiles on long heated lengths with that of localized, highly peaked, off nominal profiles.

  17. Targeted advertising, platform competition and privacy

    NARCIS (Netherlands)

    Kox, Henk; Straathof, Bas; Zwart, Gijsbert

    2017-01-01

    Targeted advertising can benefit consumers through lower prices for access to web sites. Yet, if consumers dislike that web sites collect their personal information, their welfare may go down. We study competition for consumers between web sites that can show targeted advertisements. We find that

  18. Tank farm nuclear criticality review

    International Nuclear Information System (INIS)

    Bratzel, D.R.

    1996-01-01

    The technical basis for the nuclear criticality safety of stored wastes at the Hanford Site Tank Farm Complex was reviewed by a team of senior technical personnel whose expertise covered all appropriate aspects of fissile materials chemistry and physics. The team concluded that the detailed and documented nucleonics-related studies underlying the waste tanks criticality safety basis were sound. The team concluded that, under current plutonium inventories and operating conditions, a nuclear criticality accident is incredible in any of the Hanford single-shell tanks (SST), double-shell tanks (DST), or double-contained receiver tanks (DCRTS) on the Hanford Site

  19. Temperature and pinning strength dependence of the critical current of a superconductor with a square periodic array of pinning sites

    International Nuclear Information System (INIS)

    Benkraouda, M.; Obaidat, I.M.; Al Khawaja, U.

    2006-01-01

    We have conducted extensive series of molecular dynamic simulations on driven vortex lattices interacting with periodic square arrays of pinning sites. In solving the over damped equation of vortex motion we took into account the vortex-vortex repulsion interaction, the attractive vortex-pinning interaction, and the driving Lorentz force at several values of temperature. We have studied the effect of varying the driving Lorentz force and varying the pinning strength on the critical current for several pinning densities, and temperature values. We have found that the pinning strength play an important role in enhancing the critical current over the whole temperature range. At low temperatures, the critical current was found to increase linearly with increasing the pinning strengths for all pinning densities. As the temperature increases, the effect of small pinning strengths diminishes and becomes insignificant at high temperatures

  20. Effects of functionalization on the targeting site of carbon nanotubes inside cells

    Energy Technology Data Exchange (ETDEWEB)

    Porter, A E; Bendall, J S; Welland, M [UK SuperSTEM, Daresbury Laboratory, Daresbury, Cheshire WA4 4AD (United Kingdom); Gass, M [The Nanoscience Centre, University of Cambridge, 11 J. J. Thompson Avenue, Cambridge CB3 OFF (United Kingdom); Muller, K; Skepper, J [Multiimaging Centre, Department of PDN, Physiology, Development and Neuroscience, Anatomy Building, University of Cambridge, Downing Street, Cambridge CB2 3DY (United Kingdom); Midgley, P, E-mail: a.porter@imperial.ac.u [Department of Materials Science and Metallurgy, University of Cambridge, Pembroke Street, Cambridge CB2 3QZ (United Kingdom)

    2010-07-01

    Functionalized single-walled carbon nanotubes (SWNTs) are currently being investigated for a variety of applications, including contrast agents for medical imaging{sup 1}. However before they can be used commercially it is necessary to assess whether they enter cells, the site they target within the cell and whether they cause any cytotoxicity. Here we characterize uptake of unlabelled, acid-treated, COO{sup -} functionalized SWNTs by human monocyte derived macrophage cells using both low-loss and energy loss spectroscopy and compare our findings to previous work on unpurified SWNTs. The acid-treated SWNTs were less aggregated within cells than unpurified SWNTs. Acid treatment was found to affect the distribution of intracellular SWNTs. Bundles, and also individual acid treated SWNTs, were found frequently inside lysosomes, cytoplasm and also inserting into the plasma membrane whereas unpurified non-functionalised SWNTs entered lysosomes and occasionally the nucleus.

  1. Effects of functionalization on the targeting site of carbon nanotubes inside cells

    International Nuclear Information System (INIS)

    Porter, A E; Bendall, J S; Welland, M; Gass, M; Muller, K; Skepper, J; Midgley, P

    2010-01-01

    Functionalized single-walled carbon nanotubes (SWNTs) are currently being investigated for a variety of applications, including contrast agents for medical imaging 1 . However before they can be used commercially it is necessary to assess whether they enter cells, the site they target within the cell and whether they cause any cytotoxicity. Here we characterize uptake of unlabelled, acid-treated, COO - functionalized SWNTs by human monocyte derived macrophage cells using both low-loss and energy loss spectroscopy and compare our findings to previous work on unpurified SWNTs. The acid-treated SWNTs were less aggregated within cells than unpurified SWNTs. Acid treatment was found to affect the distribution of intracellular SWNTs. Bundles, and also individual acid treated SWNTs, were found frequently inside lysosomes, cytoplasm and also inserting into the plasma membrane whereas unpurified non-functionalised SWNTs entered lysosomes and occasionally the nucleus.

  2. On-site detection of Phytophthora spp.—single-stranded target DNA as the limiting factor to improve on-chip hybridization

    International Nuclear Information System (INIS)

    Schwenkbier, Lydia; Pollok, Sibyll; Popp, Jürgen; Weber, Karina; König, Stephan; Wagner, Stefan; Werres, Sabine; Weber, Jörg; Hentschel, Martin

    2014-01-01

    We report on a lab-on-a-chip approach for on-site detection of Phytophthora species that allows visual signal readout. The results demonstrate the significance of single-stranded DNA (ssDNA) generation in terms of improving the intensity of the hybridization signal and to improve the reliability of the method. Conventional PCR with subsequent heat denaturation, sodium hydroxide-based denaturation, lambda exonuclease digestion and two asymmetric PCR methods were investigated for the species P. fragariae, P. kernoviae, and P. ramorum. The positioning of the capture probe within the amplified yeast GTP-binding protein (YPT1) target DNA was also of interest because it significantly influences the intensity of the signal. Statistical tests were used to validate the impact of the ssDNA generation methods and the capture-target probe position. The single-stranded target DNA generated by Linear-After-The-Exponential PCR (LATE-PCR) was found to produce signal intensities comparable to post-PCR exonuclease treatment. The LATE-PCR is the best method for the on-site detection of Phytophthora because the enzymatic digestion after PCR is more laborious and time-consuming. (author)

  3. Critical Role of the Sphingolipid Pathway in Stroke: a Review of Current Utility and Potential Therapeutic Targets.

    Science.gov (United States)

    Sun, Na; Keep, Richard F; Hua, Ya; Xi, Guohua

    2016-10-01

    Sphingolipids are a series of cell membrane-derived lipids which act as signaling molecules and play a critical role in cell death and survival, proliferation, recognition, and migration. Sphingosine-1-phosphate acts as a key signaling molecule and regulates lymphocyte trafficking, glial cell activation, vasoconstriction, endothelial barrier function, and neuronal death pathways which plays a critical role in numerous neurological conditions. Stroke is a second leading cause of death all over the world and effective therapies are still in great demand, including ischemic stroke and hemorrhagic stroke as well as poststroke repair. Significantly, sphingolipid activities change after stroke and correlate with stroke outcome, which has promoted efforts to testify whether the sphingolipid pathway could be a novel therapeutic target in stroke. The sphingolipid metabolic pathway, the connection between the pathway and stroke, as well as therapeutic interventions to manipulate the pathway to reduce stroke-induced brain injury are discussed in this review.

  4. Target-site resistance to neonicotinoids.

    Science.gov (United States)

    Crossthwaite, Andrew J; Rendine, Stefano; Stenta, Marco; Slater, Russell

    2014-10-01

    Neonicotinoid insecticides selectively target the invertebrate nicotinic acetylcholine receptor and disrupt excitatory cholinergic neurotransmission. First launched over 20 years ago, their broad pest spectrum, variety of application methods and relatively low risk to nontarget organisms have resulted in this class dominating the insecticide market with global annual sales in excess of $3.5 bn. This remarkable commercial success brings with it conditions in the field that favour selection of resistant phenotypes. A number of important pest species have been identified with mutations at the nicotinic acetylcholine receptor associated with insensitivity to neonicotinoids. The detailed characterization of these mutations has facilitated a greater understanding of the invertebrate nicotinic acetylcholine receptor.

  5. Targeted Nanotechnology for Cancer Imaging

    Science.gov (United States)

    Toy, Randall; Bauer, Lisa; Hoimes, Christopher; Ghaghada, Ketan B.; Karathanasis, Efstathios

    2014-01-01

    Targeted nanoparticle imaging agents provide many benefits and new opportunities to facilitate accurate diagnosis of cancer and significantly impact patient outcome. Due to the highly engineerable nature of nanotechnology, targeted nanoparticles exhibit significant advantages including increased contrast sensitivity, binding avidity and targeting specificity. Considering the various nanoparticle designs and their adjustable ability to target a specific site and generate detectable signals, nanoparticles can be optimally designed in terms of biophysical interactions (i.e., intravascular and interstitial transport) and biochemical interactions (i.e., targeting avidity towards cancer-related biomarkers) for site-specific detection of very distinct microenvironments. This review seeks to illustrate that the design of a nanoparticle dictates its in vivo journey and targeting of hard-to-reach cancer sites, facilitating early and accurate diagnosis and interrogation of the most aggressive forms of cancer. We will report various targeted nanoparticles for cancer imaging using X-ray computed tomography, ultrasound, magnetic resonance imaging, nuclear imaging and optical imaging. Finally, to realize the full potential of targeted nanotechnology for cancer imaging, we will describe the challenges and opportunities for the clinical translation and widespread adaptation of targeted nanoparticles imaging agents. PMID:25116445

  6. Monte Carlo simulation of age-dependent radiation dose from alpha- and beta-emitting radionuclides to critical trabecular bone and bone marrow targets

    Science.gov (United States)

    Dant, James T.; Richardson, Richard B.; Nie, Linda H.

    2013-05-01

    Alpha (α) particles and low-energy beta (β) particles present minimal risk for external exposure. While these particles can induce leukemia and bone cancer due to internal exposure, they can also be beneficial for targeted radiation therapies. In this paper, a trabecular bone model is presented to investigate the radiation dose from bone- and marrow-seeking α and β emitters to different critical compartments (targets) of trabecular bone for different age groups. Two main issues are addressed with Monte Carlo simulations. The first is the absorption fractions (AFs) from bone and marrow to critical targets within the bone for different age groups. The other issue is the application of 223Ra for the radiotherapy treatment of bone metastases. Both a static model and a simulated bone remodeling process are established for trabecular bone. The results show significantly lower AFs from radionuclide sources in the bone volume to the peripheral marrow and the haematopoietic marrow for adults than for newborns and children. The AFs from sources on the bone surface and in the bone marrow to peripheral marrow and haematopoietic marrow also varies for adults and children depending on the energy of the particles. Regarding the use of 223Ra as a radionuclide for the radiotherapy of bone metastases, the simulations show a significantly higher dose from 223Ra and its progeny in forming bone to the target compartment of bone metastases than that from two other more commonly used β-emitting radiopharmaceuticals, 153Sm and 89Sr. There is also a slightly lower dose from 223Ra in forming bone to haematopoietic marrow than that from 153Sm and 89Sr. These results indicate a higher therapy efficiency and lower marrow toxicity from 223Ra and its progeny. In conclusion, age-related changes in bone dimension and cellularity seem to significantly affect the internal dose from α and β emitters in the bone and marrow to critical targets, and 223Ra may be a more efficient

  7. Feasibility of subcutaneously implanted magnetic microarrays for site specific drug and gene targeting

    Directory of Open Access Journals (Sweden)

    M. Babincová

    2010-01-01

    Full Text Available The magnetic nanoparticles play a crucial role as a drug carriers in the human body. The wedge like magnetic arrays creatinga strongly non-homogeneous magnetic field are considered as a useful way to focus magnetic nanoparticles functionalizedwith various drugs or genes to desired sites. The goal of this study is to develop a numerical model of drug targetingusing subcutaneously implanted magnetic microarrays. The Finite Element Method is applied to solve partial differentialequations describing electromagnetic field (Maxwell equations and motion of these particles in a given magnetic field isobtained solving set of ordinary differential equations expressed by Newton law of motion. The results are encouragingshowing the potential to target drug to the tumour cell locally, without unwanted side effects.

  8. Cytotoxicity from coupled redox cycling of autoxidizing xenobiotics and metals: a selective critical review and commentary on work-in-progress

    Energy Technology Data Exchange (ETDEWEB)

    Borg, D C; Schaich, K M

    1984-01-01

    A comprehensive reaction schema for oxidative cytotoxicity is presented, integrating known chemical mechanisms of oxygen radical reactions and observed pathophysiology. The key features of the schema are the coupling of (1) redox cycling of autoxidizable substrates to form the equilibrium pair of superoxide anion (O/sub 2//sup -/)/and its conjugate acid, perhydroxyl radical (HO/sub 2/.); (2) hydrogen peroxide (H/sub 2/O/sub 2/) generation via O/sub 2//sup -/ dimutation; (3) catalytic redox cycling of metals reducing H/sub 2/O/sub 2/ to reactive hydroxyl radicals (OH.); (4) direct reaction of OH. with target molecules, including critical cell macromolecules and polyunsaturated lipids in membranes; (5) transfer of oxidative potential from initial to distant sites via H/sub 2/O/sub 2/ and O/sub 2/-/HO/sub 2/ diffusion, lipid free radical chain peroxidations in membranes, and migration of non-radical lipid oxidation products; and (6) cytotoxic damage at those distant sites mediated by reaction of lipid radical species and other lipid oxidation products with critical target molecules (proteins, DNA, etc.). Although there is a broad consensus of agreement within the cognizant research community concerning many aspects of this schema, there exists considerable controversy and/or misconception about several important issues. Critical analyses of four presently controversial points are presented.

  9. In silico assessment of phosphorylation and O-β-GlcNAcylation sites in human NPC1 protein critical for Ebola virus entry.

    Science.gov (United States)

    Basharat, Zarrin; Yasmin, Azra

    2015-08-01

    Ebola is a highly pathogenic enveloped virus responsible for deadly outbreaks of severe hemorrhagic fever. It enters human cells by binding a multifunctional cholesterol transporter Niemann-Pick C1 (NPC1) protein. Post translational modification (PTM) information for NPC1 is crucial to understand Ebola virus (EBOV) entry and action due to changes in phosphorylation or glycosylation at the binding site. It is difficult and costly to experimentally assess this type of interaction, so in silico strategy was employed. Identification of phosphorylation sites, including conserved residues that could be possible targets for 21 predicted kinases was followed by interplay study between phosphorylation and O-β-GlcNAc modification of NPC1. Results revealed that only 4 out of 48 predicted phosphosites exhibited O-β-GlcNAc activity. Predicted outcomes were integrated with residue conservation and 3D structural information. Three Yin Yang sites were located in the α-helix regions and were conserved in studied vertebrate and mammalian species. Only one modification site S425 was found in β-turn region located near the N-terminus of NPC1 and was found to differ in pig, mouse, cobra and humans. The predictions suggest that Yin Yang sites may not be important for virus attachment to NPC1, whereas phosphosite 473 may be important for binding and hence entry of Ebola virus. This information could be useful in addressing further experimental studies and therapeutic strategies targeting PTM events in EBOV entry. Copyright © 2015 Elsevier B.V. All rights reserved.

  10. Behavior-based safety on construction sites: a case study.

    Science.gov (United States)

    Choudhry, Rafiq M

    2014-09-01

    This work presents the results of a case study and describes an important area within the field of construction safety management, namely behavior-based safety (BBS). This paper adopts and develops a management approach for safety improvements in construction site environments. A rigorous behavioral safety system and its intervention program was implemented and deployed on target construction sites. After taking a few weeks of safety behavior measurements, the project management team implemented the designed intervention and measurements were taken. Goal-setting sessions were arranged on-site with workers' participation to set realistic and attainable targets of performance. Safety performance measurements continued and the levels of performance and the targets were presented on feedback charts. Supervisors were asked to give workers recognition and praise when they acted safely or improved critical behaviors. Observers were requested to have discussions with workers, visit the site, distribute training materials to workers, and provide feedback to crews and display charts. They were required to talk to operatives in the presence of line managers. It was necessary to develop awareness and understanding of what was being measured. In the process, operatives learned how to act safely when conducting site tasks using the designed checklists. Current weekly scores were discussed in the weekly safety meetings and other operational site meetings with emphasis on how to achieve set targets. The reliability of the safety performance measures taken by the company's observers was monitored. A clear increase in safety performance level was achieved across all categories: personal protective equipment; housekeeping; access to heights; plant and equipment, and scaffolding. The research reveals that scores of safety performance at one project improved from 86% (at the end of 3rd week) to 92.9% during the 9th week. The results of intervention demonstrated large decreases in

  11. Formation of target-specific binding sites in enzymes: solid-phase molecular imprinting of HRP

    Science.gov (United States)

    Czulak, J.; Guerreiro, A.; Metran, K.; Canfarotta, F.; Goddard, A.; Cowan, R. H.; Trochimczuk, A. W.; Piletsky, S.

    2016-05-01

    Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike complex protein engineering approaches commonly employed to generate affinity proteins, the method proposed can be used to produce protein-based ligands in a short time period using native protein molecules. These affinity materials are potentially useful tools especially for assays since they combine the catalytic properties of enzymes (for signaling) and molecular recognition properties of antibodies. We demonstrate this concept in an ELISA-format assay where HRP imprinted with vancomycin and ampicillin replaced traditional enzyme-antibody conjugates for selective detection of templates at micromolar concentrations. This approach can potentially provide a fast alternative to raising antibodies for targets that do not require high assay sensitivities; it can also find uses as a biochemical research tool, as a possible replacement for immunoperoxidase-conjugates.Here we introduce a new concept for synthesising molecularly imprinted nanoparticles by using proteins as macro-functional monomers. For a proof-of-concept, a model enzyme (HRP) was cross-linked using glutaraldehyde in the presence of glass beads (solid-phase) bearing immobilized templates such as vancomycin and ampicillin. The cross-linking process links together proteins and protein chains, which in the presence of templates leads to the formation of permanent target-specific recognition sites without adverse effects on the enzymatic activity. Unlike

  12. Management strategy for site characterization at candidate HLW repository sites

    International Nuclear Information System (INIS)

    Bartlett, J.W.

    1988-01-01

    This paper describes a management strategy for HLW repository site characterization which is aimed at producing an optimal characterization trajectory for site suitability and licensing evaluations. The core feature of the strategy is a matrix of alternative performance targets and alternative information-level targets which can be used to allocate and justify program effort. Strategies for work concerning evaluation of expected and disrupted repository performance are distinguished, and the need for issue closure criteria is discussed

  13. Kaiso Directs the Transcriptional Corepressor MTG16 to the Kaiso Binding Site in Target Promoters

    Science.gov (United States)

    Barrett, Caitlyn W.; Smith, J. Joshua; Lu, Lauren C.; Markham, Nicholas; Stengel, Kristy R.; Short, Sarah P.; Zhang, Baolin; Hunt, Aubrey A.; Fingleton, Barbara M.; Carnahan, Robert H.; Engel, Michael E.; Chen, Xi; Beauchamp, R. Daniel; Wilson, Keith T.; Hiebert, Scott W.; Reynolds, Albert B.; Williams, Christopher S.

    2012-01-01

    Myeloid translocation genes (MTGs) are transcriptional corepressors originally identified in acute myelogenous leukemia that have recently been linked to epithelial malignancy with non-synonymous mutations identified in both MTG8 and MTG16 in colon, breast, and lung carcinoma in addition to functioning as negative regulators of WNT and Notch signaling. A yeast two-hybrid approach was used to discover novel MTG binding partners. This screen identified the Zinc fingers, C2H2 and BTB domain containing (ZBTB) family members ZBTB4 and ZBTB38 as MTG16 interacting proteins. ZBTB4 is downregulated in breast cancer and modulates p53 responses. Because ZBTB33 (Kaiso), like MTG16, modulates Wnt signaling at the level of TCF4, and its deletion suppresses intestinal tumorigenesis in the ApcMin mouse, we determined that Kaiso also interacted with MTG16 to modulate transcription. The zinc finger domains of Kaiso as well as ZBTB4 and ZBTB38 bound MTG16 and the association with Kaiso was confirmed using co-immunoprecipitation. MTG family members were required to efficiently repress both a heterologous reporter construct containing Kaiso binding sites (4×KBS) and the known Kaiso target, Matrix metalloproteinase-7 (MMP-7/Matrilysin). Moreover, chromatin immunoprecipitation studies placed MTG16 in a complex occupying the Kaiso binding site on the MMP-7 promoter. The presence of MTG16 in this complex, and its contributions to transcriptional repression both required Kaiso binding to its binding site on DNA, establishing MTG16-Kaiso binding as functionally relevant in Kaiso-dependent transcriptional repression. Examination of a large multi-stage CRC expression array dataset revealed patterns of Kaiso, MTG16, and MMP-7 expression supporting the hypothesis that loss of either Kaiso or MTG16 can de-regulate a target promoter such as that of MMP-7. These findings provide new insights into the mechanisms of transcriptional control by ZBTB family members and broaden the scope of co

  14. Critical groups - basic concepts

    International Nuclear Information System (INIS)

    Carter, M.W.

    1992-01-01

    The potential exposure pathways from the land application site to man are presented. It is emphasised that the critical group is not necessary the population group closest to the source. It could be the group impact by the most significant pathways(s). Only by assessing the importance of each of these pathways and then combining them can a proper choice of critical group be made. It would be wrong to select a critical group on the basis that it seems the most probable one, before the pathways have been properly assessed. A calculation in Carter (1983) suggested that for the operating mine site, the annual doses to an Aboriginal person, a service worker and a local housewife, were all about the same and were in the range 0.1 to 0.2 mSv per year. Thus it may be that for the land application area, the critical group turns out to be non-Aboriginal rather than the expected Aboriginal group. 6 refs., 3 figs

  15. Critical target and dose and dose-rate responses for the induction of chromosomal instability by ionizing radiation

    Science.gov (United States)

    Limoli, C. L.; Corcoran, J. J.; Milligan, J. R.; Ward, J. F.; Morgan, W. F.

    1999-01-01

    To investigate the critical target, dose response and dose-rate response for the induction of chromosomal instability by ionizing radiation, bromodeoxyuridine (BrdU)-substituted and unsubstituted GM10115 cells were exposed to a range of doses (0.1-10 Gy) and different dose rates (0.092-17.45 Gy min(-1)). The status of chromosomal stability was determined by fluorescence in situ hybridization approximately 20 generations after irradiation in clonal populations derived from single progenitor cells surviving acute exposure. Overall, nearly 700 individual clones representing over 140,000 metaphases were analyzed. In cells unsubstituted with BrdU, a dose response was found, where the probability of observing delayed chromosomal instability in any given clone was 3% per gray of X rays. For cells substituted with 25-66% BrdU, however, a dose response was observed only at low doses (1.0 Gy), the incidence of chromosomal instability leveled off. There was an increase in the frequency and complexity of chromosomal instability per unit dose compared to cells unsubstituted with BrdU. The frequency of chromosomal instability appeared to saturate around approximately 30%, an effect which occurred at much lower doses in the presence of BrdU. Changing the gamma-ray dose rate by a factor of 190 (0.092 to 17.45 Gy min(-1)) produced no significant differences in the frequency of chromosomal instability. The enhancement of chromosomal instability promoted by the presence of the BrdU argues that DNA comprises at least one of the critical targets important for the induction of this end point of genomic instability.

  16. Dengue vector management using insecticide treated materials and targeted interventions on productive breeding-sites in Guatemala

    Directory of Open Access Journals (Sweden)

    Rizzo Nidia

    2012-10-01

    Full Text Available Abstract Background In view of the epidemiological expansion of dengue worldwide and the availability of new tools and strategies particularly for controlling the primary dengue vector Aedes aegypti, an intervention study was set up to test the efficacy, cost and feasibility of a combined approach of insecticide treated materials (ITMs alone and in combination with appropriate targeted interventions of the most productive vector breeding-sites. Methods The study was conducted as a cluster randomized community trial using “reduction of the vector population” as the main outcome variable. The trial had two arms: 10 intervention clusters (neighborhoods and 10 control clusters in the town of Poptun Guatemala. Activities included entomological assessments (characteristics of breeding-sites, pupal productivity, Stegomyia indices at baseline, 6 weeks after the first intervention (coverage of window and exterior doorways made of PermaNet 2.0 netting, factory treated with deltamethrin at 55 mg/m2, and of 200 L drums with similar treated material and 6 weeks after the second intervention (combination of treated materials and other suitable interventions targeting productive breeding-sites i.e larviciding with Temephos, elimination etc.. The second intervention took place 17 months after the first intervention. The insecticide residual activity and the insecticidal content were also studied at different intervals. Additionally, information about demographic characteristics, cost of the intervention, coverage of houses protected and satisfaction in the population with the interventions was collected. Results At baseline (during the dry season a variety of productive container types for Aedes pupae were identified: various container types holding >20 L, 200 L drums, washbasins and buckets (producing 83.7% of all pupae. After covering 100% of windows and exterior doorways and a small number of drums (where the commercial cover could be fixed in 970 study

  17. Dengue vector management using insecticide treated materials and targeted interventions on productive breeding-sites in Guatemala.

    Science.gov (United States)

    Rizzo, Nidia; Gramajo, Rodrigo; Escobar, Maria Cabrera; Arana, Byron; Kroeger, Axel; Manrique-Saide, Pablo; Petzold, Max

    2012-10-30

    In view of the epidemiological expansion of dengue worldwide and the availability of new tools and strategies particularly for controlling the primary dengue vector Aedes aegypti, an intervention study was set up to test the efficacy, cost and feasibility of a combined approach of insecticide treated materials (ITMs) alone and in combination with appropriate targeted interventions of the most productive vector breeding-sites. The study was conducted as a cluster randomized community trial using "reduction of the vector population" as the main outcome variable. The trial had two arms: 10 intervention clusters (neighborhoods) and 10 control clusters in the town of Poptun Guatemala. Activities included entomological assessments (characteristics of breeding-sites, pupal productivity, Stegomyia indices) at baseline, 6 weeks after the first intervention (coverage of window and exterior doorways made of PermaNet 2.0 netting, factory treated with deltamethrin at 55 mg/m2, and of 200 L drums with similar treated material) and 6 weeks after the second intervention (combination of treated materials and other suitable interventions targeting productive breeding-sites i.e larviciding with Temephos, elimination etc.). The second intervention took place 17 months after the first intervention. The insecticide residual activity and the insecticidal content were also studied at different intervals. Additionally, information about demographic characteristics, cost of the intervention, coverage of houses protected and satisfaction in the population with the interventions was collected. At baseline (during the dry season) a variety of productive container types for Aedes pupae were identified: various container types holding >20 L, 200 L drums, washbasins and buckets (producing 83.7% of all pupae). After covering 100% of windows and exterior doorways and a small number of drums (where the commercial cover could be fixed) in 970 study households, tropical rains occurred in the area and

  18. Differential regulation of the human progesterone receptor gene through an estrogen response element half site and Sp1 sites.

    Science.gov (United States)

    Petz, Larry N; Ziegler, Yvonne S; Schultz, Jennifer R; Kim, Hwajin; Kemper, J Kim; Nardulli, Ann M

    2004-02-01

    The progesterone receptor (PR) gene is regulated by estrogen in normal reproductive tissues and in MCF-7 human breast cancer cells. Although it is generally thought that estrogen responsiveness is mediated by interaction of the ligand-occupied estrogen receptor (ER) with estrogen response elements (EREs) in target genes, the human progesterone receptor (PR) gene lacks a palindromic ERE. Promoter A of the PR gene does, however, contain an ERE half site upstream of two adjacent Sp1 sites from +571 to +595, the +571 ERE/Sp1 site. We have examined the individual contributions of the ERE half site and the two Sp1 sites in regulating estrogen responsiveness. Transient transfection assays demonstrated that both Sp1 sites were critical for estrogen-mediated activation of the PR gene. Interestingly, rather than decreasing transcription, mutations in the ERE half site increased transcription substantially suggesting that this site plays a role in limiting transcription. Chromatin immunoprecipitation assays demonstrated that Sp1 was associated with the +571 ERE/Sp1 site in the endogenous PR gene in the absence and in the presence of estrogen, but that ERalpha was only associated with this region of the PR gene after MCF-7 cells had been treated with estrogen. Our studies provide evidence that effective regulation of transcription through the +571 ERE/Sp1 site requires the binding of ERalpha and Sp1 to their respective cis elements and the appropriate interaction of ERalpha and Sp1 with other coregulatory proteins and transcription factors.

  19. Interactions between the R2R3-MYB transcription factor, AtMYB61, and target DNA binding sites.

    Directory of Open Access Journals (Sweden)

    Michael B Prouse

    Full Text Available Despite the prominent roles played by R2R3-MYB transcription factors in the regulation of plant gene expression, little is known about the details of how these proteins interact with their DNA targets. For example, while Arabidopsis thaliana R2R3-MYB protein AtMYB61 is known to alter transcript abundance of a specific set of target genes, little is known about the specific DNA sequences to which AtMYB61 binds. To address this gap in knowledge, DNA sequences bound by AtMYB61 were identified using cyclic amplification and selection of targets (CASTing. The DNA targets identified using this approach corresponded to AC elements, sequences enriched in adenosine and cytosine nucleotides. The preferred target sequence that bound with the greatest affinity to AtMYB61 recombinant protein was ACCTAC, the AC-I element. Mutational analyses based on the AC-I element showed that ACC nucleotides in the AC-I element served as the core recognition motif, critical for AtMYB61 binding. Molecular modelling predicted interactions between AtMYB61 amino acid residues and corresponding nucleotides in the DNA targets. The affinity between AtMYB61 and specific target DNA sequences did not correlate with AtMYB61-driven transcriptional activation with each of the target sequences. CASTing-selected motifs were found in the regulatory regions of genes previously shown to be regulated by AtMYB61. Taken together, these findings are consistent with the hypothesis that AtMYB61 regulates transcription from specific cis-acting AC elements in vivo. The results shed light on the specifics of DNA binding by an important family of plant-specific transcriptional regulators.

  20. Targeting the eIF4F translation initiation complex: a critical nexus for cancer development.

    Science.gov (United States)

    Pelletier, Jerry; Graff, Jeremy; Ruggero, Davide; Sonenberg, Nahum

    2015-01-15

    Elevated protein synthesis is an important feature of many cancer cells and often arises as a consequence of increased signaling flux channeled to eukaryotic initiation factor 4F (eIF4F), the key regulator of the mRNA-ribosome recruitment phase of translation initiation. In many cellular and preclinical models of cancer, eIF4F deregulation results in changes in translational efficiency of specific mRNA classes. Importantly, many of these mRNAs code for proteins that potently regulate critical cellular processes, such as cell growth and proliferation, enhanced cell survival and cell migration that ultimately impinge on several hallmarks of cancer, including increased angiogenesis, deregulated growth control, enhanced cellular survival, epithelial-to-mesenchymal transition, invasion, and metastasis. By being positioned as the molecular nexus downstream of key oncogenic signaling pathways (e.g., Ras, PI3K/AKT/TOR, and MYC), eIF4F serves as a direct link between important steps in cancer development and translation initiation. Identification of mRNAs particularly responsive to elevated eIF4F activity that typifies tumorigenesis underscores the critical role of eIF4F in cancer and raises the exciting possibility of developing new-in-class small molecules targeting translation initiation as antineoplastic agents. ©2014 American Association for Cancer Research.

  1. Web-based resources for critical care education.

    Science.gov (United States)

    Kleinpell, Ruth; Ely, E Wesley; Williams, Ged; Liolios, Antonios; Ward, Nicholas; Tisherman, Samuel A

    2011-03-01

    To identify, catalog, and critically evaluate Web-based resources for critical care education. A multilevel search strategy was utilized. Literature searches were conducted (from 1996 to September 30, 2010) using OVID-MEDLINE, PubMed, and the Cumulative Index to Nursing and Allied Health Literature with the terms "Web-based learning," "computer-assisted instruction," "e-learning," "critical care," "tutorials," "continuing education," "virtual learning," and "Web-based education." The Web sites of relevant critical care organizations (American College of Chest Physicians, American Society of Anesthesiologists, American Thoracic Society, European Society of Intensive Care Medicine, Society of Critical Care Medicine, World Federation of Societies of Intensive and Critical Care Medicine, American Association of Critical Care Nurses, and World Federation of Critical Care Nurses) were reviewed for the availability of e-learning resources. Finally, Internet searches and e-mail queries to critical care medicine fellowship program directors and members of national and international acute/critical care listserves were conducted to 1) identify the use of and 2) review and critique Web-based resources for critical care education. To ensure credibility of Web site information, Web sites were reviewed by three independent reviewers on the basis of the criteria of authority, objectivity, authenticity, accuracy, timeliness, relevance, and efficiency in conjunction with suggested formats for evaluating Web sites in the medical literature. Literature searches using OVID-MEDLINE, PubMed, and the Cumulative Index to Nursing and Allied Health Literature resulted in >250 citations. Those pertinent to critical care provide examples of the integration of e-learning techniques, the development of specific resources, reports of the use of types of e-learning, including interactive tutorials, case studies, and simulation, and reports of student or learner satisfaction, among other general

  2. Determining the cortical target of transcranial magnetic stimulation.

    Science.gov (United States)

    Thielscher, A; Wichmann, F A

    2009-10-01

    Determining the cortical region that is effectively targeted by TMS to induce a reproducible behavioral effect is a non-trivial problem. In mapping experiments, a grid of coil positions is used to systematically assess the TMS effect on, e.g. muscle responses or error rates. The center-of-mass (CoM) of the response distribution is projected onto the cortex to determine the likely target site, implicitly assuming the existence of a single, contiguous target. The mapping results, however, often contain several local maxima. These could either stem from measurement noise, or hint towards a distributed target region. Critically, the calculation of a CoM, by design, treats multiple maxima as if they were noise. Here, a stringent hierarchical sigmoidal model fitting approach is developed that determines the cortical target(s) from TMS mapping based on electric field calculations. Monte-Carlo simulations are used to assess the significance and the goodness-of-fit of the sigmoidal fits, and to obtain confidence regions around the calculated targets. The approach was applied to mapping data on visual suppression (N=7). In all subjects, we reliably identified two or three neighboring targets commonly contributing to the suppression effect (average distance+/-SD: 7.7+/-2.3 mm). This demonstrates that (i) the assumption of a single CoM is not generally valid and (ii) the combination of TMS mapping with the fitting approach has a cortical resolution of TMS.

  3. Critical Protection Item classification for a waste processing facility at Savannah River Site

    International Nuclear Information System (INIS)

    Ades, M.J.; Garrett, R.J.

    1993-01-01

    This paper describes the methodology for Critical Protection Item (CPI) classification and its application to the Structures, Systems and Components (SSC) of a waste processing facility at the Savannah River Site (SRS). The WSRC methodology for CPI classification includes the evaluation of the radiological and non-radiological consequences resulting from postulated accidents at the waste processing facility and comparison of these consequences with allowable limits. The types of accidents considered include explosions and fire in the facility and postulated accidents due to natural phenomena, including earthquakes, tornadoes, and high velocity straight winds. The radiological analysis results indicate that CPIs are not required at the waste processing facility to mitigate the consequences of radiological release. The non-radiological analysis, however, shows that the Waste Storage Tank (WST) and the dike spill containment structures around the formic acid tanks in the cold chemical feed area and waste treatment area of the facility should be identified as CPIs. Accident mitigation options are provided and discussed

  4. Discrepancy of target sites between clinician and cytopathological reports in head neck fine needle aspiration: Did I miss the target or did the clinician mistake the organ site?

    International Nuclear Information System (INIS)

    Khanlari, Mahsa; Daneshbod, Yahya; Shaterzadeh Yazdi, Hanieh; Shirian, Sadegh; Negahban, Shahrzad; Aledavood, Azita; Oryan, Ahmad; Khademi, Bijan; Daneshbod, Khosrow; Field, Andrew

    2015-01-01

    The diagnostic accuracy of fine needle aspiration cytology (FNAC) of head and neck lesions is relatively high, but cytologic interpretation might be confusing if the sample is lacking typical cytologic features according to labeled site by physician. These errors may have an impact on pathology search engines, healthcare costs or even adverse outcomes. The cytology archive database of multiple institutions in southern Iran and Australia covering the period 2001–2011, were searched using keywords: salivary gland, head, neck, FNAC, and cytology. All the extracted reports were reviewed. The reports which showed discordance between the clinician's impression of the organ involved and subsequent fine needle biopsy request, and the eventual cytological diagnosis were selected. The cytological diagnosis was confirmed by histology or cell block, with assistance from imaging, clinical outcome, physical examination, molecular studies, or microbiological culture. The total number of 10,200 head and neck superficial FNAC were included in the study, from which 48 cases showed discordance between the clinicians request and the actual site of pathology. Apart from the histopathology, the imaging, clinical history, physical examination, immunohistochemical study, microbiologic culture and molecular testing helped to finalize the target organ of pathology in 23, 6, 7, 8, 2, and 1 cases respectively. The commonest discrepancies were for FNAC of “salivary gland” [total: 20 with actual final pathology in: bone (7), soft tissue (5), lymph node (3), odontogenic (3) and skin (2)], “lymph node” [total: 12 with final pathology in: soft tissue (3), skin (3), bone (1) and brain (1)], “soft tissue” [total: 11 with final pathology in: bone (5), skin (2), salivary gland (1), and ocular region (1)] and “skin” [total: 5 with final pathology in: lymph node (2), bone (1), soft tissue (1) and salivary gland (1)]. The primary physician requesting FNAC of head and neck lesions

  5. Nuclear criticality project plan for the Hanford Site tank farms

    Energy Technology Data Exchange (ETDEWEB)

    Bratzel, D.R., Westinghouse Hanford

    1996-08-06

    The mission of this project is to provide a defensible technical basis report in support of the Final Safety Analysis Report (FSAR). This technical basis report will also be used to resolve technical issues associated with the nuclear criticality safety issue. The strategy presented in this project plan includes an integrated programmatic and organizational approach. The scope of this project plan includes the provision of a criticality technical basis supporting document (CTBSD) to support the FSAR as well as for resolution of the nuclear criticality safety issue. Specifically, the CTBSD provides the requisite technical analysis to support the FSAR hazard and accident analysis as well as for the determination of the required FSAR limits and controls. The scope of The CTBSD will provide a baseline for understanding waste partitioning and distribution phenomena and mechanistics for current operational activities inclusive of single-shell tanks, double-shell tanks, double-contained receiver tanks, and miscellaneous underground storage tanks.. Although the FSAR does not include future operational activities, the waste partitioning and distribution phenomena and mechanistics work scope identified in this project plan provide a sound technical basis as a point of departure to support independent safety analyses for future activities. The CTBSD also provides the technical basis for resolution of the technical issues associated with the nuclear criticality safety issue. In addition to the CTBSD, additional documentation will be required to fully resolve U.S. Department of Energy-Headquarters administrative and programmatic issues. The strategy and activities defined in this project plan provide a CTBSD for the FSAR and for accelerated resolution of the safety issue in FY 1996. On April 30, 1992, a plant review committee reviewed the Final Safety Analysis Reports for the single-shell, double-shell, and aging waste tanks in light of the conclusions of the inadequate waste

  6. A SURVEY OF LANDNET SITES FOCUSING ON TUZ GÖLÜ SALT LAKE, TURKEY

    Directory of Open Access Journals (Sweden)

    S. Z. Gürbüz

    2012-07-01

    Full Text Available Radiometric calibration is critical to ensure the accuracy, veracity, continuity and reliability of satellite data measured from multiple sensors and platforms, and is thus recognized as a key activity by all satellite operators. For imaging sensors, vicarious methods using natural targets (such as salt lakes, deserts, or flatlands that are well-characterized and preferably temporally and spatially stable as a reference are similarly well established. However, while selecting a target site, it is important that its quality and location are selected to minimize sources of uncertainty for any given sensor. To maximize the benefit from limited resources and minimize the impact on satellite operators, the Infrared Visible Optical Sensor (IVOS sub-group of Committee on Earth Observation Satellites (CEOS Working Group on Calibration and Validation (WGCV has selected a few, well-characterized, regularly instrumented target sites, which have since become known as LANDNET sites. Currently, there are eight LANDNET sites: 1 Dome C, Antarctica; 2 Dunhuang, China, Asia; 3 Lspec Frenchman Flat, NV, USA, North America; 4 Ivanpah, NV/CA, USA, North America; 5 La Crau, France, Europe; 6 Negev, Southern Israel, Asia; 7 Railroad Valley Playa, NV, USA, North America; 8 Tuz Gölü, Central Anatolia, Turkey, Asia. This work summarizes the key characteristics, and areas of application of each of the LANDNET sites, especially that of Tuz Gölü, to guide and inform researchers on site selection, and increase international awareness and collaboration in this field. Additionally, detailed information about the Tuz Gölü, Turkey test site is provided, including geographical characteristics, spatial uniformity qualities, and opportunities for international researchers to conduct experiments and measurements. Practical, technical, and logistical experience gained through the international field campaigns organized over the last few years at Tuz Gölü is also shared in

  7. Using Critical and Post-Critical Pedagogies to Pick at the Seams of Patriarchy from "The Inside"

    Science.gov (United States)

    Lennon, Sherilyn

    2017-01-01

    This article explores the use of critical and post-critical pedagogies in a rural Australian high school for the purposes of unsettling life-limiting gender beliefs and practices. The paper problematises two examples whereby site-specific knowledges, curriculum dictates, media texts and critical pedagogies were enmeshed to create politically…

  8. Progress Report on the US Critical Zone Observatory Program

    Science.gov (United States)

    Barrera, E. C.

    2014-12-01

    The Critical Zone Observatory (CZO) program supported by the National Science Foundation originated from the recommendation of the Earth Science community published in the National Research Council report "Basic Research Opportunities in Earth Sciences" (2001) to establish natural laboratories to study processes and systems of the Critical Zone - the surface and near-surface environment sustaining nearly all terrestrial life. After a number of critical zone community workshops to develop a science plan, the CZO program was initiated in 2007 with three sites and has now grown to 10 sites and a National Office, which coordinates research, education and outreach activities of the network. Several of the CZO sites are collocated with sites supported by the US Long Term Ecological Research (LTER) and the Long Term Agricultural Research (LTAR) programs, and the National Ecological Observatory Network (NEON). Future collaboration with additional sites of these networks will add to the potential to answer questions in a more comprehensive manner and in a larger regional scale about the critical zone form and function. At the international level, CZOs have been established in many countries and strong collaborations with the US program have been in place for many years. The next step is the development of a coordinated international program of critical zone research. The success of the CZO network of sites can be measured in transformative results that elucidate properties and processes controlling the critical zone and how the critical zone structure, stores and fluxes respond to climate and land use change. This understanding of the critical zone can be used to enhance resilience and sustainability, and restore ecosystem function. Thus, CZO science can address major societal challenges. The US CZO network is a facility open to research of the critical zone community at large. Scientific data and information about the US program are available at www.criticalzone.org.

  9. Long-Term Assessment of Critical Radionuclides and Associated Environmental Media at the Savannah River Site

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, G. T.; Baker, R. A.; Lee, P. L.; Eddy, T. P.; Blount, G. C.; Whitney, G. R.

    2012-11-06

    During the operational history of the Savannah River Site (SRS), many different radionuclides have been released from site facilities. However, only a relatively small number of the released radionuclides have been significant contributors to doses and risks to the public. At SRS dose and risk assessments indicate tritium oxide in air and surface water, and Cs-137 in fish and deer have been, and continue to be, the critical radionuclides and pathways. In this assessment, indepth statistical analyses of the long-term trends of tritium oxide in atmospheric and surface water releases and Cs-137 concentrations in fish and deer are provided. Correlations also are provided with 1) operational changes and improvements, 2) geopolitical events (Cold War cessation), and 3) recent environmental remediation projects and decommissioning of excess facilities. For example, environmental remediation of the F- and H-Area Seepage Basins and the Solid Waste Disposal Facility have resulted in a measurable impact on the tritium oxide flux to the onsite Fourmile Branch stream. Airborne releases of tritium oxide have been greatly affected by operational improvements and the end of the Cold War in 1991. However, the effects of SRS environmental remediation activities and ongoing tritium operations on tritium concentrations in the environment are measurable and documented in this assessment. Controlled hunts of deer and feral hogs are conducted at SRS for approximately six weeks each year. Before any harvested animal is released to a hunter, SRS personnel perform a field analysis for Cs-137 concentrations to ensure the hunter's dose does not exceed the SRS administrative game limit of 0.22 millisievert (22 mrem). However, most of the Cs-137 found in SRS onsite deer is not from site operations but is from nuclear weapons testing fallout from the 1950's and early 1960's. This legacy source term is trended in the SRS deer, and an assessment of the ''effective'' half-life of Cs-137 in deer

  10. Target-site resistance to acetolactate synthase (ALS)-inhibiting herbicides in Amaranthus palmeri from Argentina.

    Science.gov (United States)

    Larran, Alvaro S; Palmieri, Valeria E; Perotti, Valeria E; Lieber, Lucas; Tuesca, Daniel; Permingeat, Hugo R

    2017-12-01

    Herbicide-resistant weeds are a serious problem worldwide. Recently, two populations of Amaranthus palmeri with suspected cross-resistance to acetolactate synthase (ALS)-inhibiting herbicides (R1 and R2) were found by farmers in two locations in Argentina (Vicuña Mackenna and Totoras, respectively). We conducted studies to confirm and elucidate the mechanism of resistance. We performed in vivo dose-response assays, and confirmed that both populations had strong resistance to chlorimuron-ethyl, diclosulam and imazethapyr when compared with a susceptible population (S). In vitro ALS activity inhibition tests only indicated considerable resistance to imazethapyr and chlorimuron-ethyl, indicating that other non-target mechanisms could be involved in diclosulam resistance. Subsequently, molecular analysis of als nucleotide sequences revealed three single base-pair mutations producing substitutions in amino acids previously associated with resistance to ALS inhibitors, A122, W574, and S653. This is the first report of als resistance alleles in A. palmeri in Argentina. The data support the involvement of a target-site mechanism of resistance to ALS-inhibiting herbicides. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  11. Non-Critical Covariant Superstrings

    CERN Document Server

    Grassi, P A

    2005-01-01

    We construct a covariant description of non-critical superstrings in even dimensions. We construct explicitly supersymmetric hybrid type variables in a linear dilaton background, and study an underlying N=2 twisted superconformal algebra structure. We find similarities between non-critical superstrings in 2n+2 dimensions and critical superstrings compactified on CY_(4-n) manifolds. We study the spectrum of the non-critical strings, and in particular the Ramond-Ramond massless fields. We use the supersymmetric variables to construct the non-critical superstrings sigma-model action in curved target space backgrounds with coupling to the Ramond-Ramond fields. We consider as an example non-critical type IIA strings on AdS_2 background with Ramond-Ramond 2-form flux.

  12. Target-site mutations conferring resistance to glyphosate in feathertop Rhodes grass (Chloris virgata) populations in Australia.

    Science.gov (United States)

    Ngo, The D; Krishnan, Mahima; Boutsalis, Peter; Gill, Gurjeet; Preston, Christopher

    2018-05-01

    Chloris virgata is a warm-season, C 4 , annual grass weed affecting field crops in northern Australia that has become an emerging weed in southern Australia. Four populations with suspected resistance to glyphosate were collected in South Australia, Queensland and New South Wales, Australia, and compared with one susceptible (S) population to confirm glyphosate resistance and elucidate possible mechanisms of resistance. Based on the rate of glyphosate required to kill 50% of treated plants (LD 50 ), glyphosate resistance (GR) was confirmed in four populations of C. virgata (V12, V14.2, V14.16 and V15). GR plants were 2-9.7-fold more resistant and accumulated less shikimate after glyphosate treatment than S plants. GR and S plants did not differ in glyphosate absorption and translocation. Target-site EPSPS mutations corresponding to Pro-106-Leu (V14.2) and Pro-106-Ser (V15, V14.16 and V12) substitutions were found in GR populations. The population with Pro-106-Leu substitution was 2.9-4.9-fold more resistant than the three other populations with Pro-106-Ser substitution. This report confirms glyphosate resistance in C. virgata and shows that target-site EPSPS mutations confer resistance to glyphosate in this species. The evolution of glyphosate resistance in C. virgata highlights the need to identify alternative control tactics. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  13. Adenovirus delivered short hairpin RNA targeting a conserved site in the 5' non-translated region inhibits all four serotypes of dengue viruses.

    Directory of Open Access Journals (Sweden)

    Anil Babu Korrapati

    Full Text Available BACKGROUND: Dengue is a mosquito-borne viral disease caused by four closely related serotypes of Dengue viruses (DENVs. This disease whose symptoms range from mild fever to potentially fatal haemorrhagic fever and hypovolemic shock, threatens nearly half the global population. There is neither a preventive vaccine nor an effective antiviral therapy against dengue disease. The difference between severe and mild disease appears to be dependent on the viral load. Early diagnosis may enable timely therapeutic intervention to blunt disease severity by reducing the viral load. Harnessing the therapeutic potential of RNA interference (RNAi to attenuate DENV replication may offer one approach to dengue therapy. METHODOLOGY/PRINCIPAL FINDINGS: We screened the non-translated regions (NTRs of the RNA genomes of representative members of the four DENV serotypes for putative siRNA targets mapping to known transcription/translation regulatory elements. We identified a target site in the 5' NTR that maps to the 5' upstream AUG region, a highly conserved cis-acting element essential for viral replication. We used a replication-defective human adenovirus type 5 (AdV5 vector to deliver a short-hairpin RNA (shRNA targeting this site into cells. We show that this shRNA matures to the cognate siRNA and is able to inhibit effectively antigen secretion, viral RNA replication and infectious virus production by all four DENV serotypes. CONCLUSION/SIGNIFICANCE: The data demonstrate the feasibility of using AdV5-mediated delivery of shRNAs targeting conserved sites in the viral genome to achieve inhibition of all four DENV serotypes. This paves the way towards exploration of RNAi as a possible therapeutic strategy to curtail DENV infection.

  14. Targeting hunter distribution based on host resource selection and kill sites to manage disease risk.

    Science.gov (United States)

    Dugal, Cherie J; van Beest, Floris M; Vander Wal, Eric; Brook, Ryan K

    2013-10-01

    Endemic and emerging diseases are rarely uniform in their spatial distribution or prevalence among cohorts of wildlife. Spatial models that quantify risk-driven differences in resource selection and hunter mortality of animals at fine spatial scales can assist disease management by identifying high-risk areas and individuals. We used resource selection functions (RSFs) and selection ratios (SRs) to quantify sex- and age-specific resource selection patterns of collared (n = 67) and hunter-killed (n = 796) nonmigratory elk (Cervus canadensis manitobensis) during the hunting season between 2002 and 2012, in southwestern Manitoba, Canada. Distance to protected area was the most important covariate influencing resource selection and hunter-kill sites of elk (AICw = 1.00). Collared adult males (which are most likely to be infected with bovine tuberculosis (Mycobacterium bovis) and chronic wasting disease) rarely selected for sites outside of parks during the hunting season in contrast to adult females and juvenile males. The RSFs showed selection by adult females and juvenile males to be negatively associated with landscape-level forest cover, high road density, and water cover, whereas hunter-kill sites of these cohorts were positively associated with landscape-level forest cover and increasing distance to streams and negatively associated with high road density. Local-level forest was positively associated with collared animal locations and hunter-kill sites; however, selection was stronger for collared juvenile males and hunter-killed adult females. In instances where disease infects a metapopulation and eradication is infeasible, a principle goal of management is to limit the spread of disease among infected animals. We map high-risk areas that are regularly used by potentially infectious hosts but currently underrepresented in the distribution of kill sites. We present a novel application of widely available data to target hunter distribution based on host resource

  15. Open challenges in structure-based virtual screening: Receptor modeling, target flexibility consideration and active site water molecules description.

    Science.gov (United States)

    Spyrakis, Francesca; Cavasotto, Claudio N

    2015-10-01

    Structure-based virtual screening is currently an established tool in drug lead discovery projects. Although in the last years the field saw an impressive progress in terms of algorithm development, computational performance, and retrospective and prospective applications in ligand identification, there are still long-standing challenges where further improvement is needed. In this review, we consider the conceptual frame, state-of-the-art and recent developments of three critical "structural" issues in structure-based drug lead discovery: the use of homology modeling to accurately model the binding site when no experimental structures are available, the necessity of accounting for the dynamics of intrinsically flexible systems as proteins, and the importance of considering active site water molecules in lead identification and optimization campaigns. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Rhodium(II) Proximity-Labeling Identifies a Novel Target Site on STAT3 for Inhibitors with Potent Anti-Leukemia Activity.

    Science.gov (United States)

    Minus, Matthew B; Liu, Wei; Vohidov, Farrukh; Kasembeli, Moses M; Long, Xin; Krueger, Michael J; Stevens, Alexandra; Kolosov, Mikhail I; Tweardy, David J; Sison, Edward Allan R; Redell, Michele S; Ball, Zachary T

    2015-10-26

    Nearly 40 % of children with acute myeloid leukemia (AML) suffer relapse arising from chemoresistance, often involving upregulation of the oncoprotein STAT3 (signal transducer and activator of transcription 3). Herein, rhodium(II)-catalyzed, proximity-driven modification identifies the STAT3 coiled-coil domain (CCD) as a novel ligand-binding site, and we describe a new naphthalene sulfonamide inhibitor that targets the CCD, blocks STAT3 function, and halts its disease-promoting effects in vitro, in tumor growth models, and in a leukemia mouse model, validating this new therapeutic target for resistant AML. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  17. Confirming therapeutic target of protopine using immobilized β2 -adrenoceptor coupled with site-directed molecular docking and the target-drug interaction by frontal analysis and injection amount-dependent method.

    Science.gov (United States)

    Liu, Guangxin; Wang, Pei; Li, Chan; Wang, Jing; Sun, Zhenyu; Zhao, Xinfeng; Zheng, Xiaohui

    2017-07-01

    Drug-protein interaction analysis is pregnant in designing new leads during drug discovery. We prepared the stationary phase containing immobilized β 2 -adrenoceptor (β 2 -AR) by linkage of the receptor on macroporous silica gel surface through N,N'-carbonyldiimidazole method. The stationary phase was applied in identifying antiasthmatic target of protopine guided by the prediction of site-directed molecular docking. Subsequent application of immobilized β 2 -AR in exploring the binding of protopine to the receptor was realized by frontal analysis and injection amount-dependent method. The association constants of protopine to β 2 -AR by the 2 methods were (1.00 ± 0.06) × 10 5 M -1 and (1.52 ± 0.14) × 10 4 M -1 . The numbers of binding sites were (1.23 ± 0.07) × 10 -7 M and (9.09 ± 0.06) × 10 -7 M, respectively. These results indicated that β 2 -AR is the specific target for therapeutic action of protopine in vivo. The target-drug binding occurred on Ser 169 in crystal structure of the receptor. Compared with frontal analysis, injection amount-dependent method is advantageous to drug saving, improvement of sampling efficiency, and performing speed. It has grave potential in high-throughput drug-receptor interaction analysis. Copyright © 2017 John Wiley & Sons, Ltd.

  18. Clinical Determinants of Target Non-Attainment of Linezolid in Plasma and Interstitial Space Fluid: A Pooled Population Pharmacokinetic Analysis with Focus on Critically Ill Patients.

    Science.gov (United States)

    Minichmayr, Iris K; Schaeftlein, André; Kuti, Joseph L; Zeitlinger, Markus; Kloft, Charlotte

    2017-06-01

    We aimed to assess linezolid pharmacokinetics in the plasma and interstitial space fluid (ISF) of patients with sepsis, diabetic foot infections or cystic fibrosis and healthy volunteers. The impacts of joint characteristics and disease on plasma and target-site exposure were to be identified together with the benefit of dose intensification in critically ill patients. Rich plasma (n = 1598) and ISF concentrations in subcutaneous adipose (n = 1430) and muscle tissue (n = 1089) measured by microdialysis were pooled from three clinical trials with 51 individuals receiving 600 mg of intravenous and oral linezolid. All data were analysed simultaneously by a population approach also considering methodological aspects of microdialysis. The impact of covariates on the attainment of the pharmacokinetic/pharmacodynamic targets, AUC/MIC = 100 (area under the concentration-time curve/minimum inhibitory concentration) and fT >MIC  = 99 % (time that unbound concentrations exceed the MIC), was assessed by deterministic and Monte Carlo simulations. A two-compartment pharmacokinetic model with nonlinear elimination and tissue distribution factors accounting for differences between plasma and ISF concentrations adequately predicted all measurements. Clearance (CL) was highest in septic patients (11.2 L/h vs. CL Healthy /CL Cystic fibrosis /CL Diabetic  = 7.67/6.87/6.35 L/h). Penetration into subcutaneous adipose ISF was lowest in diabetic patients (-34.9 % compared with healthy volunteers). Creatinine clearance and total body weight further impacted linezolid exposure. To achieve timely efficacious therapy, front-loaded dosing and continuous infusion seemed beneficial in septic patients. Our analysis suggests that after standard linezolid doses, particularly patients with sepsis and conserved renal function are at risk of not attaining pharmacokinetic/pharmacodynamic targets and would benefit from initial dose intensification.

  19. Seedling root targets

    Science.gov (United States)

    Diane L. Haase

    2011-01-01

    Roots are critical to seedling performance after outplanting. Although root quality is not as quick and simple to measure as shoot quality, target root characteristics should be included in any seedling quality assessment program. This paper provides a brief review of root characteristics most commonly targeted for operational seedling production. These are: root mass...

  20. From heat integration targets toward implementation – A TSA (total site analysis)-based design approach for heat recovery systems in industrial clusters

    International Nuclear Information System (INIS)

    Hackl, Roman; Harvey, Simon

    2015-01-01

    The European process industry is facing major challenges to decrease production costs. One strategy to achieve this is by increasing energy efficiency. Single chemical processes are often well-integrated and the tools to target and design such measures are well developed. Site-wide heat integration based on total site analysis tools can be used to identify opportunities to further increase energy efficiency. However, the methodology has to be developed further in order to enable identification of practical heat integration measures in a systematic way. Designing site-wide heat recovery systems across an industrial cluster is complex and involves aspects apart from thermal process and utility flows. This work presents a method for designing a roadmap of heat integration investments based on total site analysis. The method is applied to a chemical cluster in Sweden. The results of the case study show that application of the proposed method can achieve up to 42% of the previously targeted hot utility savings of 129 MW. A roadmap of heat integration systems is suggested, ranging from less complex systems that achieve a minor share of the heat recovery potential to sophisticated, strongly interdependent systems demanding large investments and a high level of collaboration. - Highlights: • Methodology focused on the practical implementation of site-wide heat recovery. • Algorithm to determine a roadmap of heat integration investments. • Case study: 42% hot utility savings potential at a pay-back period of 3.9y.

  1. Novel GABA receptor pesticide targets.

    Science.gov (United States)

    Casida, John E; Durkin, Kathleen A

    2015-06-01

    The γ-aminobutyric acid (GABA) receptor has four distinct but overlapping and coupled targets of pesticide action importantly associated with little or no cross-resistance. The target sites are differentiated by binding assays with specific radioligands, resistant strains, site-directed mutagenesis and molecular modeling. Three of the targets are for non-competitive antagonists (NCAs) or channel blockers of widely varied chemotypes. The target of the first generation (20th century) NCAs differs between the larger or elongated compounds (NCA-IA) including many important insecticides of the past (cyclodienes and polychlorocycloalkanes) or present (fiproles) and the smaller or compact compounds (NCA-IB) highly toxic to mammals and known as cage convulsants, rodenticides or chemical threat agents. The target of greatest current interest is designated NCA-II for the second generation (21st century) of NCAs consisting for now of isoxazolines and meta-diamides. This new and uniquely different NCA-II site apparently differs enough between insects and mammals to confer selective toxicity. The fourth target is the avermectin site (AVE) for allosteric modulators of the chloride channel. NCA pesticides vary in molecular surface area and solvent accessible volume relative to avermectin with NCA-IBs at 20-22%, NCA-IAs at 40-45% and NCA-IIs at 57-60%. The same type of relationship relative to ligand-docked length is 27-43% for NCA-IBs, 63-71% for NCA-IAs and 85-105% for NCA-IIs. The four targets are compared by molecular modeling for the Drosophila melanogaster GABA-R. The principal sites of interaction are proposed to be: pore V1' and A2' for NCA-IB compounds; pore A2', L6' and T9' for NCA-IA compounds; pore T9' to S15' in proximity to M1/M3 subunit interface (or alternatively an interstitial site) for NCA-II compounds; and M1/M3, M2 interfaces for AVE. Understanding the relationships of these four binding sites is important in resistance management and in the discovery and use

  2. Common features of microRNA target prediction tools

    Directory of Open Access Journals (Sweden)

    Sarah M. Peterson

    2014-02-01

    Full Text Available The human genome encodes for over 1800 microRNAs, which are short noncoding RNA molecules that function to regulate gene expression post-transcriptionally. Due to the potential for one microRNA to target multiple gene transcripts, microRNAs are recognized as a major mechanism to regulate gene expression and mRNA translation. Computational prediction of microRNA targets is a critical initial step in identifying microRNA:mRNA target interactions for experimental validation. The available tools for microRNA target prediction encompass a range of different computational approaches, from the modeling of physical interactions to the incorporation of machine learning. This review provides an overview of the major computational approaches to microRNA target prediction. Our discussion highlights three tools for their ease of use, reliance on relatively updated versions of miRBase, and range of capabilities, and these are DIANA-microT-CDS, miRanda-mirSVR, and TargetScan. In comparison across all microRNA target prediction tools, four main aspects of the microRNA:mRNA target interaction emerge as common features on which most target prediction is based: seed match, conservation, free energy, and site accessibility. This review explains these features and identifies how they are incorporated into currently available target prediction tools. MicroRNA target prediction is a dynamic field with increasing attention on development of new analysis tools. This review attempts to provide a comprehensive assessment of these tools in a manner that is accessible across disciplines. Understanding the basis of these prediction methodologies will aid in user selection of the appropriate tools and interpretation of the tool output.

  3. Targeting Critical Thinking Skills in a First-Year Undergraduate Research Course.

    Science.gov (United States)

    Carson, Susan

    2015-12-01

    TH!NK is a new initiative at NC State University focused on enhancing students' higher-order cognitive skills. As part of this initiative, I explicitly emphasized critical and creative thinking in an existing bacteriophage discovery first-year research course. In addition to the typical activities associated with undergraduate research such as review of primary literature and writing research papers, another strategy employed to enhance students' critical thinking skills was the use of discipline-specific, real-world scenarios. This paper outlines a general "formula" for writing scenarios, as well as several specific scenarios created for the described course. I also present how embedding aspects of the scenarios in reviews of the primary literature enriched the activity. I assessed student gains in critical thinking skills using a pre-/posttest model of the Critical Thinking Assessment Test (CAT), developed by Tennessee Technological University. I observed a positive gain trend in most of the individual skills assessed in the CAT, with a statistically significant large effect on critical thinking skills overall in students in the test group. I also show that a higher level of critical thinking skills was demonstrated in research papers written by students who participated in the scenarios compared with similar students who did not participate in the scenario activities. The scenario strategy described here can be modified for use in biology and other STEM disciplines, as well as in diverse disciplines in the social sciences and humanities.

  4. Glycosylation site-targeted PEGylation of glucose oxidase retains native enzymatic activity.

    Science.gov (United States)

    Ritter, Dustin W; Roberts, Jason R; McShane, Michael J

    2013-04-10

    Targeted PEGylation of glucose oxidase at its glycosylation sites was investigated to determine the effect on enzymatic activity, as well as the bioconjugate's potential in an optical biosensing assay. Methoxy-poly(ethylene glycol)-hydrazide (4.5kDa) was covalently coupled to periodate-oxidized glycosylation sites of glucose oxidase from Aspergillus niger. The bioconjugate was characterized using gel electrophoresis, liquid chromatography, mass spectrometry, and dynamic light scattering. Gel electrophoresis data showed that the PEGylation protocol resulted in a drastic increase (ca. 100kDa) in the apparent molecular mass of the protein subunit, with complete conversion to the bioconjugate; liquid chromatography data corroborated this large increase in molecular size. Mass spectrometry data proved that the extent of PEGylation was six poly(ethylene glycol) chains per glucose oxidase dimer. Dynamic light scattering data indicated the absence of higher-order oligomers in the PEGylated GOx sample. To assess stability, enzymatic activity assays were performed in triplicate at multiple time points over the course of 29 days in the absence of glucose, as well as before and after exposure to 5% w/v glucose for 24h. At a confidence level of 95%, the bioconjugate's performance was statistically equivalent to native glucose oxidase in terms of activity retention over the 29 day time period, as well as following the 24h glucose exposure. Finally, the bioconjugate was entrapped within a poly(2-hydroxyethyl methacrylate) hydrogel containing an oxygen-sensitive phosphor, and the construct was shown to respond approximately linearly with a 220±73% signal change (n=4, 95% confidence interval) over the physiologically-relevant glucose range (i.e., 0-400mg/dL); to our knowledge, this represents the first demonstration of PEGylated glucose oxidase incorporated into an optical biosensing assay. Copyright © 2013 Elsevier Inc. All rights reserved.

  5. Adenovirus-Mediated Delivery of Decoy Hyper Binding Sites Targeting Oncogenic HMGA1 Reduces Pancreatic and Liver Cancer Cell Viability.

    Science.gov (United States)

    Hassan, Faizule; Ni, Shuisong; Arnett, Tyler C; McKell, Melanie C; Kennedy, Michael A

    2018-03-30

    High mobility group AT-hook 1 (HMGA1) protein is an oncogenic architectural transcription factor that plays an essential role in early development, but it is also implicated in many human cancers. Elevated levels of HMGA1 in cancer cells cause misregulation of gene expression and are associated with increased cancer cell proliferation and increased chemotherapy resistance. We have devised a strategy of using engineered viruses to deliver decoy hyper binding sites for HMGA1 to the nucleus of cancer cells with the goal of sequestering excess HMGA1 at the decoy hyper binding sites due to binding competition. Sequestration of excess HMGA1 at the decoy binding sites is intended to reduce HMGA1 binding at the naturally occurring genomic HMGA1 binding sites, which should result in normalized gene expression and restored sensitivity to chemotherapy. As proof of principle, we engineered the replication defective adenovirus serotype 5 genome to contain hyper binding sites for HMGA1 composed of six copies of an individual HMGA1 binding site, referred to as HMGA-6. A 70%-80% reduction in cell viability and increased sensitivity to gemcitabine was observed in five different pancreatic and liver cancer cell lines 72 hr after infection with replication defective engineered adenovirus serotype 5 virus containing the HMGA-6 decoy hyper binding sites. The decoy hyper binding site strategy should be general for targeting overexpression of any double-stranded DNA-binding oncogenic transcription factor responsible for cancer cell proliferation.

  6. A critical evaluation of Web sites offering patient information on tinnitus.

    LENUS (Irish Health Repository)

    Kieran, Stephen M

    2012-02-01

    The Internet is a vast information resource for both patients and healthcare professionals. However, the quality and content often lack formal scrutiny, so we examined the quality of patient information regarding tinnitus on the Internet. Using the three most popular search engines (google.com, yahoo.com, and msn.com), we found pertinent Web sites using the search term tinnitus. Web sites\\' accountability and authorship were evaluated using previously published criteria. The quality of patient information about tinnitus was assessed using a new 10-point scale, the Tinnitus Information Value (TIV). Statistical analysis was performed using the independent sample t-test (p sites was constructed using the first 30 English-language Web sites identified by each search engine. After duplicates and sites only containing links to other Web sites were eliminated, 39 remained. The mean score for accountability was 2.13 on scale of 0 to 7. The mean TIV was 5.0 on a scale of 0 to 10. Only 12 sites (30.8%) had their authors clearly identified. Twenty-two (56.4%) sites were sponsored by commercial interests or represented private practices. The mean TIV was significantly higher (p = 0.037) for noncommercial (personal, academic institution, or charity) sites (5.88 +\\/- 2.39 SD) than those representing commercial interests (4.32 +\\/- 2.10 SD). Tinnitus information available on the Internet is indeed variable, and care should be taken in recommending tinnitus Web sites to patients.

  7. Anti-nuclear activities and critics concerning nuclear power plant sites

    International Nuclear Information System (INIS)

    Rhee, We-Beg

    2000-01-01

    Korea has dynamic nuclear power expansion programs, operating 16 nuclear units producing 13710 MW in total located on 4 different sites. Last year, nuclear power supplied over 40 % of national total electricity demands. In 1998, Korean government initiated re-designation work investigating circumstance changes to rule out the unnecessary sites in consideration of a long-term power supply. Korean government has determined to expand the Ulchin site and to designate one point of Woolju county as a new candidate site, and ruled out the rest candidate sites at the end of 1998. About such a governmental measure, the two areas show different reactions. Ulchin where nuclear power plant has been operated safely for about 10 years was likely to accept the governmental determination in spite of some opposition and called for several financial supports for local development. WooIju county, however, showed a strong opposition among local environmental groups and autonomous politicians, and they presented a variety of anti-nuclear activities including demonstrations mainly at the neighbouring metropolis, Ulsan city

  8. Conserving critical sites for biodiversity provides disproportionate benefits to people

    DEFF Research Database (Denmark)

    Larsen, Frank Wugt; Turner, Will R.; Brooks, Thomas M.

    2012-01-01

    Protecting natural habitats in priority areas is essential to halt the loss of biodiversity. Yet whether these benefits for biodiversity also yield benefits for human well-being remains controversial. Here we assess the potential human well-being benefits of safeguarding a global network of sites......) benefits to maintenance of human cultural diversity - significantly exceeding those anticipated from randomly selected sites within the same countries and ecoregions. Results suggest that safeguarding sites important for biodiversity conservation provides substantial benefits to human well-being....

  9. The mixed health messages of Millsberry: a critical study of online child-targeted food advergaming.

    Science.gov (United States)

    Thomson, Deborah M

    2011-06-01

    This paper offers a critical study of the contradictions of Millsberry.com, a General Mills (GM) advergaming website used to market GM's breakfast cereal brands to children. The paper takes a critical semiotic approach to argue that Millsberry.com sends players contradictory messages about health by simultaneously promoting nutritional wellness and consumption of high-sugar cereals, essentially conflating the two. Players on Millsberry.com create a virtual self (a Buddy) who lives in the fictional town of Millsberry, and a Buddy's health is tracked over time as players make nutritional choices for the Buddy. Health on Millsberry equates to eating from multiple food groups (nutritional balance) and eating only until full (caloric moderation). Yet both of these health messages are essentially undermined by play on the site. Nutritional balance is undermined by both the excessive promotion of high-sugar cereals and the differences between depictions of branded and unbranded foods. Caloric moderation is contradicted by digital advergames that operate on a logic of maximal consumption, by narratives of branded spokescharacters' endless appetites for cereal, and by giveaways of "free" boxes of virtual cereal that can be eaten by the Buddy in a single bite. The study concludes that such mixed messages about nutritional health are highly problematic, particularly given the alarming increase in diet and weight-related diseases among children.

  10. Critical Behaviour of Pure and Site-Random Two Dimensional Antiferromagnets

    DEFF Research Database (Denmark)

    Birgenau, R. J.; Als-Nielsen, Jens Aage; Shirane, G.

    1977-01-01

    Quasielastic neutron scattering studies of the static critical behavior in the two-dimensional antiferromagnets K2NiF4, K2MnF4, and Rb2Mn0.5Ni0.5F4 are reported. For T......Quasielastic neutron scattering studies of the static critical behavior in the two-dimensional antiferromagnets K2NiF4, K2MnF4, and Rb2Mn0.5Ni0.5F4 are reported. For T...

  11. Genetic variation in IL-16 miRNA target site and time to prostate cancer diagnosis in African American men

    Science.gov (United States)

    Hughes, Lucinda; Ruth, Karen; Rebbeck, Timothy R.; Giri, Veda N.

    2013-01-01

    Background Men with a family history of prostate cancer and African American men are at high risk for prostate cancer and in need of personalized risk estimates to inform screening decisions. This study evaluated genetic variants in genes encoding microRNA (miRNA) binding sites for informing of time to prostate cancer diagnosis among ethnically-diverse, high-risk men undergoing prostate cancer screening. Methods The Prostate Cancer Risk Assessment Program (PRAP) is a longitudinal screening program for high-risk men. Eligibility includes men ages 35-69 with a family history of prostate cancer or African descent. Participants with ≥ 1 follow-up visit were included in the analyses (n=477). Genetic variants in regions encoding miRNA binding sites in four target genes (ALOX15, IL-16, IL-18, and RAF1) previously implicated in prostate cancer development were evaluated. Genotyping methods included Taqman® SNP Genotyping Assay (Applied Biosystems) or pyrosequencing. Cox models were used to assess time to prostate cancer diagnosis by risk genotype. Results Among 256 African Americans with ≥ one follow-up visit, the TT genotype at rs1131445 in IL-16 was significantly associated with earlier time to prostate cancer diagnosis vs. the CC/CT genotypes (p=0.013), with a suggestive association after correction for false-discovery (p=0.065). Hazard ratio after controlling for age and PSA for TT vs. CC/CT among African Americans was 3.0 (95% CI 1.26-7.12). No association to time to diagnosis was detected among Caucasians by IL-16 genotype. No association to time to prostate cancer diagnosis was found for the other miRNA target genotypes. Conclusions Genetic variation in IL-16 encoding miRNA target site may be informative of time to prostate cancer diagnosis among African American men enrolled in prostate cancer risk assessment, which may inform individualized prostate cancer screening strategies in the future. PMID:24061634

  12. Permissive underfeeding versus target enteral feeding in adult critically ill patients (PermiT Trial: a study protocol of a multicenter randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Arabi Yaseen M

    2012-10-01

    Full Text Available Abstract Background Nutritional support is an essential part of the management of critically ill patients. However, optimal caloric intake has not been systematically evaluated. We aim to compare two strategies of enteral feeding: permissive underfeeding versus target feeding. Method/Design This is an international multi-center randomized controlled trial in critically ill medical- surgical adult patients. Using a centralized allocation, 862 patients will be randomized to permissive underfeeding or target feeding. Patients in the permissive group receive 50% (acceptable range is 40% to 60% of the calculated caloric requirement, while those in the targeted group receive 100% (acceptable range 70% to 100% of the calculated caloric requirement. The primary outcome is 90-day all-cause mortality. Secondary outcomes include ICU and hospital mortality, 28-day, and 180-day mortality as well as health care-associated infections, organ failure, and length of stay in the ICU and hospital. The trial has 80% power to detect an 8% absolute reduction in 90-day mortality assuming a baseline risk of death of 25% at an alpha level of 0.05. Discussion Patient recruitment started in November 2009 and is currently active in five centers. The Data Monitoring Committee advised continuation of the trial after the first interim analysis. The study is expected to finish by November 2013. Trial registration Current Controlled Trials ISRCTN68144998

  13. Comprehensive profiling of retroviral integration sites using target enrichment methods from historical koala samples without an assembled reference genome

    Directory of Open Access Journals (Sweden)

    Pin Cui

    2016-03-01

    Full Text Available Background. Retroviral integration into the host germline results in permanent viral colonization of vertebrate genomes. The koala retrovirus (KoRV is currently invading the germline of the koala (Phascolarctos cinereus and provides a unique opportunity for studying retroviral endogenization. Previous analysis of KoRV integration patterns in modern koalas demonstrate that they share integration sites primarily if they are related, indicating that the process is currently driven by vertical transmission rather than infection. However, due to methodological challenges, KoRV integrations have not been comprehensively characterized. Results. To overcome these challenges, we applied and compared three target enrichment techniques coupled with next generation sequencing (NGS and a newly customized sequence-clustering based computational pipeline to determine the integration sites for 10 museum Queensland and New South Wales (NSW koala samples collected between the 1870s and late 1980s. A secondary aim of this study sought to identify common integration sites across modern and historical specimens by comparing our dataset to previously published studies. Several million sequences were processed, and the KoRV integration sites in each koala were characterized. Conclusions. Although the three enrichment methods each exhibited bias in integration site retrieval, a combination of two methods, Primer Extension Capture and hybridization capture is recommended for future studies on historical samples. Moreover, identification of integration sites shows that the proportion of integration sites shared between any two koalas is quite small.

  14. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.

    Science.gov (United States)

    Armas, Pablo; Margarit, Ezequiel; Mouguelar, Valeria S; Allende, Miguel L; Calcaterra, Nora B

    2013-01-01

    CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2) and sporadic inclusion body myositis (sIBM) human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.

  15. Beyond the binding site: in vivo identification of tbx2, smarca5 and wnt5b as molecular targets of CNBP during embryonic development.

    Directory of Open Access Journals (Sweden)

    Pablo Armas

    Full Text Available CNBP is a nucleic acid chaperone implicated in vertebrate craniofacial development, as well as in myotonic dystrophy type 2 (DM2 and sporadic inclusion body myositis (sIBM human muscle diseases. CNBP is highly conserved among vertebrates and has been implicated in transcriptional regulation; however, its DNA binding sites and molecular targets remain elusive. The main goal of this work was to identify CNBP DNA binding sites that might reveal target genes involved in vertebrate embryonic development. To accomplish this, we used a recently described yeast one-hybrid assay to identify DNA sequences bound in vivo by CNBP. Bioinformatic analyses revealed that these sequences are G-enriched and show high frequency of putative G-quadruplex DNA secondary structure. Moreover, an in silico approach enabled us to establish the CNBP DNA-binding site and to predict CNBP putative targets based on gene ontology terms and synexpression with CNBP. The direct interaction between CNBP and candidate genes was proved by EMSA and ChIP assays. Besides, the role of CNBP upon the identified genes was validated in loss-of-function experiments in developing zebrafish. We successfully confirmed that CNBP up-regulates tbx2b and smarca5, and down-regulates wnt5b gene expression. The highly stringent strategy used in this work allowed us to identify new CNBP target genes functionally important in different contexts of vertebrate embryonic development. Furthermore, it represents a novel approach toward understanding the biological function and regulatory networks involving CNBP in the biology of vertebrates.

  16. MicroRNA target finding by comparative genomics.

    Science.gov (United States)

    Friedman, Robin C; Burge, Christopher B

    2014-01-01

    MicroRNAs (miRNAs) have been implicated in virtually every metazoan biological process, exerting a widespread impact on gene expression. MicroRNA repression is conferred by relatively short "seed match" sequences, although the degree of repression varies widely for individual target sites. The factors controlling whether, and to what extent, a target site is repressed are not fully understood. As an alternative to target prediction based on sequence alone, comparative genomics has emerged as an invaluable tool for identifying miRNA targets that are conserved by natural selection, and hence likely effective and important. Here we present a general method for quantifying conservation of miRNA seed match sites, separating it from background conservation, controlling for various biases, and predicting miRNA targets. This method is useful not only for generating predictions but also as a tool for empirically evaluating the importance of various target prediction criteria.

  17. The french criticality handbook

    International Nuclear Information System (INIS)

    Maubert, L.; Puit, J.C.

    1987-01-01

    The french criticality handbook, published in 1978 by the ''Commissariat a l'Energie Atomique'', is presented with the main targets aimed by the writer and the main choices taken relating to fissile mediums, reflection conditions, dilution curves. The validation of the critical values is presented as one of the most important aspects of this handbook which is mainly intended, in the mind of the author, to specialists well advertised in the field of criticality. The complements which have been introduced since 1978 and those which are foreseen in a near future are also detailed. (author)

  18. Physics analyses of an accelerator-driven sub-critical assembly

    Science.gov (United States)

    Naberezhnev, Dmitry G.; Gohar, Yousry; Bailey, James; Belch, Henry

    2006-06-01

    Physics analyses have been performed for an accelerator-driven sub-critical assembly as a part of the Argonne National Laboratory activity in preparation for a joint conceptual design with the Kharkov Institute of Physics and Technology (KIPT) of Ukraine. KIPT has a plan to construct an accelerator-driven sub-critical assembly targeted towards the medical isotope production and the support of the Ukraine nuclear industry. The external neutron source is produced either through photonuclear reactions in tungsten or uranium targets, or deuteron reactions in a beryllium target. KIPT intends using the high-enriched uranium (HEU) for the fuel of the sub-critical assembly. The main objective of this paper is to study the possibility of utilizing low-enriched uranium (LEU) fuel instead of HEU fuel without penalizing the sub-critical assembly performance, in particular the neutron flux level. In the course of this activity, several studies have been carried out to investigate the main choices for the system's parameters. The external neutron source has been characterized and a pre-conceptual target design has been developed. Several sub-critical configurations with different fuel enrichments and densities have been considered. Based on our analysis, it was shown that the performance of the LEU fuel is comparable with that of the HEU fuel. The LEU fuel sub-critical assembly with 200-MeV electron energy and 100-kW electron beam power has an average total flux of ˜2.50×10 13 n/s cm 2 in the irradiation channels. The corresponding total facility power is ˜204 kW divided into 91 and 113 kW deposited in the target and sub-critical assemblies, respectively.

  19. Evolution of critical day length for diapause induction enables range expansion of Diorhabda carinulata, a biological control agent against tamarisk (Tamarix spp.).

    Science.gov (United States)

    Bean, Dan W; Dalin, Peter; Dudley, Tom L

    2012-07-01

    In classical weed biological control, small collections of arthropods are made from one or a few sites in the native range of the target plant and are introduced to suppress the plant where it has become invasive, often across a wide geographic range. Ecological mismatches in the new range are likely, and success using the biocontrol agent may depend on postrelease evolution of beneficial life history traits. In this study, we measure the evolution of critical day length for diapause induction (day length at which 50% of the population enters dormancy), in a beetle (Diorhabda carinulata) introduced into North America from China to control an exotic shrub, Tamarix spp. Beetle populations were sampled from four sites in North America 7 years after introduction, and critical day length was shown to have declined, forming a cline over a latitudinal gradient At one field site, decreased critical day length was correlated with 16 additional days of reproductive activity, resulting in a closer match between beetle life history and the phenology of Tamarix. These findings indicate an enhanced efficacy and an increasingly wider range for D. carinulata in Tamarix control.

  20. Threshold Assessment: Definition of Acceptable Sites as Part of Site Selection for the Japanese HLW Program

    International Nuclear Information System (INIS)

    McKenna, S.A.; Wakasugi, Keiichiro; Webb, E.K.; Makino, Hitoshi; Ishihara, Yoshinao; Ijiri, Yuji; Sawada, Atsushi; Baba, Tomoko; Ishiguro, Katsuhiko; Umeki, Hiroyuki

    2000-01-01

    For the last ten years, the Japanese High-Level Nuclear Waste (HLW) repository program has focused on assessing the feasibility of a basic repository concept, which resulted in the recently published H12 Report. As Japan enters the implementation phase, a new organization must identify, screen and choose potential repository sites. Thus, a rapid mechanism for determining the likelihood of site suitability is critical. The threshold approach, described here, is a simple mechanism for defining the likelihood that a site is suitable given estimates of several critical parameters. We rely on the results of a companion paper, which described a probabilistic performance assessment simulation of the HLW reference case in the H12 report. The most critical two or three input parameters are plotted against each other and treated as spatial variables. Geostatistics is used to interpret the spatial correlation, which in turn is used to simulate multiple realizations of the parameter value maps. By combining an array of realizations, we can look at the probability that a given site, as represented by estimates of this combination of parameters, would be good host for a repository site

  1. Targeting Critical Thinking Skills in a First-Year Undergraduate Research Course

    Directory of Open Access Journals (Sweden)

    Susan Carson

    2015-08-01

    Full Text Available TH!NK is a new initiative at NC State University focused on enhancing students’ higher-order cognitive skills. As part of this initiative, I explicitly emphasized critical and creative thinking in an existing bacteriophagediscovery first-year research course. In addition to the typical activities associated with undergraduate research such as review of primary literature and writing research papers, another strategy employed to enhance students’ critical thinking skills was the use of discipline-specific, real-world scenarios. This paper outlines a general “formula” for writing scenarios, as well as several specific scenarios created for the described course. I also present how embedding aspects of the scenarios in reviews of the primary literature enriched the activity. I assessed student gains in critical thinking skills using a pre-/posttest model of the Critical Thinking Assessment Test (CAT, developed by Tennessee Technological University. I observed apositive gain trend in most of the individual skills assessed in the CAT, with a statistically significant large effect on critical thinking skills overall in students in the test group. I also show that a higher level of criticalthinking skills was demonstrated in research papers written by students who participated in the scenarios compared with similar students who did not participate in the scenario activities. The scenario strategy described here can be modified for use in biology and other STEM disciplines, as well as in diverse disciplines in the social sciences and humanities.

  2. The Pajarito Site operating procedures for the Los Alamos Critical Experiments Facility

    International Nuclear Information System (INIS)

    Malenfant, R.E.

    1991-12-01

    Operating procedures consistent with DOE Order 5480.6, and the American National Standard Safety Guide for the Performance of Critical Experiments are defined for the Los Alamos Critical Experiments Facility (LACEF) of the Los Alamos National Laboratory. These operating procedures supersede and update those previously published in 1983 and apply to any criticality experiment performed at the facility. 11 refs

  3. Retroviral integration: Site matters

    Science.gov (United States)

    Demeulemeester, Jonas; De Rijck, Jan

    2015-01-01

    Here, we review genomic target site selection during retroviral integration as a multistep process in which specific biases are introduced at each level. The first asymmetries are introduced when the virus takes a specific route into the nucleus. Next, by co‐opting distinct host cofactors, the integration machinery is guided to particular chromatin contexts. As the viral integrase captures a local target nucleosome, specific contacts introduce fine‐grained biases in the integration site distribution. In vivo, the established population of proviruses is subject to both positive and negative selection, thereby continuously reshaping the integration site distribution. By affecting stochastic proviral expression as well as the mutagenic potential of the virus, integration site choice may be an inherent part of the evolutionary strategies used by different retroviruses to maximise reproductive success. PMID:26293289

  4. Effect of co-administration of probiotics with polysaccharide based colon targeted delivery systems to optimize site specific drug release.

    Science.gov (United States)

    Prudhviraj, G; Vaidya, Yogyata; Singh, Sachin Kumar; Yadav, Ankit Kumar; Kaur, Puneet; Gulati, Monica; Gowthamarajan, K

    2015-11-01

    Significant clinical success of colon targeted dosage forms has been limited by their inappropriate release profile at the target site. Their failure to release the drug completely in the colon may be attributed to changes in the colonic milieu because of pathological state, drug effect and psychological stress accompanying the diseased state or, a combination of these. Alteration in normal colonic pH and bacterial picture leads to incomplete release of drug from the designed delivery system. We report the effectiveness of a targeted delivery system wherein the constant replenishment of the colonic microbiota is achieved by concomitant administration of probiotics along with the polysaccharide based drug delivery system. Guar gum coated spheroids of sulfasalazine were prepared. In the dissolution studies, these spheroids showed markedly higher release in the simulated colonic fluid. In vivo experiments conducted in rats clearly demonstrated the therapeutic advantage of co-administration of probiotics with guar gum coated spheroids. Our results suggest that concomitant use of probiotics along with the polysaccharide based delivery systems can be a simple strategy to achieve satisfactory colon targeting of drugs. Copyright © 2015 Elsevier B.V. All rights reserved.

  5. The International Criticality Safety Benchmark Evaluation Project on the Internet

    International Nuclear Information System (INIS)

    Briggs, J.B.; Brennan, S.A.; Scott, L.

    2000-01-01

    The International Criticality Safety Benchmark Evaluation Project (ICSBEP) was initiated in October 1992 by the US Department of Energy's (DOE's) defense programs and is documented in the Transactions of numerous American Nuclear Society and International Criticality Safety Conferences. The work of the ICSBEP is documented as an Organization for Economic Cooperation and Development (OECD) handbook, International Handbook of Evaluated Criticality Safety Benchmark Experiments. The ICSBEP Internet site was established in 1996 and its address is http://icsbep.inel.gov/icsbep. A copy of the ICSBEP home page is shown in Fig. 1. The ICSBEP Internet site contains the five primary links. Internal sublinks to other relevant sites are also provided within the ICSBEP Internet site. A brief description of each of the five primary ICSBEP Internet site links is given

  6. The optimal blood glucose level for critically ill adult patients.

    Science.gov (United States)

    Lv, Shaoning; Ross, Paul; Tori, Kathleen

    2017-09-01

    Glycaemic control is recognized as one of the important aspects in managing critically ill patients. Both hyperglycaemia and hypoglycaemia independently increase the risk of patient mortality. Hence, the identification of optimal glycaemic control is of paramount importance in the management of critically ill patients. The aim of this literature review is to examine the current status of glycaemic control in critically ill adult patients. This literature review will focus on randomized controlled trials comparing intensive insulin therapy to conventional insulin therapy, with an objective to identify optimal blood glucose level targets for critically ill adult patients. A literature review was conducted to identify large randomized controlled trials for the optimal targeted blood glucose level for critically ill adult patients published since 2000. A total of eight studies fulfilled the selection criteria of this review. With current human and technology resources, the results of the studies support commencing glycaemic control once the blood glucose level of critically ill patients reaches 10 mmol/L and maintaining this level between 8 mmol/L and 10 mmol/L. This literature review provides a recommendation for targeting the optimal blood glucose level for critically ill patients within moderate blood glucose level target range (8-10 mmol/L). The need for uniformed glucometrics for unbiased reporting and further research for optimal blood glucose target is required, especially in light of new technological advancements in closed-loop insulin delivery and monitoring devices. This literature review has revealed a need to call for consensus in the measurement and reporting of glycaemic control using standardized glucometrics. © 2017 British Association of Critical Care Nurses.

  7. Community-based conservation of critical sites: Uganda's experience

    African Journals Online (AJOL)

    ... of natural resources, first and foremost for their own good, and then for national and global benefit. Ecotourism and adding value to locally produced materials in communities can translate into support for conservation. This paper highlights the importance of community-based conservation for important biodiversity sites.

  8. [The optimal blood glucose target in critically ill patient: comparison of two intensive insulin therapy protocols].

    Science.gov (United States)

    Raurell Torredà, Marta; del Llano Serrano, César; Almirall Solsona, Dolors; Catalan Ibars, Rosa María; Nicolás Arfelis, José María

    2014-03-04

    Recent studies in critically ill patients receiving insulin intravenous therapy (IIT) have shown an increased incidence of severe hypoglycemia, while intermittent subcutaneous insulin «sliding scales» (conventional insulin therapy [CIT]) is associated with hyperglycemia. The objective of this study is to assess whether glycemic control range IIT can affect glucose levels and their variability and to compare it with CIT. Prospective comparative cohort study in intensive care unit, with 2 study periods: Period 1, IIT with glycemic target range 110-140 mg/dL, and Period 2, IIT of 140-180 mg/dL. In both periods CIT glycemic target was 110-180 mg/dL. We assessed severe hypoglycemia ( 216 mg/L) and the variability of blood glucose. We studied 221 patients with 12.825 blood glucose determinations. Twenty-six and 17% of patients required IIT for glycemic control in Period 1 and 2, respectively. Hypoglycemia was associated with a discontinuous nutritional intake, glycemic target 110-140 mg/dL and low body mass index (BMI) (P = .002). Hyperglycemia was exclusively associated with a history of diabetes mellitus (OR 2.6 [95% CI 1.6 to 4.5]). Glycemic variability was associated with a discontinuous nutritional intake, low BMI, CIT insulinization, diabetes mellitus, elderly and high APACHE II (P < .001). The use of IIT is useful to reduce the variability of blood glucose. Although the 140-180 mg/dL range would be more secure as to presenting greater variability and hyperglycemia, the 110-140 mg/dL range is most suitable. Copyright © 2012 Elsevier España, S.L. All rights reserved.

  9. Neutrophils in critical illness.

    Science.gov (United States)

    McDonald, Braedon

    2018-03-01

    During critical illness, dramatic alterations in neutrophil biology are observed including abnormalities of granulopoeisis and lifespan, cell trafficking and antimicrobial effector functions. As a result, neutrophils transition from powerful antimicrobial protectors into dangerous mediators of tissue injury and organ dysfunction. In this article, the role of neutrophils in the pathogenesis of critical illness (sepsis, trauma, burns and others) will be explored, including pathological changes to neutrophil function during critical illness and the utility of monitoring aspects of the neutrophil phenotype as biomarkers for diagnosis and prognostication. Lastly, we review findings from clinical trials of therapies that target the harmful effects of neutrophils, providing a bench-to-bedside perspective on neutrophils in critical illness.

  10. Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies

    Science.gov (United States)

    2017-10-01

    prostate cancer . Cancer Res 70: 7992-8002, 2010 8. Nelson PS: Molecular states underlying an- drogen receptor activation: A framework for thera- peutics...targeting androgen signaling in prostate cancer . J Clin Oncol 30:644-646, 2012 9. Thadani-Mulero M, Nanus DM, Giannakakou P: Androgen receptor on the... prostate cancer . Clin Cancer Res 21:795-807, 2015 17. van Soest RJ, de Morrée ES, Kweldam CF, et al: Targeting the androgen receptor confers in vivo

  11. Critical management practices influencing on-site waste minimization in construction projects.

    Science.gov (United States)

    Ajayi, Saheed O; Oyedele, Lukumon O; Bilal, Muhammad; Akinade, Olugbenga O; Alaka, Hafiz A; Owolabi, Hakeem A

    2017-01-01

    As a result of increasing recognition of effective site management as the strategic approach for achieving the required performance in construction projects, this study seeks to identify the key site management practices that are requisite for construction waste minimization. A mixed methods approach, involving field study and survey research were used as means of data collection. After confirmation of construct validity and reliability of scale, data analysis was carried out through a combination of Kruskal-Wallis test, descriptive statistics and exploratory factor analysis. The study suggests that site management functions could significantly reduce waste generation through strict adherence to project drawings, and by ensuring fewer or no design changes during construction process. Provision of waste skips for specific materials and maximisation of on-site reuse of materials are also found to be among the key factors for engendering waste minimization. The result of factor analysis suggests four factors underlying on-site waste management practices with 96.093% of total variance. These measures include contractual provisions for waste minimization, waste segregation, maximisation of materials reuse and effective logistic management. Strategies through which each of the underlying measures could be achieved are further discussed in the paper. Findings of this study would assist construction site managers and other site operatives in reducing waste generated by construction activities. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Early and late HIV-1 membrane fusion events are impaired by sphinganine lipidated peptides that target the fusion site.

    Science.gov (United States)

    Klug, Yoel A; Ashkenazi, Avraham; Viard, Mathias; Porat, Ziv; Blumenthal, Robert; Shai, Yechiel

    2014-07-15

    Lipid-conjugated peptides have advanced the understanding of membrane protein functions and the roles of lipids in the membrane milieu. These lipopeptides modulate various biological systems such as viral fusion. A single function has been suggested for the lipid, binding to the membrane and thus elevating the local concentration of the peptide at the target site. In the present paper, we challenged this argument by exploring in-depth the antiviral mechanism of lipopeptides, which comprise sphinganine, the lipid backbone of DHSM (dihydrosphingomyelin), and an HIV-1 envelope-derived peptide. Surprisingly, we discovered a partnership between the lipid and the peptide that impaired early membrane fusion events by reducing CD4 receptor lateral diffusion and HIV-1 fusion peptide-mediated lipid mixing. Moreover, only the joint function of sphinganine and its conjugate peptide disrupted HIV-1 fusion protein assembly and folding at the later fusion steps. Via imaging techniques we revealed for the first time the direct localization of these lipopeptides to the virus-cell and cell-cell contact sites. Overall, the findings of the present study may suggest lipid-protein interactions in various biological systems and may help uncover a role for elevated DHSM in HIV-1 and its target cell membranes.

  13. The effect of target and non-target similarity on neural classification performance: A boost from confidence

    OpenAIRE

    Amar R Marathe; Anthony J Ries; Vernon J Lawhern; Vernon J Lawhern; Brent J Lance; Jonathan eTouryan; Kaleb eMcDowell; Hubert eCecotti

    2015-01-01

    Brain computer interaction (BCI) technologies have proven effective in utilizing single-trial classification algorithms to detect target images in rapid serial visualization presentation tasks. While many factors contribute to the accuracy of these algorithms, a critical aspect that is often overlooked concerns the feature similarity between target and non-target images. In most real-world environments there are likely to be many shared features between targets and non-targets resulting in si...

  14. The effect of target and non-target similarity on neural classification performance: a boost from confidence

    OpenAIRE

    Marathe, Amar R.; Ries, Anthony J.; Lawhern, Vernon J.; Lance, Brent J.; Touryan, Jonathan; McDowell, Kaleb; Cecotti, Hubert

    2015-01-01

    Brain computer interaction (BCI) technologies have proven effective in utilizing single-trial classification algorithms to detect target images in rapid serial visualization presentation tasks. While many factors contribute to the accuracy of these algorithms, a critical aspect that is often overlooked concerns the feature similarity between target and non-target images. In most real-world environments there are likely to be many shared features between targets and non-targets resulting in si...

  15. Target loads of atmospheric sulfur deposition for the protection and recovery of acid-sensitive streams in the Southern Blue Ridge Province.

    Science.gov (United States)

    Sullivan, Timothy J; Cosby, Bernard J; Jackson, William A

    2011-11-01

    An important tool in the evaluation of acidification damage to aquatic and terrestrial ecosystems is the critical load (CL), which represents the steady-state level of acidic deposition below which ecological damage would not be expected to occur, according to current scientific understanding. A deposition load intended to be protective of a specified resource condition at a particular point in time is generally called a target load (TL). The CL or TL for protection of aquatic biota is generally based on maintaining surface water acid neutralizing capacity (ANC) at an acceptable level. This study included calibration and application of the watershed model MAGIC (Model of Acidification of Groundwater in Catchments) to estimate the target sulfur (S) deposition load for the protection of aquatic resources at several future points in time in 66 generally acid-sensitive watersheds in the southern Blue Ridge province of North Carolina and two adjoining states. Potential future change in nitrogen leaching is not considered. Estimated TLs for S deposition ranged from zero (ecological objective not attainable by the specified point in time) to values many times greater than current S deposition depending on the selected site, ANC endpoint, and evaluation year. For some sites, one or more of the selected target ANC critical levels (0, 20, 50, 100μeq/L) could not be achieved by the year 2100 even if S deposition was reduced to zero and maintained at that level throughout the simulation. Many of these highly sensitive streams were simulated by the model to have had preindustrial ANC below some of these target values. For other sites, the watershed soils contained sufficiently large buffering capacity that even very high sustained levels of atmospheric S deposition would not reduce stream ANC below common damage thresholds. Copyright © 2011 Elsevier Ltd. All rights reserved.

  16. Targeting human breast cancer cells by an oncolytic adenovirus using microRNA-targeting strategy.

    Science.gov (United States)

    Shayestehpour, Mohammad; Moghim, Sharareh; Salimi, Vahid; Jalilvand, Somayeh; Yavarian, Jila; Romani, Bizhan; Mokhtari-Azad, Talat

    2017-08-15

    MicroRNA-targeting strategy is a promising approach that enables oncolytic viruses to replicate in tumor cells but not in normal cells. In this study, we targeted adenoviral replication toward breast cancer cells by inserting ten complementary binding sites for miR-145-5p downstream of E1A gene. In addition, we evaluated the effect of increasing miR-145 binding sites on inhibition of virus replication. Ad5-control and adenoviruses carrying five or ten copies of miR145-5p target sites (Ad5-5miR145T, Ad5-10miR145T) were generated and inoculated into MDA-MB-453, BT-20, MCF-7 breast cancer cell lines and human mammary epithelial cells (HMEpC). Titer of Ad5-10miR145T in HMEpC was significantly lower than Ad5-control titer. Difference between the titer of these two viruses at 12, 24, 36, and 48h after infection was 1.25, 2.96, 3.06, and 3.77 log TCID 50 . No significant difference was observed between the titer of both adenoviruses in MDA-MB-453, BT-20 and MCF-7 cells. The infectious titer of adenovirus containing 10 miR-145 binding sites in HMEpC cells at 24, 36, and 48h post-infection was 1.7, 2.08, and 4-fold, respectively, lower than the titer of adenovirus carrying 5 miR-145 targets. Our results suggest that miR-145-targeting strategy provides selectivity for adenovirus replication in breast cancer cells. Increasing the number of miRNA binding sites within the adenoviral genome confers more selectivity for viral replication in cancer cells. Copyright © 2017. Published by Elsevier B.V.

  17. Site-targeted complement inhibition by a complement receptor 2-conjugated inhibitor (mTT30) ameliorates post-injury neuropathology in mouse brains.

    Science.gov (United States)

    Rich, Megan C; Keene, Chesleigh N; Neher, Miriam D; Johnson, Krista; Yu, Zhao-Xue; Ganivet, Antoine; Holers, V Michael; Stahel, Philip F

    2016-03-23

    Intracerebral complement activation after severe traumatic brain injury (TBI) leads to a cascade of neuroinflammatory pathological sequelae that propagate host-mediated secondary brain injury and adverse outcomes. There are currently no specific pharmacological agents on the market to prevent or mitigate the development of secondary cerebral insults after TBI. A novel chimeric CR2-fH compound (mTT30) provides targeted inhibition of the alternative complement pathway at the site of tissue injury. This experimental study was designed to test the neuroprotective effects of mTT30 in a mouse model of closed head injury. The administration of 500 μg mTT30 i.v. at 1 h, 4 h and 24 h after head injury attenuated complement C3 deposition in injured brains, reduced the extent of neuronal cell death, and decreased post-injury microglial activation, compared to vehicle-injected placebo controls. These data imply that site-targeted alternative pathway complement inhibition may represent a new promising therapeutic avenue for the future management of severe TBI. Copyright © 2016. Published by Elsevier Ireland Ltd.

  18. Direction, site and the muzzle target distance of bullet in the head and neck at close range as an indication of suicide or homicide.

    Science.gov (United States)

    Suwanjutha, T

    1988-05-01

    Direction, site and muzzle target distance can indicate suicide or homicide. This conclusion can be drawn from autopsies of 57 cases of suicide and 68 cases of homicide by handgun fired at close range to the head and neck together with going to the crimescene in some cases. This study was carried out in Bangkok during the period from January 1983 to January 1986. In order to determine whether it was suicide or homicide, the path of the bullet, the site, the muzzle target distance must be considered. The angle of the bullet would be either elevated (from below upward), horizontal or an angle of depression (from above downward). For suicide, the direction of the bullet should be at an angle of elevation in the majority of cases. The position of the handgun in relation to the head in suicide was most often in tight contact and near contact. For homicide, the direction of the bullet should be horizontal in most cases. The bullet was at close range in the majority of the cases. There are 8 common sites for suicide and homicide and 10 different sites in the case of homicide which are at neck, left cheek, left aural region, lip, left occipital area orbit, chin, left eyebrow, submental and nose.

  19. Nanoscale Synaptic Membrane Mimetic Allows Unbiased High Throughput Screen That Targets Binding Sites for Alzheimer?s-Associated A? Oligomers

    OpenAIRE

    Wilcox, Kyle C.; Marunde, Matthew R.; Das, Aditi; Velasco, Pauline T.; Kuhns, Benjamin D.; Marty, Michael T.; Jiang, Haoming; Luan, Chi-Hao; Sligar, Stephen G.; Klein, William L.

    2015-01-01

    Despite their value as sources of therapeutic drug targets, membrane proteomes are largely inaccessible to high-throughput screening (HTS) tools designed for soluble proteins. An important example comprises the membrane proteins that bind amyloid β oligomers (AβOs). AβOs are neurotoxic ligands thought to instigate the synapse damage that leads to Alzheimer's dementia. At present, the identities of initial AβO binding sites are highly uncertain, largely because of extensive protein-protein int...

  20. Target-site resistance to pyrethroids in European populations of pollen beetle, Meligethes aeneus F

    DEFF Research Database (Denmark)

    Nauen, Ralf; Zimmer, Christoph T; Andrews, Melanie

    2012-01-01

    by cytochrome P450 monooxygenases was implicated in the resistance of several pollen beetle populations from different European regions. Here, we have also investigated the possible occurrence of a target-site mechanism caused by modification of the pollen beetle para-type voltage-gated sodium channel gene. We...... resulted in high selection pressure and subsequent development of resistance. Resistance to pyrethroid insecticides in this pest is now widespread and the levels of resistance are often sufficient to result in field control failures at recommended application rates. Recently, metabolic resistance mediated...... detected a single nucleotide change that results in an amino acid substitution (L1014F) within the domain IIS6 region of the channel protein. The L1014F mutation, often termed kdr, has been found in several other insect pests and is known to confer moderate levels of resistance to pyrethroids. We developed...

  1. Toward superconducting critical current by design

    OpenAIRE

    Sadovskyy, I. A.; Jia, Y.; Leroux, M.; Kwon, J.; Hu, H.; Fang, L.; Chaparro, C.; Zhu, S.; Welp, U.; Zuo, J. -M.; Zhang, Y.; Nakasaki, R.; Selvamanickam, V.; Crabtree, G. W.; Koshelev, A. E.

    2015-01-01

    We present the new paradigm of critical current by design. Analogous to materials by design, it aims at predicting the optimal defect landscape in a superconductor for targeted applications by elucidating the vortex dynamics responsible for the bulk critical current. To highlight this approach, we demonstrate the synergistic combination of critical current measurements on commercial high-temperature superconductors containing self-assembled and irradiation tailored correlated defects by using...

  2. Toward Superconducting Critical Current by Design.

    Science.gov (United States)

    Sadovskyy, Ivan A; Jia, Ying; Leroux, Maxime; Kwon, Jihwan; Hu, Hefei; Fang, Lei; Chaparro, Carlos; Zhu, Shaofei; Welp, Ulrich; Zuo, Jian-Min; Zhang, Yifei; Nakasaki, Ryusuke; Selvamanickam, Venkat; Crabtree, George W; Koshelev, Alexei E; Glatz, Andreas; Kwok, Wai-Kwong

    2016-06-01

    A new critical-current-by-design paradigm is presented. It aims at predicting the optimal defect landscape in superconductors for targeted applications by elucidating the vortex dynamics responsible for the bulk critical current. To this end, critical current measurements on commercial high-temperature superconductors are combined with large-scale time-dependent Ginzburg-Landau simulations of vortex dynamics. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Targeting Critical Thinking Skills in a First-Year Undergraduate Research Course †

    Science.gov (United States)

    Carson, Susan

    2015-01-01

    TH!NK is a new initiative at NC State University focused on enhancing students’ higher-order cognitive skills. As part of this initiative, I explicitly emphasized critical and creative thinking in an existing bacteriophage discovery first-year research course. In addition to the typical activities associated with undergraduate research such as review of primary literature and writing research papers, another strategy employed to enhance students’ critical thinking skills was the use of discipline-specific, real-world scenarios. This paper outlines a general “formula” for writing scenarios, as well as several specific scenarios created for the described course. I also present how embedding aspects of the scenarios in reviews of the primary literature enriched the activity. I assessed student gains in critical thinking skills using a pre-/posttest model of the Critical Thinking Assessment Test (CAT), developed by Tennessee Technological University. I observed a positive gain trend in most of the individual skills assessed in the CAT, with a statistically significant large effect on critical thinking skills overall in students in the test group. I also show that a higher level of critical thinking skills was demonstrated in research papers written by students who participated in the scenarios compared with similar students who did not participate in the scenario activities. The scenario strategy described here can be modified for use in biology and other STEM disciplines, as well as in diverse disciplines in the social sciences and humanities. PMID:26753022

  4. Dosimetric management during a criticality accident

    International Nuclear Information System (INIS)

    Lebaron-Jacobs, L.; Fottorino, R.; Racine, Y.; Miele, A.; Barbry, F.; Briot, F.; Distinguin, S.; Le Goff, J.P.; Berard, P.; Boisson, P.; Cavadore, D.; Lecoix, G.; Persico, M.H.; Rongier, E.; Challeton-De Vathaire, C.; Medioni, R.; Voisin, P.; Exmelin, L.; Flury-Herard, A.; Gaillard-Lecanu, E.; Lemaire, G.; Gonin, M.; Riasse, C.

    2008-01-01

    A working group from health occupational and clinical biochemistry services on French sites has issued essential data sheets on the guidelines to follow in managing the victims of a criticality accident. Since the priority of the medical management after a criticality accident is to assess the dose and the distribution of dose, some dosimetric investigations have been selected in order to provide a prompt response and to anticipate the final dose reconstruction. Comparison exercises between clinical biochemistry laboratories on French sites were carried out to confirm that each laboratory maintained the required operational methods for hair treatment and the appropriate equipment for 32 P activity in hair and 24 Na activity in blood measurements, and to demonstrate its ability to rapidly provide neutron dose estimates after a criticality accident. As a result, a relation has been assessed to estimate the dose and the distribution of dose according to the neutron spectrum following a criticality accident. (authors)

  5. CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR-Cas9 genome-editing systems.

    Directory of Open Access Journals (Sweden)

    Lihua J Zhu

    Full Text Available CRISPR-Cas systems are a diverse family of RNA-protein complexes in bacteria that target foreign DNA sequences for cleavage. Derivatives of these complexes have been engineered to cleave specific target sequences depending on the sequence of a CRISPR-derived guide RNA (gRNA and the source of the Cas9 protein. Important considerations for the design of gRNAs are to maximize aimed activity at the desired target site while minimizing off-target cleavage. Because of the rapid advances in the understanding of existing CRISPR-Cas9-derived RNA-guided nucleases and the development of novel RNA-guided nuclease systems, it is critical to have computational tools that can accommodate a wide range of different parameters for the design of target-specific RNA-guided nuclease systems. We have developed CRISPRseek, a highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites. For applications where gRNAs are desired to discriminate between two related sequences, CRISPRseek can rank gRNAs based on the difference between predicted cleavage scores in each input sequence. CRISPRseek is implemented as a Bioconductor package within the R statistical programming environment, allowing it to be incorporated into computational pipelines to automate the design of gRNAs for target sequences identified in a wide variety of genome-wide analyses. CRISPRseek is available under the GNU General

  6. Criticality Safety Information Resource Center Web portal: www.csirc.net

    International Nuclear Information System (INIS)

    Harmon, C.D. II; Jones, T.

    2000-01-01

    The Nuclear Criticality Safety Group (ESH-6) at Los Alamos National Laboratory (LANL) is in the process of collecting and archiving historical and technical information related to nuclear criticality safety from LANL and other facilities. In an ongoing effort, this information is being made available via the Criticality Safety Information Resource Center (CSIRC) web site, which is hosted and maintained by ESH-6 staff. Recently, the CSIRC Web site was recreated as a Web portal that provides the criticality safety community with much more than just archived data

  7. Antibiotic dosing in critically ill patients receiving CRRT: underdosing is overprevalent.

    Science.gov (United States)

    Lewis, Susan J; Mueller, Bruce A

    2014-01-01

    Published CRRT drug dosing algorithms and other dosing guidelines appear to result in underdosed antibiotics, leading to failure to attain pharmacodynamic targets. High mortality rates persist with inadequate antibiotic therapy as the most important risk factor for death. Reasons for unintended antibiotic underdosing in patients receiving CRRT are many. Underdosing may result from lack of the recognition that better hepatic function in AKI patients yields higher nonrenal antibiotic clearance compared to ESRD patients. Other factors include the variability in body size and fluid composition of patients, the serious consequence of delayed achievement of antibiotic pharmacodynamic targets in septic patients, potential subtherapeutic antibiotic concentrations at the infection site, and the influence of RRT intensity on antibiotic concentrations. Too often, clinicians weigh the benefits of overcautious antibiotic dosing to avoid antibiotic toxicity too heavily against the benefits of rapid attainment of therapeutic antibiotic concentrations in critically ill patients receiving CRRT. We urge clinicians to prescribe antibiotics aggressively for these vulnerable patients. © 2014 Wiley Periodicals, Inc.

  8. CFD aspects of ADSS target design

    International Nuclear Information System (INIS)

    Shashi Kumar, G.N.; Mahendra, A.K.; Sanyal, A.; Gouthaman, G.

    2004-03-01

    The preliminary studies on CFD aspects of Accelerator Driven Sub-critical System (ADSS) target design has been presented in this report. The studies involve the thermal hydraulic analysis of the Liquid Metal Spallation Target (LMST) using Lead Bismuth Eutectic (LBE) as the target material. Apart from acting as Spallation medium LBE is used to remove the heat deposited by High Energy Proton Beam. Window of the target ( one side vacuum and other side LBE) has been reported in literature to be the most critical zone where high temperatures are reached. Numerical Simulations are carried out with Artificial Neural Network coupled Computational Fluid Dynamics (CFD) code, Various studies were carried out after the verification and validation of the initial results. Window being, the main parameter to be optimised, various designs of window were tried, along with change in the window material. The best possible combination has been proposed. The thermal hydraulic studies were carried out to arrive at the acceptable operating conditions for the target. (author)

  9. The mastermind approach to CNS drug therapy: translational prediction of human brain distribution, target site kinetics, and therapeutic effects

    OpenAIRE

    de Lange, Elizabeth CM

    2013-01-01

    Despite enormous advances in CNS research, CNS disorders remain the world?s leading cause of disability. This accounts for more hospitalizations and prolonged care than almost all other diseases combined, and indicates a high unmet need for good CNS drugs and drug therapies. Following dosing, not only the chemical properties of the drug and blood?brain barrier (BBB) transport, but also many other processes will ultimately determine brain target site kinetics and consequently the CNS effects. ...

  10. Long-Term Assessment of Critical Radionuclides and Associated Environmental Media at the Savannah River Site - 13038

    Energy Technology Data Exchange (ETDEWEB)

    Jannik, G.T.; Baker, R.A.; Lee, P.L. [Savannah River National Laboratory, Savannah River Site, Aiken, SC 29808 (United States); Eddy, T.P.; Blount, G.C. [Savannah River Nuclear Solutions, Savannah River Site, Aiken, SC 29808 (United States); Whitney, G.R. [US Department of Energy, Savannah River Operations, Aiken, SC 29808 (United States)

    2013-07-01

    During the operational history of the Savannah River Site (SRS), many different radionuclides have been released from site facilities. However, only a relatively small number of the released radionuclides have been significant contributors to doses and risks to the public. At SRS dose and risk assessments indicate tritium oxide in air and surface water, and Cs-137 in fish and deer have been, and continue to be, the critical radionuclides and pathways. In this assessment, statistical analyses of the long-term trends of tritium oxide in atmospheric and surface water releases and Cs-137 concentrations in fish and deer are provided. Correlations also are provided with 1) operational changes and improvements, 2) geopolitical events (Cold War cessation), and 3) recent environmental remediation projects and decommissioning of excess facilities. For example, environmental remediation of the F- and H-Area Seepage Basins and the Solid Waste Disposal Facility have resulted in a measurable impact on the tritium oxide flux to the onsite Fourmile Branch stream. Airborne releases of tritium oxide have been greatly affected by operational improvements and the end of the Cold War in 1991. However, the effects of SRS environmental remediation activities and ongoing tritium operations on tritium concentrations in the environment are measurable and documented in this assessment. Controlled hunts of deer and feral hogs are conducted at SRS for approximately six weeks each year. Before any harvested animal is released to a hunter, SRS personnel perform a field analysis for Cs-137 concentrations to ensure the Hunter's dose does not exceed the SRS administrative game limit of 0.22 milli-sievert (22 mrem). However, most of the Cs-137 found in SRS onsite deer is not from site operations but is from nuclear weapons testing fallout from the 1950's and early 1960's. This legacy source term is trended in the SRS deer, and an assessment of the 'effective' half-life of Cs

  11. A tale of two sequences: microRNA-target chimeric reads.

    Science.gov (United States)

    Broughton, James P; Pasquinelli, Amy E

    2016-04-04

    In animals, a functional interaction between a microRNA (miRNA) and its target RNA requires only partial base pairing. The limited number of base pair interactions required for miRNA targeting provides miRNAs with broad regulatory potential and also makes target prediction challenging. Computational approaches to target prediction have focused on identifying miRNA target sites based on known sequence features that are important for canonical targeting and may miss non-canonical targets. Current state-of-the-art experimental approaches, such as CLIP-seq (cross-linking immunoprecipitation with sequencing), PAR-CLIP (photoactivatable-ribonucleoside-enhanced CLIP), and iCLIP (individual-nucleotide resolution CLIP), require inference of which miRNA is bound at each site. Recently, the development of methods to ligate miRNAs to their target RNAs during the preparation of sequencing libraries has provided a new tool for the identification of miRNA target sites. The chimeric, or hybrid, miRNA-target reads that are produced by these methods unambiguously identify the miRNA bound at a specific target site. The information provided by these chimeric reads has revealed extensive non-canonical interactions between miRNAs and their target mRNAs, and identified many novel interactions between miRNAs and noncoding RNAs.

  12. Final work plan: Expedited Site Characterization of the IES Industries, Inc., Site at Marshalltown, Iowa. Ames Expedited Site Characterization Project, Version 1.0

    Energy Technology Data Exchange (ETDEWEB)

    1994-04-04

    The overall goal of the Ames Laboratory Expedited Site Characterization (ESC) project is to evaluate and promote both innovative and state-of-the-practice site characterization and/or monitoring technologies. This will be accomplished by fielding both types of technologies together in the context of an expedited site characterization. The first site will be at a former manufactured gas plant (FMGP) in Marshalltown, Iowa. The project will field three areas of technology: geophysical, analytical, and data fusion. Geophysical technologies are designed to understand the subsurface geology to help predict fate and transport of the target contaminants. Analytical technologies/methods are designed to detect and quantify the target contaminants. Data fusion technology consists of software systems designed to rapidly integrate or fuse all site information into a conceptual site model that then becomes the decision making tool for the site team to plan subsequent sampling activity. Not all of the contaminants present can be located at the action level. Polynuclear aromatic hydrocarbons (PAHs) are the signature organics associated with the coal tar activities that took place at the site. As a result, PAHs were selected as the target compounds. Screening analytical instruments and nonintrusive geophysical techniques will be fielded to qualitatively map the spatial contaminant distribution. Soil gas surveys, immunoassay testing (IMA), innovative optical techniques, and passive organic sorbent sensors will be deployed along with the geophysical methods. Gas chromatography/mass spectrometry (GC/MS) instruments and a cone penetrometer system equipped with a laser-induced fluorescence (LIF) probe will quantitatively map the action level edges of the PAH plume(s). Samples will be taken both by the cone penetrometer test system (CPT) and the Geoprobe {reg_sign} sampler system.

  13. Downregulation of miR-29a/b/c in placenta accreta inhibits apoptosis of implantation site intermediate trophoblast cells by targeting MCL1.

    Science.gov (United States)

    Gu, Yongzhong; Bian, Yuehong; Xu, Xiaofei; Wang, Xietong; Zuo, Changting; Meng, Jinlai; Li, Hongyan; Zhao, Shigang; Ning, Yunnan; Cao, Yongzhi; Huang, Tao; Yan, Junhao; Chen, Zi-Jiang

    2016-12-01

    Placenta accreta is defined as abnormal adhesion of placental villi to the uterine myometrium. Although this condition has become more common as a result of the increasing rate of cesarean sections, the underlying causative mechanism(s) remain elusive. Because microRNA-29a/b/c (miR-29a/b/c) have been shown to play important roles in placental development, this study evaluated the roles of these microRNAs in placenta accreta. Expression of miR-29a/b/c and myeloid cell leukemia-1 (MCL1) were quantified in patient tissues and HTR8/SVneo trophoblast cells using the real-time quantitative polymerase chain reaction. Western blotting was used to analyze expression of the MCL1 protein in HTR8/SVneo trophoblast cells with altered expression of miR-29a/b/c. To determine their role in apoptosis, miR-29a/b/c were overexpressed in HTR-8/SVneo cells, and levels of apoptosis were analyzed by flow cytometry. Luciferase activity assays were used to determine whether MCL1 is a target gene of miR-29a/b/c. Expression of miR-29a/b/c was significantly lower in creta sites compared to noncreta sites (p = 0.018, 0.041, and 0.022, respectively), but expression of MCL1 was upregulated in creta sites (p = 0.039). MCL1 expression was significantly downregulated in HTR-8/SVneo cells overexpressing miR-29a/b/c (p = 0.002, 0.008, and 0.013, respectively). Luciferase activity assays revealed that miR-29a/b/c directly target the 3' untranslated region of MCL1 in 293T cells. Over-expression of miR-29a/b/c induced apoptosis in the HTR-8/SVneo trophoblast cell line. Moreover, histopathological evaluation revealed that the number of implantation site intermediate trophoblast (ISIT) cells was increased in creta sites and that these cells were positive for MCL1. Our results demonstrate that in placenta accreta, miR-29a/b/c inhibits apoptosis of ISIT cells by targeting MCL1. These findings provide new insights into the pathogenesis of placenta accreta. Copyright © 2016 Elsevier Ltd. All rights

  14. A remote palm domain residue of RB69 DNA polymerase is critical for enzyme activity and influences the conformation of the active site.

    Directory of Open Access Journals (Sweden)

    Agata Jacewicz

    Full Text Available Non-conserved amino acids that are far removed from the active site can sometimes have an unexpected effect on enzyme catalysis. We have investigated the effects of alanine replacement of residues distant from the active site of the replicative RB69 DNA polymerase, and identified a substitution in a weakly conserved palm residue (D714A, that renders the enzyme incapable of sustaining phage replication in vivo. D714, located several angstroms away from the active site, does not contact the DNA or the incoming dNTP, and our apoenzyme and ternary crystal structures of the Pol(D714A mutant demonstrate that D714A does not affect the overall structure of the protein. The structures reveal a conformational change of several amino acid side chains, which cascade out from the site of the substitution towards the catalytic center, substantially perturbing the geometry of the active site. Consistent with these structural observations, the mutant has a significantly reduced k pol for correct incorporation. We propose that the observed structural changes underlie the severe polymerization defect and thus D714 is a remote, non-catalytic residue that is nevertheless critical for maintaining an optimal active site conformation. This represents a striking example of an action-at-a-distance interaction.

  15. Demographic survey around proposed nuclear power plant site in Haryana covering 30 km radius area from the site

    International Nuclear Information System (INIS)

    Garg, V.K.

    2013-01-01

    This study was planned to have a demographic survey of the households living within 30 km radius of the proposed site. Objectives of the present study were to attain the quantitative baseline demographic data around (within 30 km radius) the proposed site of nuclear power plant, zone-wise and sector-wise distribution of the population around proposed site up to a distance of 30 km from the site, to obtain the data on socio-economic, cultural, and religious perspectives of the target populations, to obtain the data on disease/illness pattern in the target population, health status and mortality rate

  16. Ames expedited site characterization demonstration at the former manufactured gas plant site, Marshalltown, Iowa

    International Nuclear Information System (INIS)

    Bevolo, A.J.; Kjartanson, B.H.; Wonder, J.D.

    1996-03-01

    The goal of the Ames Expedited Site Characterization (ESC) project is to evaluate and promote both innovative technologies (IT) and state-of-the-practice technologies (SOPT) for site characterization and monitoring. In April and May 1994, the ESC project conducted site characterization, technology comparison, and stakeholder demonstration activities at a former manufactured gas plant (FMGP) owned by Iowa Electric Services (IES) Utilities, Inc., in Marshalltown, Iowa. Three areas of technology were fielded at the Marshalltown FMGP site: geophysical, analytical and data integration. The geophysical technologies are designed to assess the subsurface geological conditions so that the location, fate and transport of the target contaminants may be assessed and forecasted. The analytical technologies/methods are designed to detect and quantify the target contaminants. The data integration technology area consists of hardware and software systems designed to integrate all the site information compiled and collected into a conceptual site model on a daily basis at the site; this conceptual model then becomes the decision-support tool. Simultaneous fielding of different methods within each of the three areas of technology provided data for direct comparison of the technologies fielded, both SOPT and IT. This document reports the results of the site characterization, technology comparison, and ESC demonstration activities associated with the Marshalltown FMGP site. 124 figs., 27 tabs

  17. Criticality safety basics, a study guide

    Energy Technology Data Exchange (ETDEWEB)

    V. L. Putman

    1999-09-01

    This document is a self-study and classroom guide, for criticality safety of activities with fissile materials outside nuclear reactors. This guide provides a basic overview of criticality safety and criticality accident prevention methods divided into three parts: theory, application, and history. Except for topic emphasis, theory and history information is general, while application information is specific to the Idaho National Engineering and Environmental Laboratory (INEEL). Information presented here should be useful to personnel who must know criticality safety basics to perform their assignments safely or to design critically safe equipment or operations. However, the guide's primary target audience is fissile material handler candidates.

  18. Criticality safety basics, a study guide

    International Nuclear Information System (INIS)

    Putman, V.L.

    1999-01-01

    This document is a self-study and classroom guide, for criticality safety of activities with fissile materials outside nuclear reactors. This guide provides a basic overview of criticality safety and criticality accident prevention methods divided into three parts: theory, application, and history. Except for topic emphasis, theory and history information is general, while application information is specific to the Idaho National Engineering and Environmental Laboratory (INEEL). Information presented here should be useful to personnel who must know criticality safety basics to perform their assignments safely or to design critically safe equipment or operations. However, the guide's primary target audience is fissile material handler candidates

  19. Low Herbivory among Targeted Reforestation Sites in the Andean Highlands of Southern Ecuador.

    Directory of Open Access Journals (Sweden)

    Marc-Oliver Adams

    Full Text Available Insect herbivory constitutes an important constraint in the viability and management of targeted reforestation sites. Focusing on young experimental stands at about 2000 m elevation in southern Ecuador, we examined foliar damage over one season as a function of tree species and habitat. Native tree species (Successional hardwood: Cedrela montana and Tabebuia chrysantha; fast-growing pioneer: Heliocarpus americanus have been planted among prevailing local landcover types (abandoned pasture, secondary shrub vegetation, and a Pinus patula plantation in 2003/4. Plantation trees were compared to conspecifics in the spontaneous undergrowth of adjacent undisturbed rainforest matched for height and foliar volume. Specifically, we tested the hypotheses that H. americanus as a pioneer species suffers more herbivory compared to the two successional tree species, and that damage is inversely related to habitat complexity. Overall leaf damage caused by folivorous insects (excluding leafcutter ants was low. Average leaf loss was highest among T. chrysantha (7.50% ± 0.19 SE of leaf area, followed by H. americanus (4.67% ± 0.18 SE and C. montana (3.18% ± 0.15 SE. Contrary to expectations, leaf area loss was highest among trees in closed-canopy natural rainforest, followed by pine plantation, pasture, and secondary shrub sites. Harvesting activity of leafcutter ants (Acromyrmex sp. was strongly biased towards T. chrysantha growing in open habitat (mean pasture: 2.5%; shrub: 10.5% where it could result in considerable damage (> 90.0%. Insect folivory is unlikely to pose a barrier for reforestation in the tropical Andean mountain forest zone at present, but leafcutter ants may become problematic if local temperatures increase in the wake of global warming.

  20. Targeted genome editing in Aedes aegypti using TALENs.

    Science.gov (United States)

    Aryan, Azadeh; Myles, Kevin M; Adelman, Zach N

    2014-08-15

    The Culicine mosquito, Aedes aegypti, is both a major vector of arthropod-borne viruses (arboviruses) and a genetic model organism for arbovirus transmission. TALE nucleases (TALENs), a group of artificial enzymes capable of generating site-specific DNA lesions, consist of a non-specific FokI endonuclease cleavage domain fused to an engineered DNA binding domain specific to a target site. While TALENs have become an important tool for targeted gene disruption in a variety of organisms, application to the mosquito genome is a new approach. We recently described the use of TALENs to perform heritable genetic disruptions in A. aegypti. Here, we provide detailed methods that will allow other research laboratories to capitalize on the potential of this technology for understanding mosquito gene function. We describe target site selection, transient embryo-based assays to rapidly assess TALEN activity, embryonic microinjection and downstream screening steps to identify target site mutations. Copyright © 2014 Elsevier Inc. All rights reserved.

  1. Identification of an allosteric binding site for RORγt inhibition

    Energy Technology Data Exchange (ETDEWEB)

    Scheepstra, Marcel; Leysen, Seppe; vanAlmen, Geert C.; Miller, J. Richard; Piesvaux, Jennifer; Kutilek, Victoria; van Eenennaam, Hans; Zhang, Hongjun; Barr, Kenneth; Nagpal, Sunil; Soisson, Stephen M.; Kornienko, Maria; Wiley, Kristen; Elsen, Nathaniel; Sharma, Sujata; Correll, Craig C.; Trotter, B. Wesley; van der Stelt, Mario; Oubrie, Arthur; Ottmann, Christian; Parthasarathy, Gopal; Brunsveld, Luc (Merck); (Eindhoven)

    2015-12-07

    RORγt is critical for the differentiation and proliferation of Th17 cells associated with several chronic autoimmune diseases. We report the discovery of a novel allosteric binding site on the nuclear receptor RORγt. Co-crystallization of the ligand binding domain (LBD) of RORγt with a series of small-molecule antagonists demonstrates occupancy of a previously unreported allosteric binding pocket. Binding at this non-canonical site induces an unprecedented conformational reorientation of helix 12 in the RORγt LBD, which blocks cofactor binding. The functional consequence of this allosteric ligand-mediated conformation is inhibition of function as evidenced by both biochemical and cellular studies. RORγt function is thus antagonized in a manner molecularly distinct from that of previously described orthosteric RORγt ligands. This brings forward an approach to target RORγt for the treatment of Th17-mediated autoimmune diseases. The elucidation of an unprecedented modality of pharmacological antagonism establishes a mechanism for modulation of nuclear receptors.

  2. The nucleolus: an emerging target for cancer therapy.

    Science.gov (United States)

    Hein, Nadine; Hannan, Katherine M; George, Amee J; Sanij, Elaine; Hannan, Ross D

    2013-11-01

    For over 100 years, pathologists have utilised an increase in size and number of nucleoli, the subnuclear site of ribosome synthesis, as a marker of aggressive tumours. Despite this, the contribution of the nucleolus and ribosomal RNA synthesis to cancer has been largely overlooked. This concept has recently changed with the demonstration that the nucleolus indirectly controls numerous other cellular functions, in particular, the cellular activity of the critical tumour suppressor protein, p53. Moreover, selective inhibition of ribosomal gene transcription in the nucleolus has been shown to be an effective therapeutic strategy to promote cancer-specific activation of p53. This article reviews the largely untapped potential of the nucleolus and ribosomal gene transcription as exciting new targets for cancer therapy. Copyright © 2013 Elsevier Ltd. All rights reserved.

  3. Inference of miRNA targets using evolutionary conservation and pathway analysis

    Directory of Open Access Journals (Sweden)

    van Nimwegen Erik

    2007-03-01

    Full Text Available Abstract Background MicroRNAs have emerged as important regulatory genes in a variety of cellular processes and, in recent years, hundreds of such genes have been discovered in animals. In contrast, functional annotations are available only for a very small fraction of these miRNAs, and even in these cases only partially. Results We developed a general Bayesian method for the inference of miRNA target sites, in which, for each miRNA, we explicitly model the evolution of orthologous target sites in a set of related species. Using this method we predict target sites for all known miRNAs in flies, worms, fish, and mammals. By comparing our predictions in fly with a reference set of experimentally tested miRNA-mRNA interactions we show that our general method performs at least as well as the most accurate methods available to date, including ones specifically tailored for target prediction in fly. An important novel feature of our model is that it explicitly infers the phylogenetic distribution of functional target sites, independently for each miRNA. This allows us to infer species-specific and clade-specific miRNA targeting. We also show that, in long human 3' UTRs, miRNA target sites occur preferentially near the start and near the end of the 3' UTR. To characterize miRNA function beyond the predicted lists of targets we further present a method to infer significant associations between the sets of targets predicted for individual miRNAs and specific biochemical pathways, in particular those of the KEGG pathway database. We show that this approach retrieves several known functional miRNA-mRNA associations, and predicts novel functions for known miRNAs in cell growth and in development. Conclusion We have presented a Bayesian target prediction algorithm without any tunable parameters, that can be applied to sequences from any clade of species. The algorithm automatically infers the phylogenetic distribution of functional sites for each miRNA, and

  4. EphrinA4 mimetic peptide targeted to EphA binding site impairs the formation of long-term fear memory in lateral amygdala.

    Science.gov (United States)

    Dines, M; Lamprecht, R

    2014-09-30

    Fear conditioning leads to long-term fear memory formation and is a model for studying fear-related psychopathologies conditions such as phobias and posttraumatic stress disorder. Long-term fear memory formation is believed to involve alterations of synaptic efficacy mediated by changes in synaptic transmission and morphology in lateral amygdala (LA). EphrinA4 and its cognate Eph receptors are intimately involved in regulating neuronal morphogenesis, synaptic transmission and plasticity. To assess possible roles of ephrinA4 in fear memory formation we designed and used a specific inhibitory ephrinA4 mimetic peptide (pep-ephrinA4) targeted to EphA binding site. We show that this peptide, composed of the ephrinA4 binding domain, interacts with EphA4 and inhibits ephrinA4-induced phosphorylation of EphA4. Microinjection of the pep-ephrinA4 into rat LA 30 min before training impaired long- but not short-term fear conditioning memory. Microinjection of a control peptide derived from a nonbinding E helix site of ephrinA4, that does not interact with EphA, had no effect on fear memory formation. Microinjection of pep-ephrinA4 into areas adjacent to the amygdala had no effect on fear memory. Acute systemic administration of pep-ephrinA4 1 h after training also impaired long-term fear conditioning memory formation. These results demonstrate that ephrinA4 binding sites in LA are essential for long-term fear memory formation. Moreover, our research shows that ephrinA4 binding sites may serve as a target for pharmacological treatment of fear and anxiety disorders.

  5. Site-specific quantification of lysine acetylation in the N-terminal tail of histone H4 using a double-labelling, targeted UHPLC MS/MS approach

    NARCIS (Netherlands)

    D'Urzo, Annalisa; Boichenko, Alexander P.; van den Bosch, Thea; Hermans, Jos; Dekker, Frank; Andrisano, Vincenza; Bischoff, Rainer

    We developed a targeted liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the site-specific quantification of lysine acetylation in the N-terminal region of histone H4 by combining chemical derivatization at the protein and peptide levels with digestion using chymotrypsin and

  6. Description of the Northwest hazardous waste site data base and preliminary analysis of site characteristics

    International Nuclear Information System (INIS)

    Woodruff, D.L.; Hartz, K.E.; Triplett, M.B.

    1988-08-01

    The Northwest Hazardous Waste RD and D Center (the Center) conducts research, development, and demonstration (RD and D) activities for hazardous and radioactive mixed-waste technologies applicable to remediating sites in the states of Idaho, Montana, Oregon, and Washington. To properly set priorities for these RD and D activities and to target development efforts it is necessary to understand the nature of the sites requiring remediation. A data base of hazardous waste site characteristics has been constructed to facilitate this analysis. The data base used data from EPA's Region X Comprehensive Environmental Response, Compensation, and Liability Information System (CERCLIS) and from Preliminary Assessment/Site Investigation (PA/SI) forms for sites in Montana. The Center's data base focuses on two sets of sites--those on the National Priorities List (NPL) and other sites that are denoted as ''active'' CERCLIS sites. Active CERCLIS sites are those sites that are undergoing active investigation and analysis. The data base contains information for each site covering site identification and location, type of industry associated with the site, waste categories present (e.g., heavy metals, pesticides, etc.), methods of disposal (e.g., tanks, drums, land, etc.), waste forms (e.g., liquid, solid, etc.), and hazard targets (e.g., surface water, groundwater, etc.). As part of this analysis, the Northwest region was divided into three geographic subregions to identify differences in disposal site characteristics within the Northwest. 2 refs., 18 figs., 5 tabs

  7. Public participation in decision-making for contaminated sites

    International Nuclear Information System (INIS)

    Till, J.E.; Sharp, S.L.

    2000-01-01

    Public participation is critical in environmental decision-making. This paper provides three examples of public participation in the decision making process. The first example illustrates the effectiveness of public involvement when incorporated at the beginning of a project. The second example shows the loss of trust by a community resulting from the lack of public involvement. The third example demonstrates public involvement in making risk-based decisions for corrective action in a non-radiological situation. The first site is the Los Alamos National Laboratory where a lawsuit filed by local citizens led to an independent audit of the laboratory's compliance with the Clean Air Act for radionuclides. The audit team involved the public extensively, resulting in close interaction during the audit and a better understanding by the public of the regulations. The second site is the Rocky Flats Plant nuclear weapons facility, which is being decommissioned and the surrounding property will ultimately be available for public use. The Department of Energy proposed a cleanup level but the level was developed with little public input and has been criticized widely by local residents. As a result, the target cleanup levels are being reevaluated by an independent contractor with oversight from a panel of local members of the public. Working with the independent contractor, the panel proposed new cleanup standards to the Department of Energy. The third site is a bulk oil and terminal where chemicals have migrated offsite into a residential area. Facility owners have initiated a public involvement program to help the community understand the potential risks involved and alternatives for remedial action. The public is playing a key role in the risk-based decision making process. Each of these examples illustrates the importance of public participation in different situations. (author)

  8. Hydrologic Synthesis Across the Critical Zone Observatory Network: A Step Towards Understanding the Coevolution of Critical Zone Function and Structure

    Science.gov (United States)

    Wlostowski, A. N.; Harman, C. J.; Molotch, N. P.

    2017-12-01

    The physical and biological architecture of the Earth's Critical Zone controls hydrologic partitioning, storage, and chemical evolution of precipitated water. The Critical Zone Observatory (CZO) Network provides an ideal platform to explore linkages between catchment structure and hydrologic function across a gradient of geologic and climatic settings. A legacy of hypothesis-motivated research at each site has generated a wealth of data characterizing the architecture and hydrologic function of the critical zone. We will present a synthesis of this data that aims to elucidate and explain (in the sense of making mutually intelligible) variations in hydrologic function across the CZO network. Top-down quantitative signatures of the storage and partitioning of water at catchment scales extracted from precipitation, streamflow, and meteorological data will be compared with each other, and provide quantitative benchmarks to assess differences in perceptual models of hydrologic function at each CZO site. Annual water balance analyses show that CZO sites span a wide gradient of aridity and evaporative partitioning. The aridity index (PET/P) ranges from 0.3 at Luquillo to 4.3 at Reynolds Creek, while the evaporative index (E/P) ranges from 0.3 at Luquillo (Rio Mamayes) to 0.9 at Reynolds Creek (Reynolds Creek Outlet). Snow depth and SWE observations reveal that snowpack is an important seasonal storage reservoir at three sites: Boulder, Jemez, Reynolds Creek and Southern Sierra. Simple dynamical models are also used to infer seasonal patterns of subsurface catchment storage. A root-zone water balance model reveals unique seasonal variations in plant-available water storage. Seasonal patterns of plant-available storage are driven by the asynchronicity of seasonal precipitation and evaporation cycles. Catchment sensitivity functions are derived at each site to infer relative changes in hydraulic storage (the apparent storage reservoir responsible for modulating streamflow

  9. Comparative studies of the endonucleases from two related Xenopus laevis retrotransposons, Tx1L and Tx2L: target site specificity and evolutionary implications.

    Science.gov (United States)

    Christensen, S; Pont-Kingdon, G; Carroll, D

    2000-01-01

    In the genome of the South African frog, Xenopus laevis, there are two complex families of transposable elements, Tx1 and Tx2, that have identical overall structures, but distinct sequences. In each family there are approximately 1500 copies of an apparent DNA-based element (Tx1D and Tx2D). Roughly 10% of these elements in each family are interrupted by a non-LTR retrotransposon (Tx1L and Tx2L). Each retrotransposon is flanked by a 23-bp target duplication of a specific D element sequence. In earlier work, we showed that the endonuclease domain (Tx1L EN) located in the second open reading frame (ORF2) of Tx1L encodes a protein that makes a single-strand cut precisely at the expected site within its target sequence, supporting the idea that Tx1L is a site-specific retrotransposon. In this study, we express the endonuclease domain of Tx2L (Tx2L EN) and compare the target preferences of the two enzymes. Each endonuclease shows some preference for its cognate target, on the order of 5-fold over the non-cognate target. The observed discrimination is not sufficient, however, to explain the observation that no cross-occupancy is observed - that is, L elements of one family have never been found within D elements of the other family. Possible sources of additional specificity are discussed. We also compare two hypotheses regarding the genome duplication event that led to the contemporary pseudotetraploid character of Xenopus laevis in light of the Tx1L and Tx2L data.

  10. Characterization of a Highly Conserved Binding Site of Mlh1 Required for Exonuclease I-Dependent Mismatch Repair

    DEFF Research Database (Denmark)

    Dherin, Claudine; Gueneau, Emeric; Francin, Mathilde

    2009-01-01

    Mlh1 is an essential factor of mismatch repair (MMR) and meiotic recombination. It interacts through its C-terminal region with MutL homologs and proteins involved in DNA repair and replication. In this study, we identified the site of yeast Mlh1 critical for the interaction with Exo1, Ntg2......, and Sgs1 proteins, designated as site S2 by reference to the Mlh1/Pms1 heterodimerization site S1. We show that site S2 is also involved in the interaction between human MLH1 and EXO1 or BLM. Binding at this site involves a common motif on Mlh1 partners that we called the MIP-box for the Mlh1 interacting...... protein box. Direct and specific interactions between yeast Mlh1 and peptides derived from Exo1, Ntg2, and Sgs1 and between human MLH1 and peptide derived from EXO1 and BLM were measured with K(d) values ranging from 8.1 to 17.4 microM. In Saccharomyces cerevisiae, a mutant of Mlh1 targeted at site S2...

  11. Risk-based remediation of polluted sites: A critical perspective.

    Science.gov (United States)

    Kuppusamy, Saranya; Venkateswarlu, Kadiyala; Megharaj, Mallavarapu; Mayilswami, Srinithi; Lee, Yong Bok

    2017-11-01

    Sites contaminated with chemical pollutants represent a growing challenge, and remediation of such lands is of international concern. Risk-based land management (RBLM) is an emerging approach that integrates risk assessment practices with more traditional site-specific investigations and remediation activities. Developing countries are yet to adopt RBLM strategies for remediation. RBLM is considered to be practical, scientifically defensible and cost-efficient. However, it is inherently limited by: firstly, the accuracy of risk assessment models used; secondly, ramifications of the fact that they are more likely to leave contamination in place; and thirdly, uncertainties involved and having to consider the total concentrations of all contaminants in soils that overestimate the potential risks from exposure to the contaminants. Consideration of contaminant bioavailability as the underlying basis for risk assessment and setting remediation goals of those contaminated lands that pose a risk to environmental and human health may lead to the development of a more sophisticated risk-based approach. However, employing the bioavailability concept in RBLM has not been extensively studied and/or legalized. This review highlights the extent of global land contamination, and the concept of risk-based assessment and management of contaminated sites including its advantages and disadvantages. Furthermore, the concept of bioavailability-based RBLM strategy has been proposed, and the challenges of RBLM and the priority areas for future research are summarized. Thus, the present review may help achieve a better understanding and successful implementation of a sustainable bioavailability-based RBLM strategy. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Thermal-neutron multiple scattering: critical double scattering

    International Nuclear Information System (INIS)

    Holm, W.A.

    1976-01-01

    A quantum mechanical formulation for multiple scattering of thermal-neutrons from macroscopic targets is presented and applied to single and double scattering. Critical nuclear scattering from liquids and critical magnetic scattering from ferromagnets are treated in detail in the quasielastic approximation for target systems slightly above their critical points. Numerical estimates are made of the double scattering contribution to the critical magnetic cross section using relevant parameters from actual experiments performed on various ferromagnets. The effect is to alter the usual Lorentzian line shape dependence on neutron wave vector transfer. Comparison with corresponding deviations in line shape resulting from the use of Fisher's modified form of the Ornstein-Zernike spin correlations within the framework of single scattering theory leads to values for the critical exponent eta of the modified correlations which reproduce the effect of double scattering. In addition, it is shown that by restricting the range of applicability of the multiple scattering theory from the outset to critical scattering, Glauber's high energy approximation can be used to provide a much simpler and more powerful description of multiple scattering effects. When sufficiently close to the critical point, it provides a closed form expression for the differential cross section which includes all orders of scattering and has the same form as the single scattering cross section with a modified exponent for the wave vector transfer

  13. PATTERN BASED DETECTION OF POTENTIALLY DRUGGABLE BINDING SITES BY LIGAND SCREENING

    Directory of Open Access Journals (Sweden)

    Uttam Pal

    2018-03-01

    Full Text Available This article describes an innovative way of finding the potentially druggable sites on a target protein, which can be used for orthosteric and allosteric lead detection in a single virtual screening setup. Druggability estimation for an alternate binding site other than the canonical ligand-binding pocket of an enzyme is rewarding for several inherent benefits. Allostery is a direct and efficient way of regulating biomacromolecule function. The allosteric modulators can fine-tune protein mechanics. Besides, allosteric sites are evolutionarily less conserved/more diverse even in very similarly related proteins, thus, provides high degree of specificity in targeting a particular protein. Therefore, targeting of allosteric sites is gaining attention as an emerging strategy in rational drug design. However, the experimental approaches provide a limited degree of characterization of new allosteric sites. Computational approaches are useful to analyze and select potential allosteric sites for drug discovery. Here, the use of molecular docking, which has become an integral part of the drug discovery process, has been discussed to predict the druggability of novel allosteric sites as well as the active site on target proteins by ligand screening. Genetic algorithm was used for docking and the whole protein was placed in the search space. For each ligand in the library of small molecules, the genetic algorithm was run for multiple times to populate all the druggable sites in the target protein, which was then translated into two dimensional density maps or “patterns”. High density clusters were observed for lead like molecules in these pattern diagrams. Each cluster in such a pattern diagram indicated a plausible binding site and the density gave its druggability score in terms of weighted probabilities. The patterns were filtered to find the leads for each of the druggable sites on the target protein. Such a novel pattern based analysis of the

  14. Tank farms criticality safety manual

    International Nuclear Information System (INIS)

    FORT, L.A.

    2003-01-01

    This document defines the Tank Farms Contractor (TFC) criticality safety program, as required by Title 10 Code of Federal Regulations (CFR-), Subpart 830.204(b)(6), ''Documented Safety Analysis'' (10 CFR- 830.204 (b)(6)), and US Department of Energy (DOE) 0 420.1A, Facility Safety, Section 4.3, ''Criticality Safety.'' In addition, this document contains certain best management practices, adopted by TFC management based on successful Hanford Site facility practices. Requirements in this manual are based on the contractor requirements document (CRD) found in Attachment 2 of DOE 0 420.1A, Section 4.3, ''Nuclear Criticality Safety,'' and the cited revisions of applicable standards published jointly by the American National Standards Institute (ANSI) and the American Nuclear Society (ANS) as listed in Appendix A. As an informational device, requirements directly imposed by the CRD or ANSI/ANS Standards are shown in boldface. Requirements developed as best management practices through experience and maintained consistent with Hanford Site practice are shown in italics. Recommendations and explanatory material are provided in plain type

  15. Initial source and site characterization studies for the U.C. Santa Barbara campus

    Energy Technology Data Exchange (ETDEWEB)

    Archuleta, R.; Nicholson, C.; Steidl, J.; Gurrola, L.; Alex, C.; Cochran, E.; Ely, G.; Tyler, T. [University of California, Santa Barbara (United States)

    1997-12-01

    The University of California Campus-Laboratory Collaboration (CLC) project is an integrated 3 year effort involving Lawrence Livermore National Laboratory (LLNL) and four UC campuses - Los Angeles (UCLA), Riverside (UCR), Santa Barbara (UCSB), and San Diego (UCSD) - plus additional collaborators at San Diego State University (SDSU), at Los Alamos National Laboratory and in industry. The primary purpose of the project is to estimate potential ground motions from large earthquakes and to predict site-specific ground motions for one critical structure on each campus. This project thus combines the disciplines of geology, seismology, geodesy, soil dynamics, and earthquake engineering into a fully integrated approach. Once completed, the CLC project will provide a template to evaluate other buildings at each of the four UC campuses, as well as provide a methodology for evaluating seismic hazards at other critical sites in California, including other UC locations at risk from large earthquakes. Another important objective of the CLC project is the education of students and other professional in the application of this integrated, multidisciplinary, state-of-the-art approach to the assessment of earthquake hazard. For each campus targeted by the CLC project, the seismic hazard study will consist of four phases: Phase I - Initial source and site characterization, Phase II - Drilling, logging, seismic monitoring, and laboratory dynamic soil testing, Phase III - Modeling of predicted site-specific earthquake ground motions, and Phase IV - Calculations of 3D building response. This report cover Phase I for the UCSB campus and incudes results up through March 1997.

  16. Healthcare disparities in critical illness.

    Science.gov (United States)

    Soto, Graciela J; Martin, Greg S; Gong, Michelle Ng

    2013-12-01

    To summarize the current literature on racial and gender disparities in critical care and the mechanisms underlying these disparities in the course of acute critical illness. MEDLINE search on the published literature addressing racial, ethnic, or gender disparities in acute critical illness, such as sepsis, acute lung injury, pneumonia, venous thromboembolism, and cardiac arrest. Clinical studies that evaluated general critically ill patient populations in the United States as well as specific critical care conditions were reviewed with a focus on studies evaluating factors and contributors to health disparities. Study findings are presented according to their association with the prevalence, clinical presentation, management, and outcomes in acute critical illness. This review presents potential contributors for racial and gender disparities related to genetic susceptibility, comorbidities, preventive health services, socioeconomic factors, cultural differences, and access to care. The data are organized along the course of acute critical illness. The literature to date shows that disparities in critical care are most likely multifactorial involving individual, community, and hospital-level factors at several points in the continuum of acute critical illness. The data presented identify potential targets as interventions to reduce disparities in critical care and future avenues for research.

  17. Angiogenesis and vascular targeting: Relevance for hyperthermia

    DEFF Research Database (Denmark)

    Horsman, Michael R

    2008-01-01

    The creation of a functional blood supply from the normal tissue vasculature via the process of angiogenesis is critical for the continued growth and development of solid tumours. This importance has led to the concept of targeting the tumour vasculature as a therapeutic strategy, and two major...... types of vascular targeting agents (VTAs) have developed; those that inhibit the angiogenic process-angiogenesis inhibiting agents (AIAs)-and those that specifically damage the already established neovasculature-vascular disrupting agents (VDAs). The tumour vasculature also plays a critical role...

  18. Covalent binding of benzo(a)pyrene-diol-epoxide to histone H2A in rat liver nuclei: target site specificity

    International Nuclear Information System (INIS)

    Kurokawa, M.; MacLeod, M.C.

    1986-01-01

    The authors have recently found that 7r,8t-dihydroxy-9t,10t-oxy-7,8,9,10-tetrahydrobenzo(a)pyrene (BPDE-I), a strong carcinogen, binds selectively to histone H2A-2 variant in rat liver nuclei, using a high performance liquid chromatography (HPLC) system which can separate H4, H2B, 3 different fractions of H2A variants and 3 different H3 variants in an hour. Here the authors examined the binding site of BPDE-I to the H2A-2 variant. The H2A-2 variants were purified from the acid extracted core histones of rat liver nuclei treated with ( 3 H)-BPDE-I by the HPLC system with a semi-preparative Aquapore RP-300 column. HPLC analysis of cyanogen bromide treated-H2A-2, which has one methionine residue, showed that the binding site is located in C-terminal half of H2A-2. In addition, digestions with V8-protease, trypsin and different types of carboxypeptides suggested that there are some target amino acid residues for BPDE-I in the V8-proteolytic C-terminal octapeptide which contains 2 histadine and 3 lysine residues. Currently identification of the target amino acid is proceeding, using amino acid-BPDE adducts prepared in vitro

  19. Targeted modulation of reactive oxygen species in the vascular endothelium.

    Science.gov (United States)

    Shuvaev, Vladimir V; Muzykantov, Vladimir R

    2011-07-15

    'Endothelial cells lining vascular luminal surface represent an important site of signaling and injurious effects of reactive oxygen species (ROS) produced by other cells and endothelium itself in ischemia, inflammation and other pathological conditions. Targeted delivery of ROS modulating enzymes conjugated with antibodies to endothelial surface molecules (vascular immunotargeting) provides site-specific interventions in the endothelial ROS, unattainable by other formulations including PEG-modified enzymes. Targeting of ROS generating enzymes (e.g., glucose oxidase) provides ROS- and site-specific models of endothelial oxidative stress, whereas targeting of antioxidant enzymes SOD and catalase offers site-specific quenching of superoxide anion and H(2)O(2). These targeted antioxidant interventions help to clarify specific role of endothelial ROS in vascular and pulmonary pathologies and provide basis for design of targeted therapeutics for treatment of these pathologies. In particular, antibody/catalase conjugates alleviate acute lung ischemia/reperfusion injury, whereas antibody/SOD conjugates inhibit ROS-mediated vasoconstriction and inflammatory endothelial signaling. Encapsulation in protease-resistant, ROS-permeable carriers targeted to endothelium prolongs protective effects of antioxidant enzymes, further diversifying the means for targeted modulation of endothelial ROS. Copyright © 2011 Elsevier B.V. All rights reserved.

  20. Assessing Postgraduate Students' Critical Thinking Ability

    Science.gov (United States)

    Javed, Muhammad; Nawaz, Muhammad Atif; Qurat-Ul-Ain, Ansa

    2015-01-01

    This paper addresses to assess the critical thinking ability of postgraduate students. The target population was the male and female students at University level in Pakistan. A small sample of 45 male and 45 female students were selected randomly from The Islamia University of Bahawalpur, Pakistan. Cornell Critical Thinking Test Series, The…

  1. Detection and characterization of 3D-signature phosphorylation site motifs and their contribution towards improved phosphorylation site prediction in proteins

    Directory of Open Access Journals (Sweden)

    Selbig Joachim

    2009-04-01

    Full Text Available Abstract Background Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phosphorylation process is the recognition of specific target sites by protein kinases followed by the covalent attachment of phosphate groups to the amino acids serine, threonine, or tyrosine. The experimental identification as well as computational prediction of phosphorylation sites (P-sites has proved to be a challenging problem. Computational methods have focused primarily on extracting predictive features from the local, one-dimensional sequence information surrounding phosphorylation sites. Results We characterized the spatial context of phosphorylation sites and assessed its usability for improved phosphorylation site predictions. We identified 750 non-redundant, experimentally verified sites with three-dimensional (3D structural information available in the protein data bank (PDB and grouped them according to their respective kinase family. We studied the spatial distribution of amino acids around phosphorserines, phosphothreonines, and phosphotyrosines to extract signature 3D-profiles. Characteristic spatial distributions of amino acid residue types around phosphorylation sites were indeed discernable, especially when kinase-family-specific target sites were analyzed. To test the added value of using spatial information for the computational prediction of phosphorylation sites, Support Vector Machines were applied using both sequence as well as structural information. When compared to sequence-only based prediction methods, a small but consistent performance improvement was obtained when the prediction was informed by 3D-context information. Conclusion While local one-dimensional amino acid sequence information was observed to harbor most of the discriminatory power, spatial context information was identified as

  2. Polymeric micelles as a drug carrier for tumor targeting

    Directory of Open Access Journals (Sweden)

    Neha M Dand

    2013-01-01

    Full Text Available Polymeric micelle can be targeted to tumor site by passive and active mechanism. Some inherent properties of polymeric micelle such as size in nanorange, stability in plasma, longevity in vivo, and pathological characteristics of tumor make polymeric micelles to be targeted at the tumor site by passive mechanism called enhanced permeability and retention effect. Polymeric micelle formed from the amphiphilic block copolymer is suitable for encapsulation of poorly water soluble, hydrophobic anticancer drugs. Other characteristics of polymeric micelles such as separated functionality at the outer shell are useful for targeting the anticancer drug to tumor by active mechanisms. Polymeric micelles can be conjugated with many ligands such as antibodies fragments, epidermal growth factors, α2 -glycoprotein, transferrine, and folate to target micelles to cancer cells. Application of heat and ultrasound are the alternative methods to enhance drug accumulation in tumoral cells. Targeting using micelles can also be done to tumor angiogenesis which is the potentially promising target for anticancer drugs. This review summarizes about recently available information regarding targeting the anticancer drug to the tumor site using polymeric micelles.

  3. VEGF-B is dispensable for blood vessel growth but critical for their survival, and VEGF-B targeting inhibits pathological angiogenesis

    Science.gov (United States)

    Zhang, Fan; Tang, Zhongshu; Hou, Xu; Lennartsson, Johan; Li, Yang; Koch, Alexander W.; Scotney, Pierre; Lee, Chunsik; Arjunan, Pachiappan; Dong, Lijin; Kumar, Anil; Rissanen, Tuomas T.; Wang, Bin; Nagai, Nobuo; Fons, Pierre; Fariss, Robert; Zhang, Yongqing; Wawrousek, Eric; Tansey, Ginger; Raber, James; Fong, Guo-Hua; Ding, Hao; Greenberg, David A.; Becker, Kevin G.; Herbert, Jean-Marc; Nash, Andrew; Yla-Herttuala, Seppo; Cao, Yihai; Watts, Ryan J.; Li, Xuri

    2009-01-01

    VEGF-B, a homolog of VEGF discovered a long time ago, has not been considered an important target in antiangiogenic therapy. Instead, it has received little attention from the field. In this study, using different animal models and multiple types of vascular cells, we revealed that although VEGF-B is dispensable for blood vessel growth, it is critical for their survival. Importantly, the survival effect of VEGF-B is not only on vascular endothelial cells, but also on pericytes, smooth muscle cells, and vascular stem/progenitor cells. In vivo, VEGF-B targeting inhibited both choroidal and retinal neovascularization. Mechanistically, we found that the vascular survival effect of VEGF-B is achieved by regulating the expression of many vascular prosurvival genes via both NP-1 and VEGFR-1. Our work thus indicates that the function of VEGF-B in the vascular system is to act as a “survival,” rather than an “angiogenic” factor and that VEGF-B inhibition may offer new therapeutic opportunities to treat neovascular diseases. PMID:19369214

  4. OmniSearch: a semantic search system based on the Ontology for MIcroRNA Target (OMIT) for microRNA-target gene interaction data.

    Science.gov (United States)

    Huang, Jingshan; Gutierrez, Fernando; Strachan, Harrison J; Dou, Dejing; Huang, Weili; Smith, Barry; Blake, Judith A; Eilbeck, Karen; Natale, Darren A; Lin, Yu; Wu, Bin; Silva, Nisansa de; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming; Ruttenberg, Alan

    2016-01-01

    As a special class of non-coding RNAs (ncRNAs), microRNAs (miRNAs) perform important roles in numerous biological and pathological processes. The realization of miRNA functions depends largely on how miRNAs regulate specific target genes. It is therefore critical to identify, analyze, and cross-reference miRNA-target interactions to better explore and delineate miRNA functions. Semantic technologies can help in this regard. We previously developed a miRNA domain-specific application ontology, Ontology for MIcroRNA Target (OMIT), whose goal was to serve as a foundation for semantic annotation, data integration, and semantic search in the miRNA field. In this paper we describe our continuing effort to develop the OMIT, and demonstrate its use within a semantic search system, OmniSearch, designed to facilitate knowledge capture of miRNA-target interaction data. Important changes in the current version OMIT are summarized as: (1) following a modularized ontology design (with 2559 terms imported from the NCRO ontology); (2) encoding all 1884 human miRNAs (vs. 300 in previous versions); and (3) setting up a GitHub project site along with an issue tracker for more effective community collaboration on the ontology development. The OMIT ontology is free and open to all users, accessible at: http://purl.obolibrary.org/obo/omit.owl. The OmniSearch system is also free and open to all users, accessible at: http://omnisearch.soc.southalabama.edu/index.php/Software.

  5. The Use of the Profunda Femoral Artery as the Sole Target Vessel to Bypass Aortoiliac Disease in Patients with Critical Limb Ischemia and Concomitant Unreconstructable Infrainguinal Disease.

    Science.gov (United States)

    Kontopodis, Nikolaos; Lioudaki, Stella; Chronis, Christos; Kalogerakos, Paris; Lazopoulos, George; Papaioannou, Alexandra; Ioannou, Christos V

    2018-04-01

    Critical limb ischemia (CLI) often results from multilevel occlusive disease. There are occasions where a patent profunda femoral artery (PFA) is the only target artery that can be used as outflow during reconstruction to bypass aortoiliac disease (AOID), with no further option for infrainguinal revascularization. We aim to report results of the use of PFA as the sole target vessel for the treatment of these patients. This is a retrospective, single-center study including CLI patients treated during 36 months. All procedures were included regardless of inflow site. The outcomes examined were hemodynamic improvement, clinical status change, amputation-free and overall survival, and patency of the prosthesis. Univariate analysis was performed to identify possible predictors of adverse outcomes. Twenty-three patients and 27 limbs were included (2 female, mean age 70.6). Sixteen limbs presented rest pain and 11 tissue loss. Inflow was obtained from the axillary (n = 9), contralateral femoral (n = 8), abdominal aorta (n = 2), thoracic aorta (n = 1), ipsilateral external iliac (n = 2), and contralateral external iliac artery (n = 1). Immediately postoperatively ankle-brachial index significantly increased from 0.15 (0-0.5) to 0.50 (0.25-0.9), (P-value limbs presented clinical improvement (3 minimally, 18 moderately, and 3 markedly improved) and 3 presented no change. During a mean follow-up of 15.8 (2-36) months, we recorded 4 deaths and 4 major amputations. Mean predicted overall survival and amputation-free survival were 29.8 (95% confidence interval [CI] 24.5-35.1) and 26.5 months (95% CI 21.1-31.8), respectively. Predicted primary patency was 76% at 3 years. Univariate analysis revealed significant associations only between bypass patency and limp loss (P-value = 0.021). In the presence of CLI due to AOID and unreconstructable infrainguinal disease, the use of PFA as the sole target vessel during bypass is associated with significant rates of clinical

  6. Hanford Site Performance Report - March 1999

    International Nuclear Information System (INIS)

    EDER, D.M.

    2001-01-01

    The purpose of the Hanford Site Performance Report is to provide the Department of Energy Richland Operations Office's (DOE-RL's) report of Hanford's performance by: U.S. Department of Energy, Richland Operations Office, Project Hanford Management Contract (PHMC) through Fluor Daniel Hanford, Inc. (FDH) and its subcontractors, Environmental Restoration Contract through Bechtel Hanford, Inc. (BHI), and its subcontractors, and Pacific Northwest National Laboratories (PNNL) for Science and Technology (S and T) Mission and support to the Environmental Management (EM). This report is published monthly with the intent of relating work performance and progress in the context of the Success Indicators and Critical Success Factors as outlined in the Hanford Strategic Plan. On a quarterly basis, the report also addresses performance and progress related to the Science and Technology Mission's Critical Outcomes as derived from the Hanford Strategic Plan. Section A of this report is the Executive Summary, encapsulating high-level data in this report into an overall brief. Summary information provided includes Notable Accomplishments, a performance profile with associated analyses, Critical Issues, Key Integration Activities, and a ''quick list'' of Upcoming Key Events. Section B of this report, the Site Summary section, provides Environmental Management performance data specifically organized to the pertinent Critical Success Factors and Success Indicators, and Science and Technology data in the context of the Critical Outcomes. The Site Summary demonstrates the various missions' overall progress against these strategic objectives. The information is presented in both narrative and graphical formats. The remaining sections provide performance data relative to each individual mission area (e.g., Waste Management, Spent Nuclear Fuels, etc.). The information provided in the Mission Area sections is at a level of greater detail than is presented in either the Executive Summary or

  7. Hanford Site Performance Report - May 1999

    International Nuclear Information System (INIS)

    EDER, D.M.

    2001-01-01

    The purpose of the Hanford Site Performance Report is to provide the Department of Energy Richland Operations Office's (DOE-RL's) report of Hanford's performance by: U. S. Department of Energy, Richland Operations Office, Project Hanford Management Contract (PHMC) through Fluor Daniel Hanford, Inc. (FDH) and its subcontractors, Environmental Restoration Contract through Bechtel Hanford, Inc. (BHI), and its subcontractors, and Pacific Northwest National Laboratories (PNNL) for Science and Technology (S and T) Mission and support to the Environmental Management (EM). This report is published monthly with the intent of relating work performance and progress in the context of the Success Indicators and Critical Success Factors as outlined in the Hanford Strategic Plan. On a quarterly basis, the report also addresses performance and progress related to the Science and Technology Mission's Critical Outcomes as derived from the Hanford Strategic Plan. Section A of this report is the Executive Summary, encapsulating high-level data in this report into an overall brief. Summary information provided includes Notable Accomplishments, a performance profile with associated analyses, Critical Issues, Key Integration Activities, and a ''quick list'' of Upcoming Key Events. Section B of this report, the Site Summary section, provides Environmental Management performance data specifically organized to the pertinent Critical Success Factors and Success Indicators, and Science and Technology data in the context of the Critical Outcomes. The Site Summary demonstrates the various missions' overall progress against these strategic objectives. The information is presented in both narrative and graphical formats. The remaining sections provide performance data relative to each individual mission area (e.g., Waste Management, Spent Nuclear Fuels, etc.). The information provided in the Mission Area sections is at a level of greater detail than is presented in either the Executive Summary or

  8. Hanford Site Performance Report - April 1999

    International Nuclear Information System (INIS)

    EDER, D.M.

    2001-01-01

    The purpose of the Hanford Site Performance Report is to provide the Department of Energy Richland Operations Office's (DOE-RL's) report of Hanford's performance by: U.S. Department of Energy, Richland Operations Office, Project Hanford Management Contract (PHMC) through Fluor Daniel Hanford, Inc. (FDH) and its subcontractors, Environmental Restoration Contract through Bechtel Hanford, Inc. (BHI), and its subcontractors, and Pacific Northwest National Laboratories (PNNL) for Science and Technology (S and T) Mission and support to the Environmental Management (EM). This report is published monthly with the intent of relating work performance and progress in the context of the Success Indicators and Critical Success Factors as outlined in the Hanford Strategic Plan. On a quarterly basis, the report also addresses performance and progress related to the Science and Technology Mission's Critical Outcomes as derived from the Hanford Strategic Plan. Section A of this report is the Executive Summary, encapsulating high-level data in this report into an overall brief. Summary information provided includes Notable Accomplishments, a performance profile with associated analyses, Critical Issues, Key Integration Activities, and a ''quick list'' of Upcoming Key Events. Section B of this report, the Site Summary section, provides Environmental Management performance data specifically organized to the pertinent Critical Success Factors and Success Indicators, and Science and Technology data in the context of the Critical Outcomes. The Site Summary demonstrates the various missions' overall progress against these strategic objectives. The information is presented in both narrative and graphical formats. The remaining sections provide performance data relative to each individual mission area (e.g., Waste Management, Spent Nuclear Fuels, etc.). The information provided in the Mission Area sections is at a level of greater detail than is presented in either the Executive Summary or

  9. The Pim kinases: new targets for drug development.

    Science.gov (United States)

    Swords, Ronan; Kelly, Kevin; Carew, Jennifer; Nawrocki, Stefan; Mahalingam, Devalingam; Sarantopoulos, John; Bearss, David; Giles, Francis

    2011-12-01

    The three Pim kinases are a small family of serine/threonine kinases regulating several signaling pathways that are fundamental to cancer development and progression. They were first recognized as pro-viral integration sites for the Moloney Murine Leukemia virus. Unlike other kinases, they possess a hinge region which creates a unique binding pocket for ATP. Absence of a regulatory domain means that these proteins are constitutively active once transcribed. Pim kinases are critical downstream effectors of the ABL (ableson), JAK2 (janus kinase 2), and Flt-3 (FMS related tyrosine kinase 1) oncogenes and are required by them to drive tumorigenesis. Recent investigations have established that the Pim kinases function as effective inhibitors of apoptosis and when overexpressed, produce resistance to the mTOR (mammalian target of rapamycin) inhibitor, rapamycin . Overexpression of the PIM kinases has been reported in several hematological and solid tumors (PIM 1), myeloma, lymphoma, leukemia (PIM 2) and adenocarcinomas (PIM 3). As such, the Pim kinases are a very attractive target for pharmacological inhibition in cancer therapy. Novel small molecule inhibitors of the human Pim kinases have been designed and are currently undergoing preclinical evaluation.

  10. Nuclear criticality evacuation with telemonitoring and microprocessors

    International Nuclear Information System (INIS)

    Fergus, R.W.; Moe, H.J. Sr.

    1979-01-01

    At Argonne National Laboratory, criticality alarms are required at widely separated locations to evacuate personnel in case of accident while emergency teams or maintenance personnel respond from a central location. The system functions have been divided in a similar manner. The alarm site hardware can independently detect a criticality and sound the evacuation signal while general monitoring and routine tests are handled by a communication link to a central monitoring station. The radiation detectors and evacuation sounders at each site are interconnected by a common two conductor cable in a unique telemonitoring format. This format allows both control and data information to be received or transmitted at any point on the cable which can be up to 3000 meters total length. The site microprocessor maintains a current data table, detects several faults, drives a printer, and communicates with the central telemonitoring station. The radiation detectors are made with plastic scintillators and photomultiplier tubes operated in a constant current mode with a 4 decade measurement range. The detectors also respond within microseconds to the criticality radiation burst. These characteristics can be tested with an internal light emitting diode either completely with a manual procedure or routinely with a system test initiated by the central monitoring station. Although the system was developed for a criticality alarm which requires reliable and redundant features, the basic techniques are useable for other monitoring and instrumentation applications

  11. Management and Operational Control of Criticality

    Energy Technology Data Exchange (ETDEWEB)

    Daniels, J. T. [Authority Health and Safety Branch, United Kingdom Atomic Energy Authority, Risley, Lancs. (United Kingdom)

    1966-05-15

    The evidence of the six process criticality accidents that have been reported to date shows that, without exception, they have been due to the failure of operational controls. In no instance has a criticality accident in processing been due to the use of wrong data 01 inaccurate calculation. Criticality accidents are least likely to occur in the production stream and are more likely to be associated with ancillary equipment and operations. Important as correct criticality calculations are, there are many other considerations which require the exercise of judgement in establishing the operational environment. No operation involving fissile material should be permitted without a formal review resulting in a documented statement of (a) the environmental assessment, (b) the nuclear safety arguments which demonstrate safety under that environment, and (c) the operational requirements which will ensure the validity of (b) under the conditions of (a). To ensure the continued viability of the environmental assessment and the continued reliability of clearance conditions there should be close supervision by operating management, and periodic checks made by site nuclear safety staff. Additionally, there should be periodic and systematic examinations by competent persons who are not responsible to the overall management of the site. (author)

  12. Independent criticality safety evaluation of deposits in cooler equipment in Building K-31 at the Oak Ridge K-25 Site, Oak Ridge, Tennessee

    International Nuclear Information System (INIS)

    1996-10-01

    This report provides an independent assessment of nuclear criticality issues associated with uranium deposits in the West and East Coolers for the 6A Booster Station in Building K-31 at the Oak Ridge K-25 Site. This assessment investigates the applicability of the initial assumptions used by Lockheed Martin Energy Systems (Energy Systems) and evaluates criticality calculations previously completed by Energy Systems. The calculations were independently verified. Each component was evaluated for its ability to satisfy requirements for subcriticality and meet the double contingency principle. Facility walk downs, detailed neutronics analysis, and fault tree analysis (FTA) were performed. The facility walk downs provided a better understanding of the building condition and status, equipment configuration, and uranium deposit locations. The detailed neutronics analysis focused on system geometry and moderation levels applicable to the individual components. The FTA considered the annual rate of occurrence for the events identified as potential causes of criticality issues. This report also examines the advantages of using this type of evaluation to assess the removal process for additional components and equipment

  13. Different critical perinatal periods and hypothalamic sites of oestradiol action in the defeminisation of luteinising hormone surge and lordosis capacity in the rat.

    Science.gov (United States)

    Sakakibara, M; Deura, C; Minabe, S; Iwata, Y; Uenoyama, Y; Maeda, K-I; Tsukamura, H

    2013-03-01

    Female rats show a gonadotrophin-releasing hormone (GnRH)/luteinising hormone (LH) surge in the presence of a preovulatory level of oestrogen, whereas males do not because of brain defeminisation during the developmental period by perinatal oestrogen converted from androgen. The present study aimed to identify the site(s) of oestrogen action and the critical period for defeminising the mechanism regulating the GnRH/LH surge. Animals given perinatal treatments, such as steroidal manipulations, brain local implantation of oestradiol (E(2) ) or administration of an NMDA antagonist, were examined for their ability to show an E(2) -induced LH surge at adulthood. Lordosis behaviour was examined to compare the mechanisms defeminising the GnRH/LH surge and sexual behaviour. A single s.c. oestradiol-benzoate administration on either the day before birth (E21), the day of birth (D0) or day 5 (D5) postpartum completely abolished the E(2) -induced LH surge at adulthood in female rats, although the same treatment did not inhibit lordosis. Perinatal castration on E21 or D0 partially rescued the E2-induced LH surge in genetically male rats, whereas castration from E21 to D5 totally rescued lordosis. Neonatal E(2) implantation in the anterior hypothalamus including the anteroventral periventricular nucleus (AVPV)/preoptic area (POA) abolished the E(2) -induced LH surge in female rats, whereas E(2) implantation in the mid and posterior hypothalamic regions had no inhibitory effect on the LH surge. Lordosis was not affected by neonatal E(2) implantation in any hypothalamic regions. In male rats, neonatal NMDA antagonist treatment rescued lordosis but not the LH surge. Taken together, these results suggest that an anterior hypothalamic region such as the AVPV/POA region is a perinatal site of oestrogen action where the GnRH/LH regulating system is defeminised to abolish the oestrogen-induced surge. The mechanism for defeminisation of the GnRH/LH surge system might be different from

  14. Impact of non-target-site-resistance on herbicidal activity of imazamox on blackgrass (Alopecurus myosuroides Huds. in comparison to other ALS-graminicides

    Directory of Open Access Journals (Sweden)

    Sievernich, Bernd

    2014-02-01

    Full Text Available A black-grass (Alopecurus myosuroides Huds. resistance-monitoring conducted by BASF in 2010 - 2012 revealed a high number of accessions with resistance against imazamox. However, application of imazamoxbased products in a winter crop was limited to winter beans in France and United Kingdom only until the introduction of the Clearfield®-production system in autumn 2012 in winter oilseed rape. It is therefore assumed that the resistance mechanisms were probably selected by the frequent use of ACCase- and ALSinhibitors in winter crop rotations during the last 2 decades. Resistance level for each product-biotype combination was calculated according the “R”-classification system (S, R?, RR, RRR by directly comparing the product performance on a biotype versus untreated control. Majority of resistant biotypes did not show a target-site mutation at the known codon Pro197 or Trp574. In order to better evaluate the impact of Non-Target-Site-Resistance (NTSR on the activity of BEYOND (imazamox, ATLANTIS WG (mesosulfuron+iodosulfuron and ABAK (pyroxsulam, biotypes who have shown an ALS-target-site mutation were removed from further analysis. At the dose rate of 35 g ai/ha BEYOND provided good activity on susceptible biotypes of black-grass almost matching up with ATLANTIS WG and ABAK. However, activity of BEYOND declined stronger on biotypes classified as R? or RR for that product, while ATLANTIS WG and ABAK hardly showed any decline in control on this group of biotypes when applied at the recommended dose rate. It is assumed that the underlying NTSR-mechanism is not effective enough yet to confer resistance to ATLANTIS WG and ABAK, but on BEYOND. In contrast, biotypes classified as R? for ATLANTIS WG did show a stronger impact on the activity of BEYOND and ABAK then of ATLANTIS WG. These differences in control level probably do translate into differences in selection pressure as well.

  15. Target Site Recognition by a Diversity-Generating Retroelement

    OpenAIRE

    Guo, Huatao; Tse, Longping V.; Nieh, Angela W.; Czornyj, Elizabeth; Williams, Steven; Oukil, Sabrina; Liu, Vincent B.; Miller, Jeff F.

    2011-01-01

    Diversity-generating retroelements (DGRs) are in vivo sequence diversification machines that are widely distributed in bacterial, phage, and plasmid genomes. They function to introduce vast amounts of targeted diversity into protein-encoding DNA sequences via mutagenic homing. Adenine residues are converted to random nucleotides in a retrotransposition process from a donor template repeat (TR) to a recipient variable repeat (VR). Using the Bordetella bacteriophage BPP-1 element as a prototype...

  16. A Rationally Designed Agonist Defines Subfamily IIIA Abscisic Acid Receptors As Critical Targets for Manipulating Transpiration.

    Science.gov (United States)

    Vaidya, Aditya S; Peterson, Francis C; Yarmolinsky, Dmitry; Merilo, Ebe; Verstraeten, Inge; Park, Sang-Youl; Elzinga, Dezi; Kaundal, Amita; Helander, Jonathan; Lozano-Juste, Jorge; Otani, Masato; Wu, Kevin; Jensen, Davin R; Kollist, Hannes; Volkman, Brian F; Cutler, Sean R

    2017-11-17

    Increasing drought and diminishing freshwater supplies have stimulated interest in developing small molecules that can be used to control transpiration. Receptors for the plant hormone abscisic acid (ABA) have emerged as key targets for this application, because ABA controls the apertures of stomata, which in turn regulate transpiration. Here, we describe the rational design of cyanabactin, an ABA receptor agonist that preferentially activates Pyrabactin Resistance 1 (PYR1) with low nanomolar potency. A 1.63 Å X-ray crystallographic structure of cyanabactin in complex with PYR1 illustrates that cyanabactin's arylnitrile mimics ABA's cyclohexenone oxygen and engages the tryptophan lock, a key component required to stabilize activated receptors. Further, its sulfonamide and 4-methylbenzyl substructures mimic ABA's carboxylate and C6 methyl groups, respectively. Isothermal titration calorimetry measurements show that cyanabactin's compact structure provides ready access to high ligand efficiency on a relatively simple scaffold. Cyanabactin treatments reduce Arabidopsis whole-plant stomatal conductance and activate multiple ABA responses, demonstrating that its in vitro potency translates to ABA-like activity in vivo. Genetic analyses show that the effects of cyanabactin, and the previously identified agonist quinabactin, can be abolished by the genetic removal of PYR1 and PYL1, which form subclade A within the dimeric subfamily III receptors. Thus, cyanabactin is a potent and selective agonist with a wide spectrum of ABA-like activities that defines subfamily IIIA receptors as key target sites for manipulating transpiration.

  17. Site description of Forsmark at completion of the site investigation phase. SDM-Site Forsmark

    Energy Technology Data Exchange (ETDEWEB)

    2008-12-15

    north-western part of the candidate area lacks hydraulically conductive, gently dipping fracture zones at potential repository depth and was selected as the target area for the complete site investigation work, following the initial investigations at the site. Prior to the presentation of the SDM-Site report, three versions of a site descriptive model have been completed for the Forsmark area and presented for peer review. The last version, referred to as version 1.2, was a preliminary site description that concluded the initial site investigation work and was presented in 2005. This preliminary site description formed the basis for a preliminary safety evaluation (PSE) of the Forsmark area, a preliminary repository layout (step D1), and the first evaluation of the long-term safety of this layout for KBS-3 repositories in the context of the SR-Can project. The final site descriptive model, SDM-Site, builds on a coordinated geological model in 3D, into which other discipline-specific models have been integrated without any major conflicting interpretations. In particular, the thermal properties of the bedrock at the site have been coupled to identified rock domains in the geological model and an integrated model that links the current stress regime, the hydrogeology and the chemistry of the groundwater to fracture domains and fracture zones in the geological model has evolved. These mutually consistent results demonstrate that a fundamental understanding of the current state of conditions and the on-going processes in the Forsmark area, from the surface down to potential repository depth, has been achieved. In addition, the properties of the area can be explained in the context of an understanding of the past evolution, throughout a long period of geological history. This integrated understanding of the area is presented in chapter 11 of this report and this chapter serves as an executive summary. A systematic assessment of the confidence in the model, including

  18. Site description of Forsmark at completion of the site investigation phase. SDM-Site Forsmark

    International Nuclear Information System (INIS)

    2008-12-01

    north-western part of the candidate area lacks hydraulically conductive, gently dipping fracture zones at potential repository depth and was selected as the target area for the complete site investigation work, following the initial investigations at the site. Prior to the presentation of the SDM-Site report, three versions of a site descriptive model have been completed for the Forsmark area and presented for peer review. The last version, referred to as version 1.2, was a preliminary site description that concluded the initial site investigation work and was presented in 2005. This preliminary site description formed the basis for a preliminary safety evaluation (PSE) of the Forsmark area, a preliminary repository layout (step D1), and the first evaluation of the long-term safety of this layout for KBS-3 repositories in the context of the SR-Can project. The final site descriptive model, SDM-Site, builds on a coordinated geological model in 3D, into which other discipline-specific models have been integrated without any major conflicting interpretations. In particular, the thermal properties of the bedrock at the site have been coupled to identified rock domains in the geological model and an integrated model that links the current stress regime, the hydrogeology and the chemistry of the groundwater to fracture domains and fracture zones in the geological model has evolved. These mutually consistent results demonstrate that a fundamental understanding of the current state of conditions and the on-going processes in the Forsmark area, from the surface down to potential repository depth, has been achieved. In addition, the properties of the area can be explained in the context of an understanding of the past evolution, throughout a long period of geological history. This integrated understanding of the area is presented in chapter 11 of this report and this chapter serves as an executive summary. A systematic assessment of the confidence in the model, including

  19. DeepMirTar: a deep-learning approach for predicting human miRNA targets.

    Science.gov (United States)

    Wen, Ming; Cong, Peisheng; Zhang, Zhimin; Lu, Hongmei; Li, Tonghua

    2018-06-01

    MicroRNAs (miRNAs) are small noncoding RNAs that function in RNA silencing and post-transcriptional regulation of gene expression by targeting messenger RNAs (mRNAs). Because the underlying mechanisms associated with miRNA binding to mRNA are not fully understood, a major challenge of miRNA studies involves the identification of miRNA-target sites on mRNA. In silico prediction of miRNA-target sites can expedite costly and time-consuming experimental work by providing the most promising miRNA-target-site candidates. In this study, we reported the design and implementation of DeepMirTar, a deep-learning-based approach for accurately predicting human miRNA targets at the site level. The predicted miRNA-target sites are those having canonical or non-canonical seed, and features, including high-level expert-designed, low-level expert-designed, and raw-data-level, were used to represent the miRNA-target site. Comparison with other state-of-the-art machine-learning methods and existing miRNA-target-prediction tools indicated that DeepMirTar improved overall predictive performance. DeepMirTar is freely available at https://github.com/Bjoux2/DeepMirTar_SdA. lith@tongji.edu.cn, hongmeilu@csu.edu.cn. Supplementary data are available at Bioinformatics online.

  20. Discovery of Nigri/nox and Panto/pox site-specific recombinase systems facilitates advanced genome engineering.

    Science.gov (United States)

    Karimova, Madina; Splith, Victoria; Karpinski, Janet; Pisabarro, M Teresa; Buchholz, Frank

    2016-07-22

    Precise genome engineering is instrumental for biomedical research and holds great promise for future therapeutic applications. Site-specific recombinases (SSRs) are valuable tools for genome engineering due to their exceptional ability to mediate precise excision, integration and inversion of genomic DNA in living systems. The ever-increasing complexity of genome manipulations and the desire to understand the DNA-binding specificity of these enzymes are driving efforts to identify novel SSR systems with unique properties. Here, we describe two novel tyrosine site-specific recombination systems designated Nigri/nox and Panto/pox. Nigri originates from Vibrio nigripulchritudo (plasmid VIBNI_pA) and recombines its target site nox with high efficiency and high target-site selectivity, without recombining target sites of the well established SSRs Cre, Dre, Vika and VCre. Panto, derived from Pantoea sp. aB, is less specific and in addition to its native target site, pox also recombines the target site for Dre recombinase, called rox. This relaxed specificity allowed the identification of residues that are involved in target site selectivity, thereby advancing our understanding of how SSRs recognize their respective DNA targets.

  1. Geographic spread, genetics and functional characteristics of ryanodine receptor based target-site resistance to diamide insecticides in diamondback moth, Plutella xylostella.

    Science.gov (United States)

    Steinbach, Denise; Gutbrod, Oliver; Lümmen, Peter; Matthiesen, Svend; Schorn, Corinna; Nauen, Ralf

    2015-08-01

    Anthranilic diamides and flubendiamide belong to a new chemical class of insecticides acting as conformation sensitive activators of the insect ryanodine receptor (RyR). These compounds control a diverse range of different herbivorous insects including diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae), a notorious global pest on cruciferous crops, which recently developed resistance due to target-site mutations located in the trans-membrane domain of the Plutella RyR. In the present study we further investigated the genetics and functional implications of a RyR G4946E target-site mutation we recently identified in a Philippine diamondback moth strain (Sudlon). Strain Sudlon is homozygous for the G4946E mutation and has been maintained under laboratory conditions without selection pressure for almost four years, and still exhibit stable resistance ratios of >2000-fold to all commercial diamides. Its F1 progeny resulting from reciprocal crosses with a susceptible strain (BCS-S) revealed no maternal effects and a diamide susceptible phenotype, suggesting an autosomally almost recessive mode of inheritance. Subsequent back-crosses indicate a near monogenic nature of the diamide resistance in strain Sudlon. Radioligand binding studies with Plutella thoracic microsomal membrane preparations provided direct evidence for the dramatic functional implications of the RyR G4946E mutation on both diamide specific binding and its concentration dependent modulation of [(3)H]ryanodine binding. Computational modelling based on a cryo-EM structure of rabbit RyR1 suggests that Plutella G4946E is located in trans-membrane helix S4 close to S4-S5 linker domain supposed to be involved in the modulation of the voltage sensor, and another recently described mutation, I4790M in helix S2 approx. 13 Å opposite of G4946E. Genotyping by pyrosequencing revealed the presence of the RyR G4946E mutation in larvae collected in 2013/14 in regions of ten different countries where

  2. Correction: Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges.

    Science.gov (United States)

    Martínez-Araya, Jorge Ignacio; Grand, André; Glossman-Mitnik, Daniel

    2016-01-28

    Correction for 'Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges' by Jorge Ignacio Martínez-Araya et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c5cp03822g.

  3. CERCLA site assessment workbook

    International Nuclear Information System (INIS)

    1994-08-01

    This contains comments for each chapter of exercises (in Vol. 1) which illustrate how to conduct site assessments for CERCLA regulation. A through analysis of the exercises is provided so that work and solutions from Vol 1 can be critiqued and comments are also included on the strategy of site assessment whereas the exercises illustrate the principles involved. Covered exercises include the following: A preliminary assessment of a ground water site; waste characteristics and characterization of sources; documentation of observed releases and actual contamination of targets; the strategy of an SI at a surface water site; the soil exposure pathway; the air pathway

  4. Site-specific antibody-liposome conjugation through copper-free click chemistry: a molecular biology approach for targeted photodynamic therapy (Conference Presentation)

    Science.gov (United States)

    Obaid, Girgis; Wang, Yucheng; Kuriakose, Jerrin; Broekgaarden, Mans; Alkhateeb, Ahmed; Bulin, Anne-Laure; Hui, James; Tsourkas, Andrew; Hasan, Tayyaba

    2016-03-01

    Nanocarriers, such as liposomes, have the ability to potentiate photodynamic therapy (PDT) treatment regimens by the encapsulation of high payloads of photosensitizers and enhance their passive delivery to tumors through the enhanced permeability and retention effect. By conjugating targeting moieties to the surface of the liposomal nanoconstructs, cellular selectivity is imparted on them and PDT-based therapies can be performed with significantly higher dose tolerances, as off-target toxicity is simultaneously reduced.1 However, the maximal benefits of conventional targeted nanocarriers, including liposomes, are hindered by practical limitations including chemical instability, non-selective conjugation chemistry, poor control over ligand orientation, and loss of ligand functionality following conjugation, amongst others.2 We have developed a robust, physically and chemically stable liposomal nanoplatform containing benzoporphyrin derivative photosensitizer molecules within the phospholipid bilayer and an optimized surface density of strained cyclooctyne moieties for `click' conjugation to azido-functionalized antibodies.3 The clinical chimeric anti-EGFR antibody Cetuximab is site-specifically photocrosslinked to a recombinant bioengineered that recognizes the antibody's Fc region, containing a terminal azide.4 The copper-free click conjugation of the bioengineered Cetuximab derivative to the optimized photosensitizing liposome provides exceptional control over the antibody's optimal orientation for cellular antigen binding. Importantly, the reaction occurs rapidly under physiological conditions, bioorthogonally (selectively in the presence of other biomolecules) and without the need for toxic copper catalysis.3 Such state-of-the-art conjugation strategies push the boundaries of targeted photodynamic therapy beyond the limitations of traditional chemical coupling techniques to produce more robust and effective targeted therapeutics with applications beyond

  5. Metformin: An Old Taboo yet a New Friend for Targeted Glucose Control in Critically Ill Patients

    Directory of Open Access Journals (Sweden)

    Sarvi Sanaie

    2016-04-01

    metformin may be associated with the best results only if added prior to the initial hyperinflammatory response and might have detrimental effects if added during hypoactive phase9,10. Timing of metformin administration may be an important factor contributing to its effect in critically ill patients. Finally, in patients with refractoriness to insulin who require high doses of insulin, metformin could be used as a safe adjunct therapy to reach targeted glucose levels. Metformin plus insulin appears to lower the incidence of insulin resistance, insulin requirements while maintaining blood glucose level control, and consequently the incidence of adverse effects related to high-dose insulin therapy, particularly hypoglycaemia. Declined nursing workload is also considered a major benefit.  However, two important items should be noted: first, timing of drug administration and second, characteristics of the patients like renal function, hypoperfusion status and monitoring of drug complications.

  6. Uncertainties in thick-target PIXE analysis

    International Nuclear Information System (INIS)

    Campbell, J.L.; Cookson, J.A.; Paul, H.

    1983-01-01

    Thick-target PIXE analysis insolves uncertainties arising from the calculation of thick-target X-ray production in addition to the usual PIXE uncertainties. The calculation demands knowledge of ionization cross-sections, stopping powers and photon attenuation coefficients. Information on these is reviewed critically and a computational method is used to estimate the uncertainties transmitted from this data base into results of thick-target PIXE analyses with reference to particular specimen types using beams of 2-3 MeV protons. A detailed assessment of the accuracy of thick-target PIXE is presented. (orig.)

  7. CTBT on-site inspections

    Science.gov (United States)

    Zucca, J. J.

    2014-05-01

    On-site inspection (OSI) is a critical part of the verification regime for the Comprehensive Nuclear-Test-Ban Treaty (CTBT). The OSI verification regime provides for international inspectors to make a suite of measurements and observations on site at the location of an event of interest. The other critical component of the verification regime is the International Monitoring System (IMS), which is a globally distributed network of monitoring stations. The IMS along with technical monitoring data from CTBT member countries, as appropriate, will be used to trigger an OSI. After the decision is made to carry out an OSI, it is important for the inspectors to deploy to the field site rapidly to be able to detect short-lived phenomena such as the aftershocks that may be observable after an underground nuclear explosion. The inspectors will be on site from weeks to months and will be working with many tens of tons of equipment. Parts of the OSI regime will be tested in a field exercise in the country of Jordan late in 2014. The build-up of the OSI regime has been proceeding steadily since the CTBT was signed in 1996 and is on track to becoming a deterrent to someone considering conducting a nuclear explosion in violation of the Treaty.

  8. Calcination/dissolution testing for Hanford Site tank wastes

    International Nuclear Information System (INIS)

    Colby, S.A.; Delegard, C.H.; McLaughlin, D.F.; Danielson, M.J.

    1994-07-01

    Thermal treatment by calcination offers several benefits for the treatment of Hanford Site tank wastes, including the destruction of organics and ferrocyanides and an hydroxide fusion that permits the bulk of the mostly soluble nonradioactive constituents to be easily separated from the insoluble transuranic residue. Critical design parameters were tested, including: (1) calciner equipment design, (2) hydroxide fusion chemistry, and (3) equipment corrosion. A 2 gal/minute pilot plant processed a simulated Tank 101-SY waste and produced a free flowing 700 C molten calcine with an average calciner retention time of 20 minutes and >95% organic, nitrate, and nitrite destruction. Laboratory experiments using actual radioactive tank waste and the simulated waste pilot experiments indicate that 98 wt% of the calcine produced is soluble in water, leaving an insoluble transuranic fraction. All of the Hanford Site tank wastes can benefit from calcination/dissolution processing, contingent upon blending various tank waste types to ensure a target of 70 wt% sodium hydroxide/nitrate/nitrite fluxing agent. Finally, corrosion testing indicates that a jacketed nickel liner cooled to below 400 C would corrode <2 mil/year (0.05 mm/year) from molten calcine attack

  9. EFFECTIVNESS OF TARGET ANTIMICROBIAL THERAPY OF SEVERE CHRONIC PERIODONTITIS PART I: REDUCTION OF GINGIVAL INFLAMATION AND ACTIVE PERIODONTAL DISEASE SITES

    Directory of Open Access Journals (Sweden)

    Kamen Kotsilkov

    2010-10-01

    Full Text Available The correlation between recurrent bleeding on probing and the progression of periodontal destruction is suggested in many studies. One of the main goals of the periodontal treatment is the achievement of good control of the gingival inflammation and the reduction of the active periodontal sites.Aim: Evaluation of the effectiveness of treatment of severe chronic periodontitis with additional target antibiotic administration in comparison with the therapy with adjunctive antimicrobial combination amoxicillin + metronidazole and conventional mechanical periodontal treatment regarding the achieved control of the gingival inflammation and BoP.Results: Significant reduction of the gingival bleeding and the BoP is achieved in all groups. In the group with target antibiotic administration the final mean values of the GB (gingival bleeding and BoP (bleeding on probing are the lowest and could suggest a low risk for progression of the periodontal disease.

  10. MicroRNA-467g inhibits new bone regeneration by targeting Ihh/Runx-2 signaling.

    Science.gov (United States)

    Kureel, Jyoti; John, Aijaz A; Dixit, Manisha; Singh, Divya

    2017-04-01

    MicroRNAs are important post transcriptional regulators of gene expression and play critical role in osteoblast differentiation. In this study we report miR-467g, an uncharacterized novel miRNA, in regulation of osteoblast functions. Over-expression of miR-467g inhibited osteoblast differentiation. Target prediction analysis tools and experimental validation by luciferase 3' UTR reporter assay identified Runx-2 as a direct target of miR-467g. Over expression of miR-467g in osteoblasts down regulated Runx-2 and Ihh signaling components. Furthermore, silencing of miR-467g was done to see its role in Ihh and Runx-2 mediated bone healing and regeneration in a drill hole injury model in BALB/c mice. Silencing of miR-467g led to significant increase in new bone regeneration and Ihh and Runx-2 localization at injury site in a day dependent manner. In conclusion, miR-467g negatively regulates osteogenesis by targeting Ihh/Runx-2 signaling. We, thus, propose that therapeutic approaches targeting miR-467g could be useful in enhancing the new bone formation. Copyright © 2017 Elsevier Ltd. All rights reserved.

  11. Oxygen supplementation for critically ill patients

    DEFF Research Database (Denmark)

    Barbateskovic, M; Schjørring, O L; Jakobsen, J C

    2018-01-01

    . The objective of this systematic review is to critically assess the evidence of randomised clinical trials on the effects of higher versus lower inspiratory oxygen fractions or targets of arterial oxygenation in critically ill adult patients. METHODS: We will search for randomised clinical trials in major......BACKGROUND: In critically ill patients, hypoxaemia is a common clinical manifestation of inadequate gas exchange in the lungs. Supplemental oxygen is therefore given to all critically ill patients. This can result in hyperoxaemia, and some observational studies have identified harms with hyperoxia...... in international guidelines despite lack of robust evidence of its effectiveness. To our knowledge, no systematic review of randomised clinical trials has investigated the effects of oxygen supplementation in critically ill patients. This systematic review will provide reliable evidence to better inform future...

  12. Rectal cancer: The radiation basis of radiotherapy, target volume; Cancers du rectum: volumes cible de la radiotherapie, bases rationnelles

    Energy Technology Data Exchange (ETDEWEB)

    Bosset, J.F.; Servagi-Vernat, S. [Service oncologie-radiotherapie, CHU Jean-Minjoz, 3, boulevard Fleming, 25030 Besancon (France); Crehange, G. [Service oncologie-radiotherapie, centre Georges-Francois-Leclerc, 1, rue du Pr-Marion, 21079 Dijon cedex (France); Azria, D. [Service oncologie-radiotherapie, centre Val-d' Aurelle, rue Croix-Verte, 34298 Montpellier cedex 5 (France); Gerard, J.P. [Service oncologie-radiotherapie, centre Antoine-Lacassagne, 33, avenue Valombrose, 06189 Nice (France); Hennequin, C. [Service oncologie-radiotherapie, hopital Saint-Louis, 1, avenue Claude-Vellefaux, 75475 Paris (France)

    2011-10-15

    Since the implementation of preoperative chemo-radiotherapy and meso-rectal excision, the 5-year rates of locoregional failures in T3-T4 N0-N1M0 rectal cancer fell from 25-30% thirty years ago to 5-8% nowadays. A critical analysis of the locoregional failures sites and mechanisms, as well as the identification of nodal extension, helps the radiation oncologist to optimize the radiotherapy target definition. The upper limit of the clinical target volume is usually set at the top of the third sacral vertebra. The lateral pelvic nodes should be included when the tumor is located in the distal part of the rectum. The anal sphincter and the levator muscles should be spared when a conservative surgery is planned. In case of abdomino-perineal excision, the ischio-rectal fossa and the sphincters should be included in the clinical target volume. A confrontation with radiologist and surgeon is mandatory to improve the definition of the target volumes to be treated. (authors)

  13. IMPROVING GLYCEMIC CONTROL SAFELY IN CRITICAL CARE PATIENTS: A COLLABORATIVE SYSTEMS APPROACH IN NINE HOSPITALS.

    Science.gov (United States)

    Maynard, Gregory A; Holdych, Janet; Kendall, Heather; Harrison, Karen; Montgomery, Patricia A; Kulasa, Kristen

    2017-05-01

    Safely improve glycemic control in the critical care units of nine hospitals. Critical care adult inpatients from nine hospitals with ≥4 point-of-care blood glucose (BG) readings over ≥2 days were targeted by collaborative improvement efforts to reduce hyper- and hypoglycemia. Balanced glucometric goals for each hospital were set targeting improvement from baseline or goals deemed desirable from Society of Hospital Medicine (SHM) benchmarking data. Collaborative interventions included standardized insulin infusion protocols, hypoglycemia prevention bundles, audit and feedback, education, and measure-vention (coupling measurement of patients "off protocol" with concurrent interventions to correct suboptimal care). All sites improved glycemic control. Six reached prespecified levels of improvement of the day-weighted mean BG. The day-weighted mean BG for the cohort decreased by 7.7 mg/dL (95% confidence interval [CI], 7.0 mg/dL to 8.4 mg/dL) to 151.3 mg/dL. Six of nine sites showed improvement in the percent intensive care unit (ICU) days with severe hyperglycemia (any BG >299 mg/dL). ICU severe hyperglycemic days declined from 8.6 to 7.2% for the cohort (relative risk, 0.84; 95% CI, 0.80 to 0.88). Patient days with any BG <70 mg/dL were reduced by 0.4% (95% CI, 0.06% to 0.6%), from 4.5 to 4.1%, for a small but statistically significant reduction in hypoglycemia. Seven of nine sites showed improvement. Multihospital improvements in ICU glycemic control, severe hyperglycemia, and hypoglycemia are feasible. Balanced goals for glycemic control and hypoglycemia in the ICU using SHM benchmarks and metrics enhanced successful improvement efforts with good staff acceptance and sustainability. BG = blood glucose CMI = case-mix index CY = calendar year DKA = diabetic ketoacidosis EMR = electronic medical record GBMF = Gordon and Betty Moore Foundation ICU = intensive care unit IIP = insulin infusion protocol SHM = Society of z Hospital Medicine.

  14. Site specific modification of the human plasma proteome by methylglyoxal

    International Nuclear Information System (INIS)

    Kimzey, Michael J.; Kinsky, Owen R.; Yassine, Hussein N.; Tsaprailis, George; Stump, Craig S.; Monks, Terrence J.; Lau, Serrine S.

    2015-01-01

    Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC–MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R + 72) and hydroimidazolone (R + 54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan–HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. - Highlights: • Methylglyoxal (MG) selectively modifies arginine sites in human plasma proteome. • Dihydroxyimidazolidine and hydroimidazolone adducts on serum albumin identified • MG modification on albumin R257 associated with loss of drug site I binding capacity • MRM-tandem mass spectrometry enables sensitive detection of albumin MG-R257. • Site-specific MG modification may

  15. Site specific modification of the human plasma proteome by methylglyoxal

    Energy Technology Data Exchange (ETDEWEB)

    Kimzey, Michael J.; Kinsky, Owen R. [Southwest Environmental Health Sciences Center, Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States); Yassine, Hussein N. [Department of Medicine, The University of Arizona, Tucson, AZ 85721 (United States); Tsaprailis, George [Southwest Environmental Health Sciences Center, Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States); Stump, Craig S. [Department of Medicine, The University of Arizona, Tucson, AZ 85721 (United States); Southern Arizona VA Health Care System, Tucson, AZ 85723 (United States); Monks, Terrence J. [Southwest Environmental Health Sciences Center, Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States); Lau, Serrine S., E-mail: lau@pharmacy.arizona.edu [Southwest Environmental Health Sciences Center, Department of Pharmacology & Toxicology, College of Pharmacy, The University of Arizona, Tucson, AZ 85721 (United States)

    2015-12-01

    Increasing evidence identifies dicarbonyl stress from reactive glucose metabolites, such as methylglyoxal (MG), as a major pathogenic link between hyperglycemia and complications of diabetes. MG covalently modifies arginine residues, yet the site specificity of this modification has not been thoroughly investigated. Sites of MG adduction in the plasma proteome were identified using LC–MS/MS analysis in vitro following incubation of plasma proteins with MG. Treatment of plasma proteins with MG yielded 14 putative MG hotspots from five plasma proteins (albumin [nine hotspots], serotransferrin, haptoglobin [2 hotspots], hemopexin, and Ig lambda-2 chain C regions). The search results revealed two versions of MG-arginine modification, dihydroxyimidazolidine (R + 72) and hydroimidazolone (R + 54) adducts. One of the sites identified was R257 in human serum albumin, which is a critical residue located in drug binding site I. This site was validated as a target for MG modification by a fluorescent probe displacement assay, which revealed significant drug dissociation at 300 μM MG from a prodan–HSA complex (75 μM). Moreover, twelve human plasma samples (six male, six female, with two type 2 diabetic subjects from both genders) were analyzed using multiple reaction monitoring (MRM) tandem mass spectrometry and revealed the presence of the MG-modified albumin R257 peptide. These data provide insights into the nature of the site-specificity of MG modification of arginine, which may be useful for therapeutic treatments that aim to prevent MG-mediated adverse responses in patients. - Highlights: • Methylglyoxal (MG) selectively modifies arginine sites in human plasma proteome. • Dihydroxyimidazolidine and hydroimidazolone adducts on serum albumin identified • MG modification on albumin R257 associated with loss of drug site I binding capacity • MRM-tandem mass spectrometry enables sensitive detection of albumin MG-R257. • Site-specific MG modification may

  16. Site observational work plan for the UMTRA Project site at Falls City, Texas

    International Nuclear Information System (INIS)

    1995-06-01

    Produced by the US Department of Energy (DOE), this site observational work plan (SOWP) will be used to determine site-specific activities to comply with the US Environmental Protection Agency (EPA) ground water standards at this Uranium Mill Tailings Remedial Action (UMTRA) Project site. The purpose of the SOWP is to recommend a site-specific ground water compliance strategy at the Falls City UMTRA Project site. The Falls City SOWP presents a comprehensive summary of site hydrogeological data, delineates a conceptual model of the aquifer system, and discusses the origins of milling-related ground water contamination. It also defines the magnitude of ground water contamination, potential environmental and health risks associated with ground water contamination and data gaps, and targets a proposed compliance strategy

  17. Penetrator strength effect in long-rod critical ricochet angle

    International Nuclear Information System (INIS)

    Daneshjou, K.; Shahravi, M.

    2008-01-01

    3D numerical simulations were performed in order to further investigate the role of penetrator strength in the interaction of long-rods and oblique targets. Three distinctive regimes resulting from oblique impact depending on the obliquity, namely simple ricochet, critical ricochet and target perforation, were investigated in detail. Critical ricochet angles were calculated with a full 3D explicit finite element method for various impact velocities and strength of target plates and projectiles. Numerical predictions were compared with existing two-dimensional analytical models and test results. It was predicted that critical ricochet angle increases with decreasing impact velocity and that higher ricochet angles were expected if higher strength target materials are employed. But there are differences between analytical models and 3D numerical simulation results or test results. The causes for these discrepancies are established by numerical simulations which explore the validity of the penetrator strength parameter in the analytical model as a physical entity. As a matter of fact, in this paper we first investigate the role of penetrator dynamic strength using two-dimensional simulation which resulted in different penetrator strengths out of different impact velocities. Next, by applying these amounts for penetrator strength in Rosenberg analytical model the critical ricochet angle is calculated. Finally, a comparison between the present analytical method with the 3D simulation and test results shows that the new analytical approach leads to modified results with respect to Rosenberg ones

  18. Integrated watershed- and farm-scale modeling framework for targeting critical source areas while maintaining farm economic viability.

    Science.gov (United States)

    Ghebremichael, Lula T; Veith, Tamie L; Hamlett, James M

    2013-01-15

    Quantitative risk assessments of pollution and data related to the effectiveness of mitigating best management practices (BMPs) are important aspects of nonpoint source pollution control efforts, particularly those driven by specific water quality objectives and by measurable improvement goals, such as the total maximum daily load (TMDL) requirements. Targeting critical source areas (CSAs) that generate disproportionately high pollutant loads within a watershed is a crucial step in successfully controlling nonpoint source pollution. The importance of watershed simulation models in assisting with the quantitative assessments of CSAs of pollution (relative to their magnitudes and extents) and of the effectiveness of associated BMPs has been well recognized. However, due to the distinct disconnect between the hydrological scale in which these models conduct their evaluation and the farm scale at which feasible BMPs are actually selected and implemented, and due to the difficulty and uncertainty involved in transferring watershed model data to farm fields, there are limited practical applications of these tools in the current nonpoint source pollution control efforts by conservation specialists for delineating CSAs and planning targeting measures. There are also limited approaches developed that can assess impacts of CSA-targeted BMPs on farm productivity and profitability together with the assessment of water quality improvements expected from applying these measures. This study developed a modeling framework that integrates farm economics and environmental aspects (such as identification and mitigation of CSAs) through joint use of watershed- and farm-scale models in a closed feedback loop. The integration of models in a closed feedback loop provides a way for environmental changes to be evaluated with regard to the impact on the practical aspects of farm management and economics, adjusted or reformulated as necessary, and revaluated with respect to effectiveness of

  19. Local Delivery Is Critical for Monocyte Chemotactic Protein-1 Mediated Site-Specific Murine Aneurysm Healing.

    Science.gov (United States)

    Hourani, Siham; Motwani, Kartik; Wajima, Daisuke; Fazal, Hanain; Jones, Chad H; Doré, Sylvain; Hosaka, Koji; Hoh, Brian L

    2018-01-01

    Local delivery of monocyte chemotactic protein-1 (MCP-1/CCL2) via our drug-eluting coil has been shown to promote intrasaccular aneurysm healing via an inflammatory pathway. In this study, we validate the importance of local MCP-1 in murine aneurysm healing. Whether systemic, rather than local, delivery of MCP-1 can direct site-specific aneurysm healing has significant translational implications. If systemic MCP-1 is effective, then MCP-1 could be administered as a pill rather than by endovascular procedure. Furthermore, we confirm that MCP-1 is the primary effector in our MCP-1 eluting coil-mediated murine aneurysm healing model. We compare aneurysm healing with repeated intraperitoneal MCP-1 versus vehicle injection, in animals with control poly(lactic-co-glycolic) acid (PLGA)-coated coils. We demonstrate elimination of the MCP-1-associated tissue-healing response by knockout of MCP-1 or CCR2 (MCP-1 receptor) and by selectively inhibiting MCP-1 or CCR2. Using immunofluorescent probing, we explore the cell populations found in healed aneurysm tissue following each intervention. Systemically administered MCP-1 with PLGA coil control does not produce comparable aneurysm healing, as seen with MCP-1 eluting coils. MCP-1-directed aneurysm healing is eliminated by selective inhibition of MCP-1 or CCR2 and in MCP-1-deficient or CCR2-deficient mice. No difference was detected in M2 macrophage and myofibroblast/smooth muscle cell staining with systemic MCP-1 versus vehicle in aneurysm wall, but a significant increase in these cell types was observed with MCP-1 eluting coil implant and attenuated by MCP-1/CCR2 blockade or deficiency. We show that systemic MCP-1 concurrent with PLGA-coated platinum coil implant is not sufficient to produce site-specific aneurysm healing. MCP-1 is a critical, not merely complementary, actor in the aneurysm healing pathway.

  20. Nanoscale Synaptic Membrane Mimetic Allows Unbiased High Throughput Screen That Targets Binding Sites for Alzheimer's-Associated Aβ Oligomers.

    Directory of Open Access Journals (Sweden)

    Kyle C Wilcox

    Full Text Available Despite their value as sources of therapeutic drug targets, membrane proteomes are largely inaccessible to high-throughput screening (HTS tools designed for soluble proteins. An important example comprises the membrane proteins that bind amyloid β oligomers (AβOs. AβOs are neurotoxic ligands thought to instigate the synapse damage that leads to Alzheimer's dementia. At present, the identities of initial AβO binding sites are highly uncertain, largely because of extensive protein-protein interactions that occur following attachment of AβOs to surface membranes. Here, we show that AβO binding sites can be obtained in a state suitable for unbiased HTS by encapsulating the solubilized synaptic membrane proteome into nanoscale lipid bilayers (Nanodiscs. This method gives a soluble membrane protein library (SMPL--a collection of individualized synaptic proteins in a soluble state. Proteins within SMPL Nanodiscs showed enzymatic and ligand binding activity consistent with conformational integrity. AβOs were found to bind SMPL Nanodiscs with high affinity and specificity, with binding dependent on intact synaptic membrane proteins, and selective for the higher molecular weight oligomers known to accumulate at synapses. Combining SMPL Nanodiscs with a mix-incubate-read chemiluminescence assay provided a solution-based HTS platform to discover antagonists of AβO binding. Screening a library of 2700 drug-like compounds and natural products yielded one compound that potently reduced AβO binding to SMPL Nanodiscs, synaptosomes, and synapses in nerve cell cultures. Although not a therapeutic candidate, this small molecule inhibitor of synaptic AβO binding will provide a useful experimental antagonist for future mechanistic studies of AβOs in Alzheimer's model systems. Overall, results provide proof of concept for using SMPLs in high throughput screening for AβO binding antagonists, and illustrate in general how a SMPL Nanodisc system can

  1. Nanoscale Synaptic Membrane Mimetic Allows Unbiased High Throughput Screen That Targets Binding Sites for Alzheimer's-Associated Aβ Oligomers.

    Science.gov (United States)

    Wilcox, Kyle C; Marunde, Matthew R; Das, Aditi; Velasco, Pauline T; Kuhns, Benjamin D; Marty, Michael T; Jiang, Haoming; Luan, Chi-Hao; Sligar, Stephen G; Klein, William L

    2015-01-01

    Despite their value as sources of therapeutic drug targets, membrane proteomes are largely inaccessible to high-throughput screening (HTS) tools designed for soluble proteins. An important example comprises the membrane proteins that bind amyloid β oligomers (AβOs). AβOs are neurotoxic ligands thought to instigate the synapse damage that leads to Alzheimer's dementia. At present, the identities of initial AβO binding sites are highly uncertain, largely because of extensive protein-protein interactions that occur following attachment of AβOs to surface membranes. Here, we show that AβO binding sites can be obtained in a state suitable for unbiased HTS by encapsulating the solubilized synaptic membrane proteome into nanoscale lipid bilayers (Nanodiscs). This method gives a soluble membrane protein library (SMPL)--a collection of individualized synaptic proteins in a soluble state. Proteins within SMPL Nanodiscs showed enzymatic and ligand binding activity consistent with conformational integrity. AβOs were found to bind SMPL Nanodiscs with high affinity and specificity, with binding dependent on intact synaptic membrane proteins, and selective for the higher molecular weight oligomers known to accumulate at synapses. Combining SMPL Nanodiscs with a mix-incubate-read chemiluminescence assay provided a solution-based HTS platform to discover antagonists of AβO binding. Screening a library of 2700 drug-like compounds and natural products yielded one compound that potently reduced AβO binding to SMPL Nanodiscs, synaptosomes, and synapses in nerve cell cultures. Although not a therapeutic candidate, this small molecule inhibitor of synaptic AβO binding will provide a useful experimental antagonist for future mechanistic studies of AβOs in Alzheimer's model systems. Overall, results provide proof of concept for using SMPLs in high throughput screening for AβO binding antagonists, and illustrate in general how a SMPL Nanodisc system can facilitate drug discovery

  2. Targeted ethnography as a critical step to inform cultural adaptations of HIV prevention interventions for adults with severe mental illness.

    Science.gov (United States)

    Wainberg, Milton L; Alfredo González, M; McKinnon, Karen; Elkington, Katherine S; Pinto, Diana; Gruber Mann, Claudio; Mattos, Paulo E

    2007-07-01

    As in other countries worldwide, adults with severe mental illness (SMI) in Brazil are disproportionately infected with HIV relative to the general population. Brazilian psychiatric facilities lack tested HIV prevention interventions. To adapt existing interventions, developed only in the US, we conducted targeted ethnography with adults with SMI and staff from two psychiatric institutions in Brazil. We sought to characterize individual, institutional, and interpersonal factors that may affect HIV risk behavior in this population. We conducted 350 hours of ethnographic field observations in two mental health service settings in Rio de Janeiro, and 9 focus groups (n=72) and 16 key-informant interviews with patients and staff in these settings. Data comprised field notes and audiotapes of all exchanges, which were transcribed, coded, and systematically analyzed. The ethnography identified and/or characterized the institutional culture: (1) patients' risk behaviors; (2) the institutional setting; (3) intervention content; and (4) intervention format and delivery strategies. Targeted ethnography also illuminated broader contextual issues for development and implementation of HIV prevention interventions for adults with SMI in Brazil, including an institutional culture that did not systematically address patients' sexual behavior, sexual health, or HIV sexual risk, yet strongly impacted the structure of patients' sexual networks. Further, ethnography identified the Brazilian concept of "social responsibility" as important to prevention work with psychiatric patients. Targeted ethnography with adults with SMI and institutional staff provided information critical to the adaptation of tested US HIV prevention interventions for Brazilians with SMI.

  3. [Resistance to target-based therapy and its circumvention].

    Science.gov (United States)

    Nishio, Kazuto

    2004-07-01

    Intrinsic and acquired resistance to molecular target therapy critically limits the outcome of cancer treatments. Target levels including quantitative and gene alteration should be determinants for the resistance. Downstream of the target molecules, drug metabolism, and drug transport influences the tumor sensitivity to molecular target therapy. The mechanisms of resistance to antibody therapy have not been fully clarified. Correlative clinical studies using these biomarkers of resistance are extremely important for circumvention of clinical resistance to target based therapy.

  4. Target-Rich Environment

    Science.gov (United States)

    Perna, Mark C.

    2005-01-01

    Target marketing is defining school enrollment goals and then developing a strategic plan to accomplish those goals through the use of specific communication vehicles and community focus. It is critical to reach the right audience, with the right message, at the right time, for the right cost. In this brief article, the author describes several…

  5. Identification of direct regulatory targets of the transcription factor Sox10 based on function and conservation

    Directory of Open Access Journals (Sweden)

    Lee Sanghyuk

    2008-09-01

    Full Text Available Abstract Background Sox10, a member of the Sry-related HMG-Box gene family, is a critical transcription factor for several important cell lineages, most notably the neural crest stem cells and the derivative peripheral glial cells and melanocytes. Thus far, only a handful of direct target genes are known for this transcription factor limiting our understanding of the biological network it governs. Results We describe identification of multiple direct regulatory target genes of Sox10 through a procedure based on function and conservation. By combining RNA interference technique and DNA microarray technology, we have identified a set of genes that show significant down-regulation upon introduction of Sox10 specific siRNA into Schwannoma cells. Subsequent comparative genomics analyses led to potential binding sites for Sox10 protein conserved across several mammalian species within the genomic region proximal to these genes. Multiple sites belonging to 4 different genes (proteolipid protein, Sox10, extracellular superoxide dismutase, and pleiotrophin were shown to directly interact with Sox10 by chromatin immunoprecipitation assay. We further confirmed the direct regulation through the identified cis-element for one of the genes, extracellular superoxide dismutase, using electrophoretic mobility shift assay and reporter assay. Conclusion In sum, the process of combining differential expression profiling and comparative genomics successfully led to further defining the role of Sox10, a critical transcription factor for the development of peripheral glia. Our strategy utilizing relatively accessible techniques and tools should be applicable to studying the function of other transcription factors.

  6. Power load limits of the WENDELSTEIN 7-X target elements-comparison of experimental results and design values for power loads up to the critical heat flux

    International Nuclear Information System (INIS)

    Greuner, H; Boeswirth, B; Boscary, J; Leuprecht, A; Plankensteiner, A

    2007-01-01

    The power load limits of the WENDELSTEIN7-X divertor target elements were experimentally evaluated with heat loads considerably exceeding the expected operating conditions. The water-cooled elements are designed for steady-state heat flux of 10 MW m -2 and to remove a power load up to 100 kW. The elements must allow a limited operation time at 12 MW m -2 steady-state and should not fail for short pulses of up to 15 MW m -2 for cooling conditions in the subcooled nucleate boiling regime. In the framework of the qualification phase, pre-series target elements were loaded up to 24 MW m -2 without loss of CFC tiles. A critical heat flux at the target of 31 MW m -2 was achieved. The paper discusses the results of the tests performed at the high heat flux test facility GLADIS. The experimental results compared to transient nonlinear fine element method (FEM) calculations confirm a high thermal safety margin of the target design sufficient for plasma operation in W7-X

  7. FLP recombinase-mediated site-specific recombination in silkworm, Bombyx mori.

    Directory of Open Access Journals (Sweden)

    Ding-Pei Long

    Full Text Available A comprehensive understanding of gene function and the production of site-specific genetically modified mutants are two major goals of genetic engineering in the post-genomic era. Although site-specific recombination systems have been powerful tools for genome manipulation of many organisms, they have not yet been established for use in the manipulation of the silkworm Bombyx mori genome. In this study, we achieved site-specific excision of a target gene at predefined chromosomal sites in the silkworm using a FLP/FRT site-specific recombination system. We first constructed two stable transgenic target silkworm strains that both contain a single copy of the transgene construct comprising a target gene expression cassette flanked by FRT sites. Using pre-blastoderm microinjection of a FLP recombinase helper expression vector, 32 G3 site-specific recombinant transgenic individuals were isolated from five of 143 broods. The average frequency of FLP recombinase-mediated site-specific excision in the two target strains genome was approximately 3.5%. This study shows that it is feasible to achieve site-specific recombination in silkworms using the FLP/FRT system. We conclude that the FLP/FRT system is a useful tool for genome manipulation in the silkworm. Furthermore, this is the first reported use of the FLP/FRT system for the genetic manipulation of a lepidopteran genome and thus provides a useful reference for the establishment of genome manipulation technologies in other lepidopteran species.

  8. Cdc7 kinase - a new target for drug development.

    Science.gov (United States)

    Swords, Ronan; Mahalingam, Devalingam; O'Dwyer, Michael; Santocanale, Corrado; Kelly, Kevin; Carew, Jennifer; Giles, Francis

    2010-01-01

    The cell division cycle 7 (Cdc7) is a serine threonine kinase that is of critical importance in the regulation of normal cell cycle progression. Cdc7 kinase is highly conserved during evolution and much has been learned about its biological roles in humans through the study of lower eukaryotes, particularly yeasts. Two important regulator proteins, Dbf4 and Drf1, bind to and modulate the kinase activity of human Cdc7 which phosphorylates several sites on Mcm2 (minichromosome maintenance protein 2), one of the six subunits of the replicative DNA helicase needed for duplication of the genome. Through regulation of both DNA synthesis and DNA damage response, both key functions in the survival of tumour cells, Cdc7 becomes an attractive target for pharmacological inhibition. There are much data available on the pre-clinical anti-cancer effects of Cdc7 depletion and although there are no available Cdc7 inhibitors in clinical trials as yet, several lead compounds are being optimised for this purpose. In this review, we will address the current status of Cdc7 as an important target for new drug development.

  9. Numerical prediction of a dip effect in the critical current density

    International Nuclear Information System (INIS)

    Al Khawaja, U.; Benkraouda, M.; Obaidat, I.M.

    2007-01-01

    We have conducted extensive series of molecular dynamic simulations on the properties of the critical current density in systems with periodic square arrays of pinning sites. The density of the pinning sites was kept fixed while the density of vortices, pinning strength, and temperature were varied several times. At zero temperature, we have observed a substantial dip in the critical current density that occurs only at a fixed value of the vortex density and for specific values of pinning strength. We have found that the occurrence of the dip depends mainly on the initial positions of the vortices with respect to the positions of the pinning sites. At the dip, we have found that the interstitial vortices form moving channels leading to the observed drop in the critical current density

  10. A Bioinorganic Approach to Fragment-Based Drug Discovery Targeting Metalloenzymes.

    Science.gov (United States)

    Cohen, Seth M

    2017-08-15

    Metal-dependent enzymes (i.e., metalloenzymes) make up a large fraction of all enzymes and are critically important in a wide range of biological processes, including DNA modification, protein homeostasis, antibiotic resistance, and many others. Consequently, metalloenzymes represent a vast and largely untapped space for drug development. The discovery of effective therapeutics that target metalloenzymes lies squarely at the interface of bioinorganic and medicinal chemistry and requires expertise, methods, and strategies from both fields to mount an effective campaign. In this Account, our research program that brings together the principles and methods of bioinorganic and medicinal chemistry are described, in an effort to bridge the gap between these fields and address an important class of medicinal targets. Fragment-based drug discovery (FBDD) is an important drug discovery approach that is particularly well suited for metalloenzyme inhibitor development. FBDD uses relatively small but diverse chemical structures that allow for the assembly of privileged molecular collections that focus on a specific feature of the target enzyme. For metalloenzyme inhibition, the specific feature is rather obvious, namely, a metal-dependent active site. Surprisingly, prior to our work, the exploration of diverse molecular fragments for binding the metal active sites of metalloenzymes was largely unexplored. By assembling a modest library of metal-binding pharmacophores (MBPs), we have been able to find lead hits for many metalloenzymes and, from these hits, develop inhibitors that act via novel mechanisms of action. A specific case study on the use of this strategy to identify a first-in-class inhibitor of zinc-dependent Rpn11 (a component of the proteasome) is highlighted. The application of FBDD for the development of metalloenzyme inhibitors has raised several other compelling questions, such as how the metalloenzyme active site influences the coordination chemistry of bound

  11. CRITICAL EVENTS IN CONSTRUCTION PROCESS

    DEFF Research Database (Denmark)

    Jørgensen, Kirsten; Rasmussen, Grane Mikael Gregaard

    2009-01-01

    cause-effects of failures and defects in the construction industry by using an analytical approach (The bowtie model) which is developed in the accident research. Using this model clarifies the relationships within the chain of failures that causes critical events with undesirable consequences......Function failures, defects and poor communication are major problems in the construction industry. These failures and defects are caused by a row of critical events in the construction process. The purpose of this paper is to define “critical events” in the construction process and to investigate....... In this way the causes of failures and the relationships between various failures are rendered visible. A large construction site was observed from start to finish as the empirical element in the research. The research focuses on all kinds of critical events identified throughout every phase during...

  12. Criticizing politicians in Ancient Comedy

    Directory of Open Access Journals (Sweden)

    María José García Soler

    2016-08-01

    Full Text Available Old Comedy brought into focus all aspects of life in Athens, with an infinitefreedom of speech. One of its main targets were the politicians who ruled thedestinies of the polis, criticized mercilessly for their public activities, but also fortheir physical and moral characteristics.

  13. Global Identification of EVI1 Target Genes in Acute Myeloid Leukemia.

    Directory of Open Access Journals (Sweden)

    Carolyn Glass

    Full Text Available The ecotropic virus integration site 1 (EVI1 transcription factor is associated with human myeloid malignancy of poor prognosis and is overexpressed in 8-10% of adult AML and strikingly up to 27% of pediatric MLL-rearranged leukemias. For the first time, we report comprehensive genomewide EVI1 binding and whole transcriptome gene deregulation in leukemic cells using a combination of ChIP-Seq and RNA-Seq expression profiling. We found disruption of terminal myeloid differentiation and cell cycle regulation to be prominent in EVI-induced leukemogenesis. Specifically, we identified EVI1 directly binds to and downregulates the master myeloid differentiation gene Cebpe and several of its downstream gene targets critical for terminal myeloid differentiation. We also found EVI1 binds to and downregulates Serpinb2 as well as numerous genes involved in the Jak-Stat signaling pathway. Finally, we identified decreased expression of several ATP-dependent P2X purinoreceptors genes involved in apoptosis mechanisms. These findings provide a foundation for future study of potential therapeutic gene targets for EVI1-induced leukemia.

  14. Targeting the SH2-kinase interface in Bcr-Abl inhibits leukemogenesis.

    Science.gov (United States)

    Grebien, Florian; Hantschel, Oliver; Wojcik, John; Kaupe, Ines; Kovacic, Boris; Wyrzucki, Arkadiusz M; Gish, Gerald D; Cerny-Reiterer, Sabine; Koide, Akiko; Beug, Hartmut; Pawson, Tony; Valent, Peter; Koide, Shohei; Superti-Furga, Giulio

    2011-10-14

    Chronic myelogenous leukemia (CML) is caused by the constitutively active tyrosine kinase Bcr-Abl and treated with the tyrosine kinase inhibitor (TKI) imatinib. However, emerging TKI resistance prevents complete cure. Therefore, alternative strategies targeting regulatory modules of Bcr-Abl in addition to the kinase active site are strongly desirable. Here, we show that an intramolecular interaction between the SH2 and kinase domains in Bcr-Abl is both necessary and sufficient for high catalytic activity of the enzyme. Disruption of this interface led to inhibition of downstream events critical for CML signaling and, importantly, completely abolished leukemia formation in mice. Furthermore, disruption of the SH2-kinase interface increased sensitivity of imatinib-resistant Bcr-Abl mutants to TKI inhibition. An engineered Abl SH2-binding fibronectin type III monobody inhibited Bcr-Abl kinase activity both in vitro and in primary CML cells, where it induced apoptosis. This work validates the SH2-kinase interface as an allosteric target for therapeutic intervention. Copyright © 2011 Elsevier Inc. All rights reserved.

  15. Los Alamos Critical Experiments Facility

    International Nuclear Information System (INIS)

    Malenfant, R.E.

    1991-01-01

    The Critical Experiments Facility of the Los Alamos National Laboratory has been in existence for 45 years. In that period of time, thousands of measurements have been made on assemblies containing every fissionable material in various configurations that included bare metal and compounds of the nitrate, sulfate, fluoride, carbide, and oxide. Techniques developed or applied include Rossi-α, source-jerk, rod oscillator, and replacement measurements. Many of the original measurements of delay neutrons were performed at the site, and a replica of the Hiroshima weapon was operated at steady state to assist in evaluating the relative biological effectiveness (RBE) of neutrons. Solid, liquid, and gas fissioning systems were run at critical. Operation of this original critical facility has demonstrated the margin of safety that can be obtained through remote operation. Eight accidental excursions have occurred on the site, ranging from 1.5 x 10 16 to 1.2 x 10 17 fissions, with no significant exposure to personnel or damage to the facility beyond the machines themselves -- and in only one case was the machine damaged beyond further use. The present status of the facility, operating procedures, and complement of machines will be described in the context of programmatic activity. New programs will focus on training, validation of criticality alarm systems, experimental safety assessment of process applications, and dosimetry. Special emphasis will be placed on the incorporation of experience from 45 years of operation into present procedures and programs. 3 refs

  16. Increasing the Structural Coverage of Tuberculosis Drug Targets

    Science.gov (United States)

    Baugh, Loren; Phan, Isabelle; Begley, Darren W.; Clifton, Matthew C.; Armour, Brianna; Dranow, David M.; Taylor, Brandy M.; Muruthi, Marvin M.; Abendroth, Jan; Fairman, James W.; Fox, David; Dieterich, Shellie H.; Staker, Bart L.; Gardberg, Anna S.; Choi, Ryan; Hewitt, Stephen N.; Napuli, Alberto J.; Myers, Janette; Barrett, Lynn K.; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W.; Stacy, Robin; Stewart, Lance J.; Edwards, Thomas E.; Van Voorhis, Wesley C.; Myler, Peter J.

    2015-01-01

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus “homolog-rescue” strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD 85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. PMID:25613812

  17. Combinatorial microRNA target predictions

    DEFF Research Database (Denmark)

    Krek, Azra; Grün, Dominic; Poy, Matthew N.

    2005-01-01

    MicroRNAs are small noncoding RNAs that recognize and bind to partially complementary sites in the 3' untranslated regions of target genes in animals and, by unknown mechanisms, regulate protein production of the target transcript1, 2, 3. Different combinations of microRNAs are expressed...... in different cell types and may coordinately regulate cell-specific target genes. Here, we present PicTar, a computational method for identifying common targets of microRNAs. Statistical tests using genome-wide alignments of eight vertebrate genomes, PicTar's ability to specifically recover published micro......RNA targets, and experimental validation of seven predicted targets suggest that PicTar has an excellent success rate in predicting targets for single microRNAs and for combinations of microRNAs. We find that vertebrate microRNAs target, on average, roughly 200 transcripts each. Furthermore, our results...

  18. Continuing pollution from the Rum Jungle U-Cu project: A critical evaluation of environmental monitoring and rehabilitation

    Energy Technology Data Exchange (ETDEWEB)

    Mudd, Gavin M., E-mail: Gavin.Mudd@eng.monash.edu.a [Environmental Engineering, Dept of Civil Engineering, Monash University, Clayton, VIC 3800 (Australia); Patterson, James [Environmental Engineering Consultant, Sydney, NSW (Australia)

    2010-05-15

    The former Rum Jungle uranium-copper project, Australia, is an internationally important case study on environmental pollution from and rehabilitation of mining. The Rum Jungle mining project is briefly reviewed, followed by a critical evaluation of monitoring data and pollution loads prior to and after rehabilitation - leading to the conclusion that rehabilitation has clearly failed the test of time after just two decades. The most critical findings are the need to understand pollution cycles holistically, and designing monitoring regimes to match, explicit inclusion of radiological criteria (lacking in original planning), and finally the need to set targets based on environmental criteria. Two examples include polluted groundwater which was excluded from rehabilitation and the poor design, construction and/or performance of engineered soil covers - both leading to increasing acid drainage impacts on the Finniss River. The critical review therefore presents a valuable case study of the environmental performance of uranium mine site rehabilitation. - The Rum Jungle U-Cu project underwent extensive rehabilitation in the 1980's, however, it remains a major cause of pollution to the Finniss River.

  19. The site selection process

    International Nuclear Information System (INIS)

    Kittel, J.H.

    1989-01-01

    One of the most arduous tasks associated with the management of radioactive wastes is the siting of new disposal facilities. Experience has shown that the performance of the disposal facility during and after disposal operations is critically dependent on the characteristics of the site itself. The site selection process consists of defining needs and objectives, identifying geographic regions of interest, screening and selecting candidate sites, collecting data on the candidate sites, and finally selecting the preferred site. Before the site selection procedures can be implemented, however, a formal legal system must be in place that defines broad objectives and, most importantly, clearly establishes responsibilities and accompanying authorities for the decision-making steps in the procedure. Site selection authorities should make every effort to develop trust and credibility with the public, local officials, and the news media. The responsibilities of supporting agencies must also be spelled out. Finally, a stable funding arrangement must be established so that activities such as data collection can proceed without interruption. Several examples, both international and within the US, are given

  20. Hierarchical effects on target detection and conflict monitoring

    Science.gov (United States)

    Cao, Bihua; Gao, Feng; Ren, Maofang; Li, Fuhong

    2016-01-01

    Previous neuroimaging studies have demonstrated a hierarchical functional structure of the frontal cortices of the human brain, but the temporal course and the electrophysiological signature of the hierarchical representation remains unaddressed. In the present study, twenty-one volunteers were asked to perform a nested cue-target task, while their scalp potentials were recorded. The results showed that: (1) in comparison with the lower-level hierarchical targets, the higher-level targets elicited a larger N2 component (220–350 ms) at the frontal sites, and a smaller P3 component (350–500 ms) across the frontal and parietal sites; (2) conflict-related negativity (non-target minus target) was greater for the lower-level hierarchy than the higher-level, reflecting a more intensive process of conflict monitoring at the final step of target detection. These results imply that decision making, context updating, and conflict monitoring differ among different hierarchical levels of abstraction. PMID:27561989

  1. Unusually effective microRNA targeting within repeat-rich coding regions of mammalian mRNAs

    Science.gov (United States)

    Schnall-Levin, Michael; Rissland, Olivia S.; Johnston, Wendy K.; Perrimon, Norbert; Bartel, David P.; Berger, Bonnie

    2011-01-01

    MicroRNAs (miRNAs) regulate numerous biological processes by base-pairing with target messenger RNAs (mRNAs), primarily through sites in 3′ untranslated regions (UTRs), to direct the repression of these targets. Although miRNAs have sometimes been observed to target genes through sites in open reading frames (ORFs), large-scale studies have shown such targeting to be generally less effective than 3′ UTR targeting. Here, we show that several miRNAs each target significant groups of genes through multiple sites within their coding regions. This ORF targeting, which mediates both predictable and effective repression, arises from highly repeated sequences containing miRNA target sites. We show that such sequence repeats largely arise through evolutionary duplications and occur particularly frequently within families of paralogous C2H2 zinc-finger genes, suggesting the potential for their coordinated regulation. Examples of ORFs targeted by miR-181 include both the well-known tumor suppressor RB1 and RBAK, encoding a C2H2 zinc-finger protein and transcriptional binding partner of RB1. Our results indicate a function for repeat-rich coding sequences in mediating post-transcriptional regulation and reveal circumstances in which miRNA-mediated repression through ORF sites can be reliably predicted. PMID:21685129

  2. Non-target-site resistance to ALS-inhibiting herbicides in a Sagittaria trifolia L. population.

    Science.gov (United States)

    Zhao, Bochui; Fu, Danni; Yu, Yang; Huang, Chengtian; Yan, Kecheng; Li, Pingsheng; Shafi, Jamil; Zhu, He; Wei, Songhong; Ji, Mingshan

    2017-08-01

    Sagittaria trifolia L. is one of the most competitive weeds in rice fields in northeastern China. The continuous use of acetolactate synthase (ALS)-inhibitors has led to the evolution of herbicide resistant S. trifolia. A subpopulation BC1, which was derived from the L1 population, was analyzed using DNA sequencing and ALS enzyme activity assays and levels of resistance to five ALS-inhibiting herbicides was determined. DNA sequencing and ALS enzyme assays revealed no amino acid substitutions and no significant differences in enzyme sensitivity between susceptible and resistant populations. Whole-plant dose-response experiments showed that the BC1 population exhibited different levels of resistance (resistance ratios ranging from 2.14 to 51.53) to five ALS herbicides, and the addition of malathion (P450 inhibitor) to bensulfuron-methyl, penoxsulam and bispyribac-sodium strongly reduced the dry weight accumulation of the BC1 population compared with the effects of the three herbicides alone. The results of the present study demonstrated that the BC1 population has evolved non-target-site resistance to ALS-inhibiting herbicides. Copyright © 2017 Elsevier Inc. All rights reserved.

  3. Strong Earthquake Motion Estimates for Three Sites on the U.C. Riverside Campus; TOPICAL

    International Nuclear Information System (INIS)

    Archuleta, R.; Elgamal, A.; Heuze, F.; Lai, T.; Lavalle, D.; Lawrence, B.; Liu, P.C.; Matesic, L.; Park, S.; Riemar, M.; Steidl, J.; Vucetic, M.; Wagoner, J.; Yang, Z.

    2000-01-01

    The approach of the Campus Earthquake Program (CEP) is to combine the substantial expertise that exists within the UC system in geology, seismology, and geotechnical engineering, to estimate the earthquake strong motion exposure of UC facilities. These estimates draw upon recent advances in hazard assessment, seismic wave propagation modeling in rocks and soils, and dynamic soil testing. The UC campuses currently chosen for application of our integrated methodology are Riverside, San Diego, and Santa Barbara. The procedure starts with the identification of possible earthquake sources in the region and the determination of the most critical fault(s) related to earthquake exposure of the campus. Combined geological, geophysical, and geotechnical studies are then conducted to characterize each campus with specific focus on the location of particular target buildings of special interest to the campus administrators. We drill and geophysically log deep boreholes next to the target structure, to provide direct in-situ measurements of subsurface material properties, and to install uphole and downhole 3-component seismic sensors capable of recording both weak and strong motions. The boreholes provide access below the soil layers, to deeper materials that have relatively high seismic shear-wave velocities. Analyses of conjugate downhole and uphole records provide a basis for optimizing the representation of the low-strain response of the sites. Earthquake rupture scenarios of identified causative faults are combined with the earthquake records and with nonlinear soil models to provide site-specific estimates of strong motions at the selected target locations. The predicted ground motions are shared with the UC consultants, so that they can be used as input to the dynamic analysis of the buildings. Thus, for each campus targeted by the CEP project, the strong motion studies consist of two phases, Phase 1-initial source and site characterization, drilling, geophysical logging

  4. Critical examination of information related to the ecological impact of mining sites on Ritord drainage basin and Saint-Pardoux lake. Preliminary study

    International Nuclear Information System (INIS)

    Garnier-Laplace, J.; Beaugelin-Seiller, K.

    2006-01-01

    This expertise report addresses the potential impact of liquid releases of any kind due to mining sites managed by AREVA on aquatic ecosystems (rivers, dams, lakes, and so on). The analysis comprises a detailed analysis of a report published by SENES Consultants on the potential effects on the roach and other fish species present in the St-Pardoux lake in relationship with their exposure to radionuclides, and a proposition of additional studies for the assessment of the ecological risk associated with releases of radioactive substances and of metals in relationship with the past and present exploitation and management of mining sites. A second part proposes an overview of European methods of assessment of the ecological risk and impact. The traditional method comprises an identification of hazards, an analysis of effects through a critical examination of relationship between dose and associated effects for each substance with a determination of predicted no-effect concentrations (PNEC), an analysis of exposure ways through a calculation or measurement of concentrations to which a part of an ecosystem may be exposed (PEC, predicted environmental concentration), and the risk characterization. Evolutions and approaches are discussed. The third part discusses the study performed by SENES Consultants. The method is presented as well as main general criteria for radiological and chemical aspects. Critics are formulated on the approach to the radiological and chemical aspects, and on the conclusions of this study. The fourth part proposes a brief discussion of the AREVA decennial environmental review and proposes additional studies regarding the screening performed on ecosystems

  5. Towards soft robotic devices for site-specific drug delivery.

    Science.gov (United States)

    Alici, Gursel

    2015-01-01

    Considerable research efforts have recently been dedicated to the establishment of various drug delivery systems (DDS) that are mechanical/physical, chemical and biological/molecular DDS. In this paper, we report on the recent advances in site-specific drug delivery (site-specific, controlled, targeted or smart drug delivery are terms used interchangeably in the literature, to mean to transport a drug or a therapeutic agent to a desired location within the body and release it as desired with negligibly small toxicity and side effect compared to classical drug administration means such as peroral, parenteral, transmucosal, topical and inhalation) based on mechanical/physical systems consisting of implantable and robotic drug delivery systems. While we specifically focus on the robotic or autonomous DDS, which can be reprogrammable and provide multiple doses of a drug at a required time and rate, we briefly cover the implanted DDS, which are well-developed relative to the robotic DDS, to highlight the design and performance requirements, and investigate issues associated with the robotic DDS. Critical research issues associated with both DDSs are presented to describe the research challenges ahead of us in order to establish soft robotic devices for clinical and biomedical applications.

  6. Mapping the heparin-binding site of the BMP antagonist gremlin by site-directed mutagenesis based on predictive modelling.

    Science.gov (United States)

    Tatsinkam, Arnold Junior; Mulloy, Barbara; Rider, Christopher C

    2015-08-15

    Gremlin is a member of the CAN (cerberus and DAN) family of secreted BMP (bone morphogenetic protein) antagonists and also an agonist of VEGF (vascular endothelial growth factor) receptor-2. It is critical in limb skeleton and kidney development and is re-expressed during tissue fibrosis. Gremlin binds strongly to heparin and heparan sulfate and, in the present study, we sought to investigate its heparin-binding site. In order to explore a putative non-contiguous binding site predicted by computational molecular modelling, we substituted a total of 11 key arginines and lysines located in three basic residue sequence clusters with homologous sequences from cerberus and DAN (differential screening selected gene abberative in neuroblastoma), CAN proteins which lack basic residues in these positions. A panel of six Myc-tagged gremlin mutants, MGR-1-MGR-6 (MGR, mutant gremlin), each containing different combinations of targeted substitutions, all showed markedly reduced affinity for heparin as demonstrated by their NaCl elution on heparin affinity chromatography, thus verifying our predictions. Both MGR-5 and MGR-6 retained BMP-4-binding activity comparable to that of wild-type gremlin. Low-molecular-mass heparin neither promoted nor inhibited BMP-4 binding. Finally, glutaraldehyde cross-linking demonstrated that gremlin forms non-covalent dimers, similar behaviour to that of DAN and also PRDC (protein related to cerberus and DAN), another CAN protein. The resulting dimer would possess two heparin-binding sites, each running along an exposed surface on the second β-strand finger loop of one of the monomers. © 2015 Authors; published by Portland Press Limited.

  7. Fusion facility siting considerations

    International Nuclear Information System (INIS)

    Bussell, G.T.

    1985-01-01

    Inherent in the fusion program's transition from hydrogen devices to commercial power machines is a general increase in the size and scope of succeeding projects. This growth will lead to increased emphasis on safety, environmental impact, and the external effects of fusion in general, and of each new device in particular. A critically important consideration in this regard is site selection. The purpose of this paper is to examine major siting issues that may affect the economics, safety, and environmental impact of fusion

  8. Monoubiquitination of Tob/BTG family proteins competes with degradation-targeting polyubiquitination

    Energy Technology Data Exchange (ETDEWEB)

    Suzuki, Toru, E-mail: toru@ims.u-tokyo.ac.jp [Division of Oncology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Kim, Minsoo [Division of Bacterial Infection, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Kozuka-Hata, Hiroko [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Watanabe, Masato [Department of Medical Genome Science, School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562 (Japan); Oyama, Masaaki [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Tsumoto, Kouhei [Medical Proteomics Laboratory, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Department of Medical Genome Science, School of Frontier Sciences, University of Tokyo, 5-1-5 Kashiwanoha, Kashiwa 277-8562 (Japan); Yamamoto, Tadashi, E-mail: tyamamot@ims.u-tokyo.ac.jp [Division of Oncology, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639 (Japan); Cell Signal Unit, Okinawa Institute of Science and Technology, 1919-1 Onna-son, Kunigami, Okinawa 904-0412 (Japan)

    2011-05-27

    Highlights: {yields} Tob/BTG family proteins are monoubiquitinated in the absence of E3s in vitro. {yields} Monoubiquitination sites of Tob are identified by mass spectrometry. {yields} The monoubiquitination event correlates with lower levels of polyubiquitination. -- Abstract: Tob belongs to the anti-proliferative Tob/BTG protein family. The expression level of Tob family proteins is strictly regulated both transcriptionally and through post-translational modification. Ubiquitin (Ub)/proteosome-dependent degradation of Tob family proteins is critical in controlling cell cycle progression and DNA damage responses. Various Ub ligases (E3s) are responsible for degradation of Tob protein. Here, we show that Tob family proteins undergo monoubiquitination even in the absence of E3s in vitro. Determination of the ubiquitination site(s) in Tob by mass spectrometric analysis revealed that two lysine residues (Lys48 and Lys63) located in Tob/BTG homology domain are ubiquitinated. A mutant Tob, in which both Lys48 and Lys63 are substituted with alanine, is more strongly polyubiquitinated than wild-type Tob in vivo. These data suggest that monoubiquitination of Tob family proteins confers resistance against polyubiquitination, which targets proteins for degradation. The strategy for regulating the stability of Tob family proteins suggests a novel role for monoubiquitination.

  9. Monoubiquitination of Tob/BTG family proteins competes with degradation-targeting polyubiquitination

    International Nuclear Information System (INIS)

    Suzuki, Toru; Kim, Minsoo; Kozuka-Hata, Hiroko; Watanabe, Masato; Oyama, Masaaki; Tsumoto, Kouhei; Yamamoto, Tadashi

    2011-01-01

    Highlights: → Tob/BTG family proteins are monoubiquitinated in the absence of E3s in vitro. → Monoubiquitination sites of Tob are identified by mass spectrometry. → The monoubiquitination event correlates with lower levels of polyubiquitination. -- Abstract: Tob belongs to the anti-proliferative Tob/BTG protein family. The expression level of Tob family proteins is strictly regulated both transcriptionally and through post-translational modification. Ubiquitin (Ub)/proteosome-dependent degradation of Tob family proteins is critical in controlling cell cycle progression and DNA damage responses. Various Ub ligases (E3s) are responsible for degradation of Tob protein. Here, we show that Tob family proteins undergo monoubiquitination even in the absence of E3s in vitro. Determination of the ubiquitination site(s) in Tob by mass spectrometric analysis revealed that two lysine residues (Lys48 and Lys63) located in Tob/BTG homology domain are ubiquitinated. A mutant Tob, in which both Lys48 and Lys63 are substituted with alanine, is more strongly polyubiquitinated than wild-type Tob in vivo. These data suggest that monoubiquitination of Tob family proteins confers resistance against polyubiquitination, which targets proteins for degradation. The strategy for regulating the stability of Tob family proteins suggests a novel role for monoubiquitination.

  10. Radiation-Force Assisted Targeting Facilitates Ultrasonic Molecular Imaging

    Directory of Open Access Journals (Sweden)

    Shukui Zhao

    2004-07-01

    Full Text Available Ultrasonic molecular imaging employs contrast agents, such as microbubbles, nanoparticles, or liposomes, coated with ligands specific for receptors expressed on cells at sites of angiogenesis, inflammation, or thrombus. Concentration of these highly echogenic contrast agents at a target site enhances the ultrasound signal received from that site, promoting ultrasonic detection and analysis of disease states. In this article, we show that acoustic radiation force can be used to displace targeted contrast agents to a vessel wall, greatly increasing the number of agents binding to available surface receptors. We provide a theoretical evaluation of the magnitude of acoustic radiation force and show that it is possible to displace micron-sized agents physiologically relevant distances. Following this, we show in a series of experiments that acoustic radiation force can enhance the binding of targeted agents: The number of biotinylated microbubbles adherent to a synthetic vessel coated with avidin increases as much as 20-fold when acoustic radiation force is applied; the adhesion of contrast agents targeted to αvβ3 expressed on human umbilical vein endothelial cells increases 27-fold within a mimetic vessel when radiation force is applied; and finally, the image signal-to-noise ratio in a phantom vessel increases up to 25 dB using a combination of radiation force and a targeted contrast agent, over use of a targeted contrast agent alone.

  11. Quantum mechanical design of enzyme active sites.

    Science.gov (United States)

    Zhang, Xiyun; DeChancie, Jason; Gunaydin, Hakan; Chowdry, Arnab B; Clemente, Fernando R; Smith, Adam J T; Handel, T M; Houk, K N

    2008-02-01

    The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

  12. SRTC criticality safety technical review: Nuclear Criticality Safety Evaluation 93-04 enriched uranium receipt

    International Nuclear Information System (INIS)

    Rathbun, R.

    1993-01-01

    Review of NMP-NCS-930087, open-quotes Nuclear Criticality Safety Evaluation 93-04 Enriched Uranium Receipt (U), July 30, 1993, close quotes was requested of SRTC (Savannah River Technology Center) Applied Physics Group. The NCSE is a criticality assessment to determine the mass limit for Engineered Low Level Trench (ELLT) waste uranium burial. The intent is to bury uranium in pits that would be separated by a specified amount of undisturbed soil. The scope of the technical review, documented in this report, consisted of (1) an independent check of the methods and models employed, (2) independent HRXN/KENO-V.a calculations of alternate configurations, (3) application of ANSI/ANS 8.1, and (4) verification of WSRC Nuclear Criticality Safety Manual procedures. The NCSE under review concludes that a 500 gram limit per burial position is acceptable to ensure the burial site remains in a critically safe configuration for all normal and single credible abnormal conditions. This reviewer agrees with that conclusion

  13. Targeting for energy efficiency and improved energy collaboration between different companies using total site analysis (TSA)

    International Nuclear Information System (INIS)

    Hackl, Roman; Andersson, Eva; Harvey, Simon

    2011-01-01

    Rising fuel prices, increasing costs associated with emissions of green house gases and the threat of global warming make efficient use of energy more and more important. Industrial clusters have the potential to significantly increase energy efficiency by energy collaboration. In this paper Sweden's largest chemical cluster is analysed using the total site analysis (TSA) method. TSA delivers targets for the amount of utility consumed and generated through excess energy recovery by the different processes. The method enables investigation of opportunities to deliver waste heat from one process to another using a common utility system. The cluster consists of 5 chemical companies producing a variety of products, including polyethylene (PE), polyvinyl chloride (PVC), amines, ethylene, oxygen/nitrogen and plasticisers. The companies already work together by exchanging material streams. In this study the potential for energy collaboration is analysed in order to reach an industrial symbiosis. The overall heating and cooling demands of the site are around 442 MW and 953 MW, respectively. 122 MW of heat is produced in boilers and delivered to the processes. TSA is used to stepwise design a site-wide utility system which improves energy efficiency. It is shown that heat recovery in the cluster can be increased by 129 MW, i.e. the current utility demand could be completely eliminated and further 7 MW excess steam can be made available. The proposed retrofitted utility system involves the introduction of a site-wide hot water circuit, increased recovery of low pressure steam and shifting of heating steam pressure to lower levels in a number heat exchangers when possible. Qualitative evaluation of the suggested measures shows that 60 MW of the savings potential could to be achieved with moderate changes to the process utility system corresponding to 50% of the heat produced from purchased fuel in the boilers of the cluster. Further analysis showed that after implementation

  14. Canonical A-to-I and C-to-U RNA editing is enriched at 3'UTRs and microRNA target sites in multiple mouse tissues.

    Directory of Open Access Journals (Sweden)

    Tongjun Gu

    Full Text Available RNA editing is a process that modifies RNA nucleotides and changes the efficiency and fidelity of the central dogma. Enzymes that catalyze RNA editing are required for life, and defects in RNA editing are associated with many diseases. Recent advances in sequencing have enabled the genome-wide identification of RNA editing sites in mammalian transcriptomes. Here, we demonstrate that canonical RNA editing (A-to-I and C-to-U occurs in liver, white adipose, and bone tissues of the laboratory mouse, and we show that apparent non-canonical editing (all other possible base substitutions is an artifact of current high-throughput sequencing technology. Further, we report that high-confidence canonical RNA editing sites can cause non-synonymous amino acid changes and are significantly enriched in 3' UTRs, specifically at microRNA target sites, suggesting both regulatory and functional consequences for RNA editing.

  15. Target specific proteochemometric model development for BACE1 - protein flexibility and structural water are critical in virtual screening.

    Science.gov (United States)

    Manoharan, Prabu; Chennoju, Kiranmai; Ghoshal, Nanda

    2015-07-01

    BACE1 is an attractive target in Alzheimer's disease (AD) treatment. A rational drug design effort for the inhibition of BACE1 is actively pursued by researchers in both academic and pharmaceutical industries. This continued effort led to the steady accumulation of BACE1 crystal structures, co-complexed with different classes of inhibitors. This wealth of information is used in this study to develop target specific proteochemometric models and these models are exploited for predicting the prospective BACE1 inhibitors. The models developed in this study have performed excellently in predicting the computationally generated poses, separately obtained from single and ensemble docking approaches. The simple protein-ligand contact (SPLC) model outperforms other sophisticated high end models, in virtual screening performance, developed during this study. In an attempt to account for BACE1 protein active site flexibility information in predictive models, we included the change in the area of solvent accessible surface and the change in the volume of solvent accessible surface in our models. The ensemble and single receptor docking results obtained from this study indicate that the structural water mediated interactions improve the virtual screening results. Also, these waters are essential for recapitulating bioactive conformation during docking study. The proteochemometric models developed in this study can be used for the prediction of BACE1 inhibitors, during the early stage of AD drug discovery.

  16. Critical examination of emergency plans for nuclear accidents

    International Nuclear Information System (INIS)

    Catsaros, Nicolas.

    1986-08-01

    An analysis of emergency plans of various countries for nuclear installations on- and off-site emergency preparedness is presented. The analysis is focused on the off-site organization and countermeasures to protect public health and safety. A critical examination of the different approaches is performed and recommendations for effectiveness improvement and optimization are formulated. (author)

  17. Critical analysis of the potential for therapeutic targeting of mammalian target of rapamycin (mTOR in gastric cancer

    Directory of Open Access Journals (Sweden)

    Inokuchi M

    2014-04-01

    Full Text Available Mikito Inokuchi,1 Keiji Kato,1 Kazuyuki Kojima,2 Kenichi Sugihara1 1Department of Surgical Oncology, 2Department of Minimally Invasive Surgery, Tokyo Medical and Dental University, Tokyo, Japan Abstract: Multidisciplinary treatment including chemotherapy has become the global standard of care for patients with metastatic gastric cancer (mGC; nonetheless, survival remains poor. Although many molecular-targeted therapies have been developed for various cancers, only anti-HER2 treatment has produced promising results in patients with mGC. Mammalian target of rapamycin (mTOR plays a key role in cell proliferation, antiapoptosis, and metastasis in signaling pathways from the tyrosine kinase receptor, and its activation has been demonstrated in gastric cancer (GC cells. This review discusses the clinical relevance of mTOR in GC and examines its potential as a therapeutic target in patients with mGC. Preclinical studies in animal models suggest that suppression of the mTOR pathway inhibits the proliferation of GC cells and delays tumor progression. The mTOR inhibitor everolimus has been evaluated as second- or third-line treatment in clinical trials. Adverse events were well tolerated although the effectiveness of everolimus alone was limited. Everolimus is now being evaluated in combination with chemotherapy in Phase III clinical studies in this subgroup of patients. Two Phase III studies include exploratory biomarker research designed to evaluate the predictive value of the expression or mutation of molecules related to the Akt/mTOR signaling pathway. These biomarker studies may lead to the realization of targeted therapy for selected patients with mGC in the future. Keywords: gastric cancer, mTOR, everolimus

  18. MiR-181b targets Six2 and inhibits the proliferation of metanephric mesenchymal cells in vitro

    International Nuclear Information System (INIS)

    Lyu, Zhongshi; Mao, Zhaomin; Wang, Honglian; Fang, Yin; Chen, Tielin; Wan, Qianya; Wang, Ming; Wang, Nian; Xiao, Jiangming; Wei, Hongyuan; Li, Xun; Liu, Yi; Zhou, Qin

    2013-01-01

    Highlights: •We do bio-informatics websites to analysis of Six2 3′UTR. •MiR181b is a putative miRNA which can targets Six2 3′UTR. •MiR-181b binding site in the 3′UTR of Six2 is functional. •MiR-181b suppresses MK3 cells cell proliferation by targeting Six2. -- Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that down-regulate gene expression by binding to target mRNA for cleavage or translational repression, and play important regulatory roles in renal development. Despite increasing genes have been predicted to be miRNA targets by bioinformatic analysis during kidney development, few of them have been verified by experiment. The objective of our study is to identify the miRNAs targeting Six2, a critical transcription factor that maintains the mesenchymal progenitor pool via self-renewal (proliferation) during renal development. We initially analyzed the 3′UTR of Six2 and found 37 binding sites targeted by 50 putative miRNAs in the 3′UTR of Six2. Among the 50 miRNAs, miR-181b is the miRNAs predicted by the three used websites. In our study, the results of luciferase reporter assay, realtime-PCR and Western blot demonstrated that miR-181b directly targeted on the 3′UTR of Six2 and down-regulate the expression of Six2 at mRNA and protein levels. Furthermore, EdU proliferation assay along with the Six2 rescue strategy showed that miR-181b suppresses the proliferation of metanephric mesenchymal by targeting Six2 in part. In our research, we concluded that by targeting the transcription factor gene Six2, miR-181b inhibits the proliferation of metanephric mesenchymal cells in vitro and might play an important role in the formation of nephrons

  19. MiR-181b targets Six2 and inhibits the proliferation of metanephric mesenchymal cells in vitro

    Energy Technology Data Exchange (ETDEWEB)

    Lyu, Zhongshi; Mao, Zhaomin; Wang, Honglian; Fang, Yin; Chen, Tielin [The Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); Wan, Qianya [The Undergraduates Class of 2011 entry, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); Wang, Ming; Wang, Nian; Xiao, Jiangming; Wei, Hongyuan; Li, Xun; Liu, Yi [The Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China); Zhou, Qin, E-mail: zhouqin@cqmu.edu.cn [The Division of Molecular Nephrology and the Creative Training Center for Undergraduates, The M.O.E. Key Laboratory of Laboratory Medical Diagnostics, The College of Laboratory Medicine, Chongqing Medical University, Chongqing 400016 (China)

    2013-11-01

    Highlights: •We do bio-informatics websites to analysis of Six2 3′UTR. •MiR181b is a putative miRNA which can targets Six2 3′UTR. •MiR-181b binding site in the 3′UTR of Six2 is functional. •MiR-181b suppresses MK3 cells cell proliferation by targeting Six2. -- Abstract: MicroRNAs (miRNAs) are small non-coding RNAs that down-regulate gene expression by binding to target mRNA for cleavage or translational repression, and play important regulatory roles in renal development. Despite increasing genes have been predicted to be miRNA targets by bioinformatic analysis during kidney development, few of them have been verified by experiment. The objective of our study is to identify the miRNAs targeting Six2, a critical transcription factor that maintains the mesenchymal progenitor pool via self-renewal (proliferation) during renal development. We initially analyzed the 3′UTR of Six2 and found 37 binding sites targeted by 50 putative miRNAs in the 3′UTR of Six2. Among the 50 miRNAs, miR-181b is the miRNAs predicted by the three used websites. In our study, the results of luciferase reporter assay, realtime-PCR and Western blot demonstrated that miR-181b directly targeted on the 3′UTR of Six2 and down-regulate the expression of Six2 at mRNA and protein levels. Furthermore, EdU proliferation assay along with the Six2 rescue strategy showed that miR-181b suppresses the proliferation of metanephric mesenchymal by targeting Six2 in part. In our research, we concluded that by targeting the transcription factor gene Six2, miR-181b inhibits the proliferation of metanephric mesenchymal cells in vitro and might play an important role in the formation of nephrons.

  20. Increasing the structural coverage of tuberculosis drug targets.

    Science.gov (United States)

    Baugh, Loren; Phan, Isabelle; Begley, Darren W; Clifton, Matthew C; Armour, Brianna; Dranow, David M; Taylor, Brandy M; Muruthi, Marvin M; Abendroth, Jan; Fairman, James W; Fox, David; Dieterich, Shellie H; Staker, Bart L; Gardberg, Anna S; Choi, Ryan; Hewitt, Stephen N; Napuli, Alberto J; Myers, Janette; Barrett, Lynn K; Zhang, Yang; Ferrell, Micah; Mundt, Elizabeth; Thompkins, Katie; Tran, Ngoc; Lyons-Abbott, Sally; Abramov, Ariel; Sekar, Aarthi; Serbzhinskiy, Dmitri; Lorimer, Don; Buchko, Garry W; Stacy, Robin; Stewart, Lance J; Edwards, Thomas E; Van Voorhis, Wesley C; Myler, Peter J

    2015-03-01

    High-resolution three-dimensional structures of essential Mycobacterium tuberculosis (Mtb) proteins provide templates for TB drug design, but are available for only a small fraction of the Mtb proteome. Here we evaluate an intra-genus "homolog-rescue" strategy to increase the structural information available for TB drug discovery by using mycobacterial homologs with conserved active sites. Of 179 potential TB drug targets selected for x-ray structure determination, only 16 yielded a crystal structure. By adding 1675 homologs from nine other mycobacterial species to the pipeline, structures representing an additional 52 otherwise intractable targets were solved. To determine whether these homolog structures would be useful surrogates in TB drug design, we compared the active sites of 106 pairs of Mtb and non-TB mycobacterial (NTM) enzyme homologs with experimentally determined structures, using three metrics of active site similarity, including superposition of continuous pharmacophoric property distributions. Pair-wise structural comparisons revealed that 19/22 pairs with >55% overall sequence identity had active site Cα RMSD 85% side chain identity, and ≥80% PSAPF (similarity based on pharmacophoric properties) indicating highly conserved active site shape and chemistry. Applying these results to the 52 NTM structures described above, 41 shared >55% sequence identity with the Mtb target, thus increasing the effective structural coverage of the 179 Mtb targets over three-fold (from 9% to 32%). The utility of these structures in TB drug design can be tested by designing inhibitors using the homolog structure and assaying the cognate Mtb enzyme; a promising test case, Mtb cytidylate kinase, is described. The homolog-rescue strategy evaluated here for TB is also generalizable to drug targets for other diseases. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Contamination and UV ageing of diffuser targets used in satellite inflight and ground reference test site calibrations

    Science.gov (United States)

    Vaskuri, Anna; Greenwell, Claire; Hessey, Isabel; Tompkins, Jordan; Woolliams, Emma

    2018-02-01

    Diffuser reflectance targets are key components in in-orbit calibrations and for verifying ground reference test sites. In this work, Spectralon, Diffusil, and Heraeus diffusers were exposed to exhaust gases and ultraviolet (UV) radiation in the ambient air conditions and their degradations were monitored by measuring changes in spectral reflectances. Spectralon is a state-of-the-art diffuser made of polytetrafluoroethylene, and Diffusil and Heraeus diffusers are made of fused silica with gas bubbles inside. Based on the contamination tests, Spectralon degrades faster than fused silica diffusers. For the samples exposed to contamination for 20 minutes, the 250 nm - 400 nm total diffuse spectral reflectance of Spectralon degraded 3-5 times more when exposed to petrol-like emission and 16-23 times more when exposed to diesel-like emission, compared with Diffusil. When the reflectance changes of Spectralon were compared with those of Heraeus, Spectralon degraded 3-4 times more when exposed to petrol-like emission for 20 minutes and 5-7 times more when exposed to diesel-like emission for 7.5 minutes. When the samples contaminated were exposed to UV radiation in the ambient air, their reflectance gradually restored back to the original level. In conclusion, fused silica diffusers are more resistant to hydrocarbon contaminants present in ground reference test sites, and thus more stable under UV radiation in the air.

  2. A Cross-Industry Review of B2B Critical Success Factors.

    Science.gov (United States)

    Eid, Riyad; Trueman, Myfanwy; Ahmed, Abdel Moneim

    2002-01-01

    Presents a comprehensive review of B2B (business-to- business) international Internet marketing and identifies 21 critical success factors in five categories: marketing strategy, including management support, strategic goals, and collaboration; Web site factors, including Web site design; global factors, including multilanguage sites and cultural…

  3. Targeted enzyme prodrug therapies.

    Science.gov (United States)

    Schellmann, N; Deckert, P M; Bachran, D; Fuchs, H; Bachran, C

    2010-09-01

    The cure of cancer is still a formidable challenge in medical science. Long-known modalities including surgery, chemotherapy and radiotherapy are successful in a number of cases; however, invasive, metastasized and inaccessible tumors still pose an unresolved and ongoing problem. Targeted therapies designed to locate, detect and specifically kill tumor cells have been developed in the past three decades as an alternative to treat troublesome cancers. Most of these therapies are either based on antibody-dependent cellular cytotoxicity, targeted delivery of cytotoxic drugs or tumor site-specific activation of prodrugs. The latter is a two-step procedure. In the first step, a selected enzyme is accumulated in the tumor by guiding the enzyme or its gene to the neoplastic cells. In the second step, a harmless prodrug is applied and specifically converted by this enzyme into a cytotoxic drug only at the tumor site. A number of targeting systems, enzymes and prodrugs were investigated and improved since the concept was first envisioned in 1974. This review presents a concise overview on the history and latest developments in targeted therapies for cancer treatment. We cover the relevant technologies such as antibody-directed enzyme prodrug therapy (ADEPT), gene-directed enzyme prodrug therapy (GDEPT) as well as related therapies such as clostridial- (CDEPT) and polymer-directed enzyme prodrug therapy (PDEPT) with emphasis on prodrug-converting enzymes, prodrugs and drugs.

  4. Nanoscale Synaptic Membrane Mimetic Allows Unbiased High Throughput Screen That Targets Binding Sites for Alzheimer’s-Associated Aβ Oligomers

    Science.gov (United States)

    Wilcox, Kyle C.; Marunde, Matthew R.; Das, Aditi; Velasco, Pauline T.; Kuhns, Benjamin D.; Marty, Michael T.; Jiang, Haoming; Luan, Chi-Hao; Sligar, Stephen G.; Klein, William L.

    2015-01-01

    Despite their value as sources of therapeutic drug targets, membrane proteomes are largely inaccessible to high-throughput screening (HTS) tools designed for soluble proteins. An important example comprises the membrane proteins that bind amyloid β oligomers (AβOs). AβOs are neurotoxic ligands thought to instigate the synapse damage that leads to Alzheimer’s dementia. At present, the identities of initial AβO binding sites are highly uncertain, largely because of extensive protein-protein interactions that occur following attachment of AβOs to surface membranes. Here, we show that AβO binding sites can be obtained in a state suitable for unbiased HTS by encapsulating the solubilized synaptic membrane proteome into nanoscale lipid bilayers (Nanodiscs). This method gives a soluble membrane protein library (SMPL)—a collection of individualized synaptic proteins in a soluble state. Proteins within SMPL Nanodiscs showed enzymatic and ligand binding activity consistent with conformational integrity. AβOs were found to bind SMPL Nanodiscs with high affinity and specificity, with binding dependent on intact synaptic membrane proteins, and selective for the higher molecular weight oligomers known to accumulate at synapses. Combining SMPL Nanodiscs with a mix-incubate-read chemiluminescence assay provided a solution-based HTS platform to discover antagonists of AβO binding. Screening a library of 2700 drug-like compounds and natural products yielded one compound that potently reduced AβO binding to SMPL Nanodiscs, synaptosomes, and synapses in nerve cell cultures. Although not a therapeutic candidate, this small molecule inhibitor of synaptic AβO binding will provide a useful experimental antagonist for future mechanistic studies of AβOs in Alzheimer’s model systems. Overall, results provide proof of concept for using SMPLs in high throughput screening for AβO binding antagonists, and illustrate in general how a SMPL Nanodisc system can facilitate drug

  5. Targeted gene insertion for molecular medicine.

    Science.gov (United States)

    Voigt, Katrin; Izsvák, Zsuzsanna; Ivics, Zoltán

    2008-11-01

    Genomic insertion of a functional gene together with suitable transcriptional regulatory elements is often required for long-term therapeutical benefit in gene therapy for several genetic diseases. A variety of integrating vectors for gene delivery exist. Some of them exhibit random genomic integration, whereas others have integration preferences based on attributes of the targeted site, such as primary DNA sequence and physical structure of the DNA, or through tethering to certain DNA sequences by host-encoded cellular factors. Uncontrolled genomic insertion bears the risk of the transgene being silenced due to chromosomal position effects, and can lead to genotoxic effects due to mutagenesis of cellular genes. None of the vector systems currently used in either preclinical experiments or clinical trials displays sufficient preferences for target DNA sequences that would ensure appropriate and reliable expression of the transgene and simultaneously prevent hazardous side effects. We review in this paper the advantages and disadvantages of both viral and non-viral gene delivery technologies, discuss mechanisms of target site selection of integrating genetic elements (viruses and transposons), and suggest distinct molecular strategies for targeted gene delivery.

  6. Criticality calculations in reactor accelerator coupling experiment (Race)

    International Nuclear Information System (INIS)

    Reda, M.A.; Spaulding, R.; Hunt, A.; Harmon, J.F.; Beller, D.E.

    2005-01-01

    A Reactor Accelerator Coupling Experiment (RACE) is to be performed at the Idaho State University Idaho Accelerator Center (IAC). The electron accelerator is used to generate neutrons by inducing Bremsstrahlung photon-neutron reactions in a Tungsten- Copper target. This accelerator/target system produces a source of ∼1012 n/s, which can initiate fission reactions in the subcritical system. This coupling experiment between a 40-MeV electron accelerator and a subcritical system will allow us to predict and measure coupling efficiency, reactivity, and multiplication. In this paper, the results of the criticality and multiplication calculations, which were carried out using the Monte Carlo radiation transport code MCNPX, for different coupling design options are presented. The fuel plate arrangements and the surrounding tank dimensions have been optimized. Criticality using graphite instead of water for reflector/moderator outside of the core region has been studied. The RACE configuration at the IAC will have a criticality (k-effective) of about 0,92 and a multiplication of about 10. (authors)

  7. Critical review of decision support tools for sustainability assessment of site remediation options.

    Science.gov (United States)

    Huysegoms, Lies; Cappuyns, Valérie

    2017-07-01

    In Europe alone, there are more than 2,5 million potentially contaminated sites of which 14% are expected to require remediation. Contaminated soil and groundwater can cause damage to human health as well as to valuable ecosystems. Globally more attention has been paid to this problem of soil contamination in the past decades. For example, more than 58 000 sites have been remediated in Europe between 2006 and 2011. Together with this increase in remediation projects there has been a surge in the development of new remediation technologies and decision support tools to be able to match every site and its specific characteristics to the best possible remediation alternative. In the past years the development of decision support tools (DST) has evolved in a more sustainable direction. Several DSTs added the claim not only to denote effective or technologically and economically feasible remediation alternatives but also to point out the more or most sustainable remediation alternatives. These trends in the evaluation of site remediation options left users with a confusing clew of possibly applicable tools to assist them in decision making for contaminated site remediation. This review provides a structured overview on the extent decision support tools for contaminated site remediation, that claim to assist in choosing the most sustainable remediation alternative, actually include the different elements of sustainability proposed in our assessment framework. The review contains an in-depth analysis of thirteen tools specifically developed to assess the sustainability of site remediation alternatives. This analysis is based on six criteria derived from the definition of sustainable development of the Brundtland report. The six criteria were concretized by using the three pillars of sustainability, applied to site remediation according to the SuRF-UK framework, two criteria derived from Life Cycle Assessment and Cost-Benefit Analysis, and an 'User friendly' criterion

  8. Novel epigenetic target therapy for prostate cancer: a preclinical study.

    Directory of Open Access Journals (Sweden)

    Ilaria Naldi

    Full Text Available Epigenetic events are critical contributors to the pathogenesis of cancer, and targeting epigenetic mechanisms represents a novel strategy in anticancer therapy. Classic demethylating agents, such as 5-Aza-2'-deoxycytidine (Decitabine, hold the potential for reprograming somatic cancer cells demonstrating high therapeutic efficacy in haematological malignancies. On the other hand, epigenetic treatment of solid tumours often gives rise to undesired cytotoxic side effects. Appropriate delivery systems able to enrich Decitabine at the site of action and improve its bioavailability would reduce the incidence of toxicity on healthy tissues. In this work we provide preclinical evidences of a safe, versatile and efficient targeted epigenetic therapy to treat hormone sensitive (LNCap and hormone refractory (DU145 prostate cancers. A novel Decitabine formulation, based on the use of engineered erythrocyte (Erythro-Magneto-Hemagglutinin Virosomes, EMHVs drug delivery system (DDS carrying this drug, has been refined. Inside the EMHVs, the drug was shielded from the environment and phosphorylated in its active form. The novel magnetic EMHV DDS, endowed with fusogenic protein, improved the stability of the carried drug and exhibited a high efficiency in confining its delivery at the site of action in vivo by applying an external static magnetic field. Here we show that Decitabine loaded into EMHVs induces a significant tumour mass reduction in prostate cancer xenograft models at a concentration, which is seven hundred times lower than the therapeutic dose, suggesting an improved pharmacokinetics/pharmacodynamics of drug. These results are relevant for and discussed in light of developing personalised autologous therapies and innovative clinical approach for the treatment of solid tumours.

  9. Novel epigenetic target therapy for prostate cancer: a preclinical study.

    Science.gov (United States)

    Naldi, Ilaria; Taranta, Monia; Gherardini, Lisa; Pelosi, Gualtiero; Viglione, Federica; Grimaldi, Settimio; Pani, Luca; Cinti, Caterina

    2014-01-01

    Epigenetic events are critical contributors to the pathogenesis of cancer, and targeting epigenetic mechanisms represents a novel strategy in anticancer therapy. Classic demethylating agents, such as 5-Aza-2'-deoxycytidine (Decitabine), hold the potential for reprograming somatic cancer cells demonstrating high therapeutic efficacy in haematological malignancies. On the other hand, epigenetic treatment of solid tumours often gives rise to undesired cytotoxic side effects. Appropriate delivery systems able to enrich Decitabine at the site of action and improve its bioavailability would reduce the incidence of toxicity on healthy tissues. In this work we provide preclinical evidences of a safe, versatile and efficient targeted epigenetic therapy to treat hormone sensitive (LNCap) and hormone refractory (DU145) prostate cancers. A novel Decitabine formulation, based on the use of engineered erythrocyte (Erythro-Magneto-Hemagglutinin Virosomes, EMHVs) drug delivery system (DDS) carrying this drug, has been refined. Inside the EMHVs, the drug was shielded from the environment and phosphorylated in its active form. The novel magnetic EMHV DDS, endowed with fusogenic protein, improved the stability of the carried drug and exhibited a high efficiency in confining its delivery at the site of action in vivo by applying an external static magnetic field. Here we show that Decitabine loaded into EMHVs induces a significant tumour mass reduction in prostate cancer xenograft models at a concentration, which is seven hundred times lower than the therapeutic dose, suggesting an improved pharmacokinetics/pharmacodynamics of drug. These results are relevant for and discussed in light of developing personalised autologous therapies and innovative clinical approach for the treatment of solid tumours.

  10. Understanding pathways of exposure using site-specific habits surveys, particularly new pathways and methodologies

    International Nuclear Information System (INIS)

    Grzechnik, M.; McTaggart, K.; Clyne, F.

    2006-01-01

    Full text of publication follows: UK policy on the control of radiation exposure via routine discharges from nuclear licensed sites has long been based on ICRP recommendations that embody the principles of justification of practices, optimisation of protection, and dose limitation. Radiological protection of the public is based on the concept of a critical group of individuals. This group is defined as those people who, as a result of the area they reside and their habits, receive the highest radiation dose due to the operations of a site. Therefore, if the dose to this critical group is acceptable in relation to relevant dose limits and constraints, then other members of the public will receive lower doses. Thus, the principle of critical groups provides overall protection for the public. Surveys to determine local habits involve an integrated methodology, whereby the potential radioactive exposure pathways from liquid and gaseous discharges and direct radiation from the site are investigated. Surveys to identify these habits must be undertaken rigorously for consistency, and have been known to reveal unexpected pathways of radiation exposure. Pathways typically include consumption of local foodstuffs and external exposure. Furthermore, a number of critical groups ma y be identified within a single survey area if the habits of one group do not adequately describe those of the other inhabitants of the area. Survey preparation involves the initial identification of high producers and consumers of local foods in a geographically defined area surrounding the nuclear facility. Pathways can be broken down into three general groups, which include exposure arising from; 1) Terrestrial (gaseous) discharges surveyed within 5 km of the site 2) Direct radiation surveyed within 1 km of the site 3) Aquatic (liquid) discharges surveyed within local areas affected by the discharges, including seas, rivers and sewage works. The survey fieldwork involves interviewing members of the

  11. Establishing a Critical Zone Observatory site in Turkey

    Science.gov (United States)

    Demir, Gokben; Akyurek, Zuhal; Binley, Andrew; Yucel, Ismail; Kentel, Elcin; Merzi, Nuri; Yilmaz, Tugrul; Yanmaz, Melih

    2017-04-01

    The Earth's Critical Zone (CZ) is the planetary veneer that extends from the air above our treetops to the layers of rocks below, which supports human activity. This includes life-sustaining resources for energy, food, and water. The CZ also includes places where we dispose and store toxic materials, and expose to other contaminants. The fate of change in the CZ is important to the government and business planners to help respond to effects of disease, drought, and land degradation in agricultural and urban settings. Critical Zone Observatory's are outdoor laboratories that are highly instrumented and becoming integrated into a global network. Turkey has a diversified landscape, representing most terrestrial ecosystems on Earth. Turkey is unique because some regions have been subject to high-impact human influence for thousands of years. This millennial-scale anthropogenic affect on the CZ does not exist at most other CZO's. In this study the establishment of a CZO at a basin located in the south part of Turkey which the instrumentation that has been already completed is presented. The mean altitude of the basin is 1601 m and it has 526km2 area. The cherry trees along the river, agricultural areas and the natural vegetation composed of pasture and shrub are the main land cover in the basin. The brown forest and brown soil are the main soil types. The basin has a complex geology. There are two main tributaries of the stream: one of them is fed by gypsum ground waters and mine drainage and the other one is fed by shallow fresh ground water. Three meteorological stations were established within this project at 1246 m, 1580m and 1790m. At these stations besides the meteorological variables, soil water content are measured. The discharge observations are carried out at three discharge observation stations where the water stage, temperature and electrical conductivity values are measured. A CRS200B soil moisture probe is installed at 1459 m and the soil water content is

  12. Enhancers Are Major Targets for Murine Leukemia Virus Vector Integration

    Science.gov (United States)

    De Ravin, Suk See; Su, Ling; Theobald, Narda; Choi, Uimook; Macpherson, Janet L.; Poidinger, Michael; Symonds, Geoff; Pond, Susan M.; Ferris, Andrea L.; Hughes, Stephen H.

    2014-01-01

    ABSTRACT Retroviral vectors have been used in successful gene therapies. However, in some patients, insertional mutagenesis led to leukemia or myelodysplasia. Both the strong promoter/enhancer elements in the long terminal repeats (LTRs) of murine leukemia virus (MLV)-based vectors and the vector-specific integration site preferences played an important role in these adverse clinical events. MLV integration is known to prefer regions in or near transcription start sites (TSS). Recently, BET family proteins were shown to be the major cellular proteins responsible for targeting MLV integration. Although MLV integration sites are significantly enriched at TSS, only a small fraction of the MLV integration sites (integration map of more than one million integration sites from CD34+ hematopoietic stem cells transduced with a clinically relevant MLV-based vector. The integration sites form ∼60,000 tight clusters. These clusters comprise ∼1.9% of the genome. The vast majority (87%) of the integration sites are located within histone H3K4me1 islands, a hallmark of enhancers. The majority of these clusters also have H3K27ac histone modifications, which mark active enhancers. The enhancers of some oncogenes, including LMO2, are highly preferred targets for integration without in vivo selection. IMPORTANCE We show that active enhancer regions are the major targets for MLV integration; this means that MLV preferentially integrates in regions that are favorable for viral gene expression in a variety of cell types. The results provide insights for MLV integration target site selection and also explain the high risk of insertional mutagenesis that is associated with gene therapy trials using MLV vectors. PMID:24501411

  13. DOE site performance assessment activities

    International Nuclear Information System (INIS)

    1990-07-01

    Information on performance assessment capabilities and activities was collected from eight DOE sites. All eight sites either currently dispose of low-level radioactive waste (LLW) or plan to dispose of LLW in the near future. A survey questionnaire was developed and sent to key individuals involved in DOE Order 5820.2A performance assessment activities at each site. The sites surveyed included: Hanford Site (Hanford), Idaho National Engineering Laboratory (INEL), Los Alamos National Laboratory (LANL), Nevada Test Site (NTS), Oak Ridge National Laboratory (ORNL), Paducah Gaseous Diffusion Plant (Paducah), Portsmouth Gaseous Diffusion Plant (Portsmouth), and Savannah River Site (SRS). The questionnaire addressed all aspects of the performance assessment process; from waste source term to dose conversion factors. This report presents the information developed from the site questionnaire and provides a comparison of site-specific performance assessment approaches, data needs, and ongoing and planned activities. All sites are engaged in completing the radioactive waste disposal facility performance assessment required by DOE Order 5820.2A. Each site has achieved various degrees of progress and have identified a set of critical needs. Within several areas, however, the sites identified common needs and questions

  14. Social Networking Sites: A premise on enhancement

    OpenAIRE

    MANINDERPAL SINGH SAINI; GYEWON MOON

    2013-01-01

    This article address five constructs that are paramount toward continued evolution of social networking sites (SNS`s) they include, - stabilisation, visual, language, security and flexibility. These constructs add to our proposed framework. Firmly grounded research on social networking sites and literature, we propose that user feedback, is the critical component that stimulates the development and growth of social networking sites online. We offer a framework that can aid new and current soc...

  15. Targets development at Sandia National Laboratories

    International Nuclear Information System (INIS)

    Smith, M.L.; Hebron, D.; Derzon, M.; Olson, R.; Alberts, T.

    1997-01-01

    For many years, Sandia National Laboratories under contract to the Department of Energy has produced targets designed to understand complex ion beam and z-pinch plasma physics. This poster focuses on the features of target designs that make them suitable for Z-pinch plasma physics applications. Precision diagnostic targets will prove critical in understanding the plasma physics model needed for future ion beam and z-pinch design. Targets are designed to meet specific physics needs; in this case the authors have fabricated targets to maximize information about the end-on versus side-on x-ray emission and z-pinch hohlraum development. In this poster, they describe the fabrication and characterization techniques. They include discussion of current targets under development as well as target fabrication capabilities. Advanced target designs are fabricated by Sandia National Laboratories in cooperation with General Atomics of San Diego, CA and W.J. Schafer Associates, Inc. of Livermore, CA

  16. Hydrogen peroxide (H2O2) irreversibly inactivates creatine kinase from Pelodiscus sinensis by targeting the active site cysteine.

    Science.gov (United States)

    Wang, Wei; Lee, Jinhyuk; Hao, Hao; Park, Yong-Doo; Qian, Guo-Ying

    2017-12-01

    Creatine kinase (EC 2.7.3.2, CK) plays an important role in cellular energy metabolism and homeostasis by catalysing the transfer of phosphate between ATP and creatine phosphate. In this study, we investigated the effects of H 2 O 2 on PSCKM (muscle type creatine kinase from Pelodiscus sinensis) by the integrating method between enzyme kinetics and docking simulations. We found that H 2 O 2 strongly inactivated PSCKM (IC 50 =0.25mM) in a first-order kinetic process, and targeted the active site cysteine directly. A conformational study showed that H 2 O 2 did not induce the tertiary structural changes in PSCKM with no extensive exposure of hydrophobic surfaces. Sequential docking simulations between PSCKM and H 2 O 2 indicated that H 2 O 2 interacts with the ADP binding region of the active site, consistent with experimental results that demonstrated H 2 O 2 -induced inactivation. Our study demonstrates the effect of H 2 O 2 on PSCKM enzymatic function and unfolding, and provides important insight into the changes undergone by this central metabolic enzyme in ectothermic animals in response to the environment. Copyright © 2017 Elsevier B.V. All rights reserved.

  17. New "persona" concept helps site designers cater to target user segments' needs.

    Science.gov (United States)

    2004-09-01

    Using the relatively new "persona" design concept, Web strategists create a set of archetypical user characters, each one representing one of their site's primary audiences. Then, as their site is constructed or upgraded, they champion the personas, arguing on their behalf and forcing the design team to take each audience's needs and wants into account.

  18. 20-20-20: the target of European energy policy

    International Nuclear Information System (INIS)

    Clo, R.; Verde, S.

    2007-01-01

    The last Spring European Council set ambitious targets in its new EU energy policy. Reaching these objectives is far from going without saying and without hidden dangers, if the EU aims at these targets uncritically, national and European energy systems will be exposed to additional risks and problems. Hence, the critical issues must be born in mind negotiating national targets in Brussels [it

  19. ALARP considerations in criticality safety assessments

    International Nuclear Information System (INIS)

    Bowden, Russell L.; Barnes, Andrew; Thorne, Peter R.; Venner, Jack

    2003-01-01

    Demonstrating that the risk to the public and workers is As Low As Reasonably Practicable (ALARP) is a fundamental requirement of safety cases for nuclear facilities in the United Kingdom. This is embodied in the Safety Assessment Principles (SAPs) published by the Regulator, the essence of which is incorporated within the safety assessment processes of the various nuclear site licensees. The concept of ALARP within criticality safety assessments has taken some time to establish in the United Kingdom. In principle, the licensee is obliged to search for a deterministic criticality safety solution, such as safe geometry vessels and passive control features, rather than placing reliance on active measurement devices and plant administrative controls. This paper presents a consideration of some ALARP issues in relation to the development of criticality safety cases. The paper utilises some idealised examples covering a range of issues facing the criticality safety assessor, including new plant design, operational plant and decommissioning activities. These examples are used to outline the elements of the criticality safety cases and present a discussion of ALARP in the context of criticality safety assessments. (author)

  20. Targeted marketing and public health.

    Science.gov (United States)

    Grier, Sonya A; Kumanyika, Shiriki

    2010-01-01

    Targeted marketing techniques, which identify consumers who share common needs or characteristics and position products or services to appeal to and reach these consumers, are now the core of all marketing and facilitate its effectiveness. However, targeted marketing, particularly of products with proven or potential adverse effects (e.g., tobacco, alcohol, entertainment violence, or unhealthful foods) to consumer segments defined as vulnerable raises complex concerns for public health. It is critical that practitioners, academics, and policy makers in marketing, public health, and other fields recognize and understand targeted marketing as a specific contextual influence on the health of children and adolescents and, for different reasons, ethnic minority populations and other populations who may benefit from public health protections. For beneficial products, such understanding can foster more socially productive targeting. For potentially harmful products, understanding the nature and scope of targeted marketing influences will support identification and implementation of corrective policies.

  1. Target sites for chemical regulation of strigolactone signaling

    Directory of Open Access Journals (Sweden)

    Hidemitsu eNakamura

    2014-11-01

    Full Text Available Demands for plant growth regulators (chemicals that control plant growth are increasing globally, especially in developing countries. Both positive and negative plant growth regulators are widely used to enhance crop production and to suppress unwanted shoot growth, respectively. Strigolactones (SLs are multifunctional molecules that function as phytohormones, inhibiting shoot branching and also functioning in the rhizospheric communication with symbiotic fungi and parasitic weeds. Therefore, it is anticipated that chemicals that regulate the functions of SLs will be widely used in agricultural applications. Although the SL biosynthetic pathway is not fully understood, it has been demonstrated that beta-carotene isomerases, carotenoid cleavage dioxygenases (CCDs, and a cytochrome P450 monooxygenase are involved in strigolactone biosynthesis. A CCD inhibitor, abamine, which is also an inhibitor of abscisic acid biosynthesis, reduces the levels of SL in several plant species and reduces the germination rate of Orobanche minor seeds grown with tobacco. On the basis of the structure of abamine, several chemicals have been designed to specifically inhibit CCDs during SL synthesis. Cytochrome P450 monooxygenase is another target enzyme in the development of SL biosynthesis inhibitors, and the triazole-derived TIS series of chemicals is known to include SL biosynthesis inhibitors, although their target enzyme has not been identified. Recently, DWARF14 (D14 has been shown to be a receptor for SLs, and the D-ring moiety of SL is essential for its recognition by D14. A variety of SL agonists are currently under development and most agonists commonly contain the D-ring or a D-ring-like moiety. Several research groups have also resolved the crystal structure of D14 in the last two years. It is expected that this information on the D14 structure will be invaluable not only for developing SL agonists with novel structures but also in the design of inhibitors

  2. Finding flicker: Critical differences in temporal frequency capture attention

    Directory of Open Access Journals (Sweden)

    John eCass

    2011-11-01

    Full Text Available Rapid visual flicker is known to capture attention. Here we show slow flicker can also capture attention under reciprocal temporal conditions. Observers searched for a target line (vertical or horizontal among tilted distractors. Distractor lines were surrounded by luminance modulating annuli, all flickering sinusoidally at 1.3 or 12.1 Hz, while the target’s annulus flickered at frequencies within this range. Search times improved with increasing target/distractor frequency differences. For target-distractor frequency separations > 5 Hz reaction times were minimal with high frequency targets correctly identified more rapidly than low frequency targets (~400ms. Critically, however, at these optimal frequency separations search times for low and high frequency targets were unaffected by set size (slow flicker popped out from high flicker, and vice versa, indicating parallel and symmetric search performance when searching for high or low frequency targets. In a ‘cost’ experiment using 1.3 and 12.1 Hz flicker, the unique flickering annulus sometimes surrounded a distractor and, on other trials, surrounded the target. When centred on a distractor, the unique frequency produced a clear and symmetrical search cost. Together, these symmetric pop-out and search costs demonstrate that temporal frequency is a pre-attentive visual feature capable of capturing attention, and that it is relative rather than absolute frequencies that are critical. The shape of the search functions strongly suggest that early visual temporal frequency filters underlie these effects.

  3. Identification of critical contaminants in wastewater effluent for managed aquifer recharge.

    Science.gov (United States)

    Yuan, Jie; Van Dyke, Michele I; Huck, Peter M

    2017-04-01

    Managed aquifer recharge (MAR) using highly treated effluent from municipal wastewater treatment plants has been recognized as a promising strategy for indirect potable water reuse. Treated wastewater effluent can contain a number of residual contaminants that could have adverse effects on human health, and some jurisdictions have regulations in place to govern these. For those that do not, but where reuse may be under consideration, it is of crucial importance to develop a strategy for identifying priority contaminants, which can then be used to understand the water treatment technologies that might be required. In this study, a multi-criteria approach to identify critical contaminants in wastewater effluent for MAR was developed and applied using a case study site located in southern Ontario, Canada. An important aspect of this approach was the selection of representative compounds for each group of contaminants, based on potential for occurrence in wastewater and expected health or environmental impacts. Due to a lack of MAR regulations in Canada, the study first proposed potential recharge water quality targets. Predominant contaminants, potential additional contaminants, and potential emerging contaminants, which together comprise critical contaminants for MAR with reclaimed water, were then selected based on the case study wastewater effluent monitoring data and literature data. This paper proposes an approach for critical contaminant selection, which will be helpful to guide future implementation of MAR projects using wastewater treatment plant effluents. Copyright © 2016 Elsevier Ltd. All rights reserved.

  4. Endothelial Cell-Targeted Adenoviral Vector for Suppressing Breast Malignancies

    National Research Council Canada - National Science Library

    Huang, Shuang

    2004-01-01

    .... Our proposal is designed to develop an endothelial cell-targeted adenoviral vector and to use the targeted vector to express high levels of anticancer therapeutic genes in the sites of angiogenenic...

  5. Optimization of radiotherapy to target volumes with concave outlines: target-dose homogenization and selective sparing of critical structures by constrained matrix inversion

    Energy Technology Data Exchange (ETDEWEB)

    Colle, C; Van den Berge, D; De Wagter, C; Fortan, L; Van Duyse, B; De Neve, W

    1995-12-01

    The design of 3D-conformal dose distributions for targets with concave outlines is a technical challenge in conformal radiotherapy. For these targets, it is impossible to find beam incidences for which the target volume can be isolated from the tissues at risk. Commonly occurring examples are most thyroid cancers and the targets located at the lower neck and upper mediastinal levels related to some head and neck. A solution to this problem was developed, using beam intensity modulation executed with a multileaf collimator by applying a static beam-segmentation technique. The method includes the definition of beam incidences and beam segments of specific shape as well as the calculation of segment weights. Tests on Sherouse`s GRATISTM planning system allowed to escalate the dose to these targets to 65-70 Gy without exceeding spinal cord tolerance. Further optimization by constrained matrix inversion was investigated to explore the possibility of further dose escalation.

  6. Confronting "Difficult Knowledge": Critical Aesthetics and War in the Classroom

    Science.gov (United States)

    Heybach Vivirito, Jessica A.

    2012-01-01

    This qualitative multi-site case study explores critical aesthetic experiences in teacher education classrooms, and advocates for the inclusion of theoretical and practical knowledge of "difficult knowledge," visual culture, and critical aesthetics in the classroom. Social reality consists of a perpetual stream of tragic and horrific…

  7. Geographic Hotspots of Critical National Infrastructure.

    Science.gov (United States)

    Thacker, Scott; Barr, Stuart; Pant, Raghav; Hall, Jim W; Alderson, David

    2017-12-01

    Failure of critical national infrastructures can result in major disruptions to society and the economy. Understanding the criticality of individual assets and the geographic areas in which they are located is essential for targeting investments to reduce risks and enhance system resilience. Within this study we provide new insights into the criticality of real-life critical infrastructure networks by integrating high-resolution data on infrastructure location, connectivity, interdependence, and usage. We propose a metric of infrastructure criticality in terms of the number of users who may be directly or indirectly disrupted by the failure of physically interdependent infrastructures. Kernel density estimation is used to integrate spatially discrete criticality values associated with individual infrastructure assets, producing a continuous surface from which statistically significant infrastructure criticality hotspots are identified. We develop a comprehensive and unique national-scale demonstration for England and Wales that utilizes previously unavailable data from the energy, transport, water, waste, and digital communications sectors. The testing of 200,000 failure scenarios identifies that hotspots are typically located around the periphery of urban areas where there are large facilities upon which many users depend or where several critical infrastructures are concentrated in one location. © 2017 Society for Risk Analysis.

  8. Target surface condition during reactive glow discharge sputtering of copper

    International Nuclear Information System (INIS)

    Depla, D; Haemers, J; Gryse, R De

    2002-01-01

    During reactive glow discharge sputtering of copper in an argon/nitrogen plasma, we noticed an abrupt change of the target voltage and the deposition rate when the nitrogen concentration in the plasma exceeds a critical value. To explain this behaviour, the target surface after reactive glow discharge sputtering was examined by x-ray photoelectron spectroscopy (XPS). An experimental arrangement was constructed that allows direct transfer of the glow discharge cathode to the XPS analysis chamber without air exposure. These XPS measurements revealed that several different chemical states of nitrogen are present in the layer that forms on the target surface. The relative concentration of these different states changes when the critical nitrogen concentration in the plasma is exceeded

  9. Drug-targeting methodologies with applications: A review

    Science.gov (United States)

    Kleinstreuer, Clement; Feng, Yu; Childress, Emily

    2014-01-01

    Targeted drug delivery to solid tumors is a very active research area, focusing mainly on improved drug formulation and associated best delivery methods/devices. Drug-targeting has the potential to greatly improve drug-delivery efficacy, reduce side effects, and lower the treatment costs. However, the vast majority of drug-targeting studies assume that the drug-particles are already at the target site or at least in its direct vicinity. In this review, drug-delivery methodologies, drug types and drug-delivery devices are discussed with examples in two major application areas: (1) inhaled drug-aerosol delivery into human lung-airways; and (2) intravascular drug-delivery for solid tumor targeting. The major problem addressed is how to deliver efficiently the drug-particles from the entry/infusion point to the target site. So far, most experimental results are based on animal studies. Concerning pulmonary drug delivery, the focus is on the pros and cons of three inhaler types, i.e., pressurized metered dose inhaler, dry powder inhaler and nebulizer, in addition to drug-aerosol formulations. Computational fluid-particle dynamics techniques and the underlying methodology for a smart inhaler system are discussed as well. Concerning intravascular drug-delivery for solid tumor targeting, passive and active targeting are reviewed as well as direct drug-targeting, using optimal delivery of radioactive microspheres to liver tumors as an example. The review concludes with suggestions for future work, considereing both pulmonary drug targeting and direct drug delivery to solid tumors in the vascular system. PMID:25516850

  10. Critical currents and fields of disordered nanocrystalline superconductors

    International Nuclear Information System (INIS)

    Yavary, H.; Shahzamanian, M.A.; Rabbani, H.

    2007-01-01

    Full text: There is an enormous effort directed at increasing the upper critical field of the superconducting materials because this upper critical field provides a fundamental limit to the maximum field a magnet system can produce. High-energy particle accelerators and medical resonance imaging body scanners are limited by the for NbTi (10 T). Gigahertz class nuclear-magnetic-resonance and high field laboratory magnets are limited by for Nb 3 Sn (23 T) [1]. However, the values of critical current density are too low for industrial use, possibly because of degraded or nonsuperconducting phases, such as MoS 2 or Mo 2 S 3 , at the grain boundaries or because the pinning site density is not high enough. It has long been known that decreasing the grain size of low-temperature superconducting (LTS) materials, such as Nb 3 Sn, increases the density of flux pinning sites and hence. Nanocrystalline materials are characterized by ultrafine grains and a high density of grain boundaries [2]. Hence nanocrystalline materials can exhibit unusual physical, chemical, and mechanical properties with respect to conventional polycrystalline materials. The purpose of this paper is to investigate the structure of currents and fields in disordered nanocrystalline superconducting materials by the use of quasiclassical many body techniques. The Keldish Greens functions are used to calculate the current density of the system. Since the disorder and microstructure of these nanocrystalline materials are on a sufficiently short length scale as to increase both the density of pinning site and the upper critical field. (authors)

  11. The SKI SITE-94 project approach to analyzing confidence in site-specific data

    International Nuclear Information System (INIS)

    Dverstorp, B.; Andersson, J.

    1995-01-01

    The ongoing SKI SITE-94 project is a fully integrated performance assessment based on a hypothetical repository at 500 m depth in crystalline rock. One main objective of the project is to develop a methodology for incorporating data from a site characterization into the performance assessment. The hypothetical repository is located at SKB's Hard Rock Laboratory at Aspo in south-eastern Sweden. The site evaluation in SITE-94 uses data from the pre-excavation phase that comprised measurements performed on the ground and in boreholes, including cross-hole hydraulic and tracer experiments. Uncertainties related to measurement technique, equipment and methods for interpretation were evaluated through a critical review of geohydraulic measurement methods and a complete re-evaluation of the hydraulic packer tests using the generalised radial flow (GRF) theory. Groundwater chemistry samples were analyzed for representativeness and sampling errors. A wide range of site models within geology, hydrogeology, geochemistry and rock mechanics has been developed and tested with the site characterization data. (authors). 10 refs., 3 figs., 2 tabs

  12. Structural basis of sterol recognition and nonvesicular transport by lipid transfer proteins anchored at membrane contact sites.

    Science.gov (United States)

    Tong, Junsen; Manik, Mohammad Kawsar; Im, Young Jun

    2018-01-30

    Membrane contact sites (MCSs) in eukaryotic cells are hotspots for lipid exchange, which is essential for many biological functions, including regulation of membrane properties and protein trafficking. Lipid transfer proteins anchored at membrane contact sites (LAMs) contain sterol-specific lipid transfer domains [StARkin domain (SD)] and multiple targeting modules to specific membrane organelles. Elucidating the structural mechanisms of targeting and ligand recognition by LAMs is important for understanding the interorganelle communication and exchange at MCSs. Here, we determined the crystal structures of the yeast Lam6 pleckstrin homology (PH)-like domain and the SDs of Lam2 and Lam4 in the apo form and in complex with ergosterol. The Lam6 PH-like domain displays a unique PH domain fold with a conserved N-terminal α-helix. The Lam6 PH-like domain lacks the basic surface for phosphoinositide binding, but contains hydrophobic patches on its surface, which are critical for targeting to endoplasmic reticulum (ER)-mitochondrial contacts. Structures of the LAM SDs display a helix-grip fold with a hydrophobic cavity and a flexible Ω1-loop as a lid. Ergosterol is bound to the pocket in a head-down orientation, with its hydrophobic acyl group located in the tunnel entrance. The Ω1-loop in an open conformation is essential for ergosterol binding by direct hydrophobic interaction. Structural comparison suggested that the sterol binding mode of the Lam2 SD2 is likely conserved among the sterol transfer proteins of the StARkin superfamily. Structural models of full-length Lam2 correlated with the sterol transport function at the membrane contact sites.

  13. Pripper: prediction of caspase cleavage sites from whole proteomes

    Directory of Open Access Journals (Sweden)

    Salmi Jussi

    2010-06-01

    Full Text Available Abstract Background Caspases are a family of proteases that have central functions in programmed cell death (apoptosis and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed well in predicting caspase cleavage sites, and when combining different classifiers the accuracy increased further. A new tool, Pripper, was developed to utilize the classifiers and predict the caspase cut sites from an arbitrary number of input sequences. A database was constructed with the developed tool, and it was used to identify caspase target proteins from tandem mass spectrometry data from two different proteomic experiments. Both known caspase cleavage products as well as novel cleavage products were identified using the database demonstrating the usefulness of the tool. Pripper is not restricted to predicting only caspase cut sites, but it gives the possibility to scan protein sequences for any given motif(s and predict cut sites once a suitable cut site prediction model for any other protease has been developed. Pripper is freely available and can be downloaded from http://users.utu.fi/mijopi/Pripper. Conclusions We have developed Pripper, a tool for

  14. Subject Gateway Sites and Search Engine Ranking.

    Science.gov (United States)

    Thelwall, Mike

    2002-01-01

    Discusses subject gateway sites and commercial search engines for the Web and presents an explanation of Google's PageRank algorithm. The principle question addressed is the conditions under which a gateway site will increase the likelihood that a target page is found in search engines. (LRW)

  15. Systematic risk assessment methodology for critical infrastructure elements - Oil and Gas subsectors

    Science.gov (United States)

    Gheorghiu, A.-D.; Ozunu, A.

    2012-04-01

    The concern for the protection of critical infrastructure has been rapidly growing in the last few years in Europe. The level of knowledge and preparedness in this field is beginning to develop in a lawfully organized manner, for the identification and designation of critical infrastructure elements of national and European interest. Oil and gas production, refining, treatment, storage and transmission by pipelines facilities, are considered European critical infrastructure sectors, as per Annex I of the Council Directive 2008/114/EC of 8 December 2008 on the identification and designation of European critical infrastructures and the assessment of the need to improve their protection. Besides identifying European and national critical infrastructure elements, member states also need to perform a risk analysis for these infrastructure items, as stated in Annex II of the above mentioned Directive. In the field of risk assessment, there are a series of acknowledged and successfully used methods in the world, but not all hazard identification and assessment methods and techniques are suitable for a given site, situation, or type of hazard. As Theoharidou, M. et al. noted (Theoharidou, M., P. Kotzanikolaou, and D. Gritzalis 2009. Risk-Based Criticality Analysis. In Critical Infrastructure Protection III. Proceedings. Third Annual IFIP WG 11.10 International Conference on Critical Infrastructure Protection. Hanover, New Hampshire, USA, March 23-25, 2009: revised selected papers, edited by C. Palmer and S. Shenoi, 35-49. Berlin: Springer.), despite the wealth of knowledge already created, there is a need for simple, feasible, and standardized criticality analyses. The proposed systematic risk assessment methodology includes three basic steps: the first step (preliminary analysis) includes the identification of hazards (including possible natural hazards) for each installation/section within a given site, followed by a criterial analysis and then a detailed analysis step

  16. Structuring a cost-effective site characterization

    International Nuclear Information System (INIS)

    Berven, B.A.; Little, C.A.; Swaja, R.E.

    1990-01-01

    Successful chemical and radiological site characterizations are complex activities which require meticulously detailed planning. Each layer of investigation is based upon previously generated information about the site. Baseline historical, physical, geological, and regulatory information is prerequisite for preliminary studies at a site. Preliminary studies then provide samples and measurements which define the identity of potential contaminants and define boundaries around the area to be investigated. The goal of a full site characterization is to accurately determine the extent and magnitude of contaminants and carefully define the site conditions such that the future movements of site contaminants can be assessed for potential exposure to human occupants and/or environmental impacts. Critical to this process is the selection of appropriate measurement and sampling methodology, selection and use of appropriate instrumentation and management/interpretation of site information. Site investigations require optimization between the need of information to maximize the understanding of site conditions and the cost of acquiring that information. 5 refs., 1 tab

  17. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Science.gov (United States)

    Joseph, Thomas T; Osman, Roman

    2012-01-01

    In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA) is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC) that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the cumulative effects of

  18. Autism: A “Critical Period” Disorder?

    Directory of Open Access Journals (Sweden)

    Jocelyn J. LeBlanc

    2011-01-01

    Full Text Available Cortical circuits in the brain are refined by experience during critical periods early in postnatal life. Critical periods are regulated by the balance of excitatory and inhibitory (E/I neurotransmission in the brain during development. There is now increasing evidence of E/I imbalance in autism, a complex genetic neurodevelopmental disorder diagnosed by abnormal socialization, impaired communication, and repetitive behaviors or restricted interests. The underlying cause is still largely unknown and there is no fully effective treatment or cure. We propose that alteration of the expression and/or timing of critical period circuit refinement in primary sensory brain areas may significantly contribute to autistic phenotypes, including cognitive and behavioral impairments. Dissection of the cellular and molecular mechanisms governing well-established critical periods represents a powerful tool to identify new potential therapeutic targets to restore normal plasticity and function in affected neuronal circuits.

  19. SU-E-T-170: Characterization of the Location, Extent, and Proximity to Critical Structures of Target Volumes Provides Detail for Improved Outcome Predictions Among Pancreatic Cancer Patients

    International Nuclear Information System (INIS)

    Cheng, Z; Moore, J; Rosati, L; Mian, O; Narang, A; Herman, J; McNutt, T

    2015-01-01

    Purpose: In radiotherapy, size, location and proximity of the target to critical structures influence treatment decisions. It has been shown that proximity of the target predicts dosimetric sparing of critical structures. In addition to dosimetry, precise location of disease has further implications such as tumor invasion, or proximity to major arteries that inhibit surgery. Knowledge of which patients can be converted to surgical candidates by radiation may have high impact on future treat/no-treat decisions. We propose a method to improve our characterization of the location of pancreatic cancer and treatment volume extent with respect to nearby arteries with the goal of developing features to improve clinical predictions and decisions. Methods: Oncospace is a local learning health system that systematically captures clinical outcomes and all aspects of radiotherapy treatment plans, including overlap volume histograms (OVH) – a measure of spatial relationships between two structures. Minimum and maximum distances of PTV and OARs based on OVH, PTV volume, anatomic location by ICD-9 code, and surgical outcome were queried. Normalized distance to center from the left and right kidney was calculated to indicate tumor location and laterality. Distance to critical arteries (celiac, superior mesenteric, common hepatic) is validated by surgical status (borderline resectable, locally advanced converted to resectable). Results: There were 205 pancreas stereotactic body radiotherapy patients treated from 2009–2015 queried. Location/laterality of tumor based on kidney OVH show strong trends between location by OVH and by ICD-9. Compared to the locally advanced group, the borderline resectable group showed larger geometrical distance from critical arteries (p=0.03). Conclusion: Our platform enabled analysis of shape/size-location relationships. These data suggest that PTV volume and attention to distance between PTVs and surrounding OARs and major arteries may be

  20. SU-E-T-170: Characterization of the Location, Extent, and Proximity to Critical Structures of Target Volumes Provides Detail for Improved Outcome Predictions Among Pancreatic Cancer Patients

    Energy Technology Data Exchange (ETDEWEB)

    Cheng, Z; Moore, J; Rosati, L; Mian, O; Narang, A; Herman, J; McNutt, T [Johns Hopkins University, Baltimore, MD (United States)

    2015-06-15

    Purpose: In radiotherapy, size, location and proximity of the target to critical structures influence treatment decisions. It has been shown that proximity of the target predicts dosimetric sparing of critical structures. In addition to dosimetry, precise location of disease has further implications such as tumor invasion, or proximity to major arteries that inhibit surgery. Knowledge of which patients can be converted to surgical candidates by radiation may have high impact on future treat/no-treat decisions. We propose a method to improve our characterization of the location of pancreatic cancer and treatment volume extent with respect to nearby arteries with the goal of developing features to improve clinical predictions and decisions. Methods: Oncospace is a local learning health system that systematically captures clinical outcomes and all aspects of radiotherapy treatment plans, including overlap volume histograms (OVH) – a measure of spatial relationships between two structures. Minimum and maximum distances of PTV and OARs based on OVH, PTV volume, anatomic location by ICD-9 code, and surgical outcome were queried. Normalized distance to center from the left and right kidney was calculated to indicate tumor location and laterality. Distance to critical arteries (celiac, superior mesenteric, common hepatic) is validated by surgical status (borderline resectable, locally advanced converted to resectable). Results: There were 205 pancreas stereotactic body radiotherapy patients treated from 2009–2015 queried. Location/laterality of tumor based on kidney OVH show strong trends between location by OVH and by ICD-9. Compared to the locally advanced group, the borderline resectable group showed larger geometrical distance from critical arteries (p=0.03). Conclusion: Our platform enabled analysis of shape/size-location relationships. These data suggest that PTV volume and attention to distance between PTVs and surrounding OARs and major arteries may be

  1. CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool.

    Directory of Open Access Journals (Sweden)

    Manuel Stemmer

    Full Text Available Engineering of the CRISPR/Cas9 system has opened a plethora of new opportunities for site-directed mutagenesis and targeted genome modification. Fundamental to this is a stretch of twenty nucleotides at the 5' end of a guide RNA that provides specificity to the bound Cas9 endonuclease. Since a sequence of twenty nucleotides can occur multiple times in a given genome and some mismatches seem to be accepted by the CRISPR/Cas9 complex, an efficient and reliable in silico selection and evaluation of the targeting site is key prerequisite for the experimental success. Here we present the CRISPR/Cas9 target online predictor (CCTop, http://crispr.cos.uni-heidelberg.de to overcome limitations of already available tools. CCTop provides an intuitive user interface with reasonable default parameters that can easily be tuned by the user. From a given query sequence, CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. Thus, CCTop provides the bench biologist with a tool for the rapid and efficient identification of high quality target sites.

  2. Effective intermolecular potential and critical point for C60 molecule

    Science.gov (United States)

    Ramos, J. Eloy

    2017-07-01

    The approximate nonconformal (ANC) theory is applied to the C60 molecule. A new binary potential function is developed for C60, which has three parameters only and is obtained by averaging the site-site carbon interactions on the surface of two C60 molecules. It is shown that the C60 molecule follows, to a good approximation, the corresponding states principle with n-C8H18, n-C4F10 and n-C5F12. The critical point of C60 is estimated in two ways: first by applying the corresponding states principle under the framework of the ANC theory, and then by using previous computer simulations. The critical parameters obtained by applying the corresponding states principle, although very different from those reported in the literature, are consistent with the previous results of the ANC theory. It is shown that the Girifalco potential does not correspond to an average of the site-site carbon-carbon interaction.

  3. Responses of Lyngbya wollei to exposures of copper-based algaecides: the critical burden concept.

    Science.gov (United States)

    Bishop, W M; Rodgers, J H

    2012-04-01

    The formulation of a specific algaecide can greatly influence the bioavailability, uptake, and consequent control of the targeted alga. In this research, three copper-based algaecide formulations were evaluated in terms of copper sorption to a specific problematic alga and amount of copper required to achieve control. The objectives of this study were (1) to compare the masses of copper required to achieve control of Lyngbya wollei using the algaecide formulations Algimycin-PWF, Clearigate, and copper sulfate pentahydrate in laboratory toxicity experiments; (2) to relate the responses of L. wollei to the masses of copper adsorbed and absorbed (i.e., dose) as well as the concentrations of copper in the exposure water; and (3) to discern the relation between the mass of copper required to achieve control of a certain mass of L. wollei among different algaecide formulations. The critical burden of copper (i.e., threshold algaecide concentration that must be absorbed or adsorbed to achieve control) for L. wollei averaged 3.3 and 1.9 mg Cu/g algae for Algimycin-PWF and Clearigate, respectively, in experiments with a series of aqueous copper concentrations, water volumes, and masses of algae. With reasonable exposures in these experiments, control was not achieved with single applications of copper sulfate despite copper sorption >13 mg Cu/g algae in one experiment. Factors governing the critical burden of copper required for control of problematic cyanobacteria include algaecide formulation and concentration, volume of water, and mass of algae. By measuring the critical burden of copper from an algaecide formulation necessary to achieve control of the targeted algae, selection of an effective product and treatment rate can be calculated at a given field site.

  4. Canadian critical environmental zones: Concepts, goals and resources

    International Nuclear Information System (INIS)

    Meredith, T.C.; Moore, C.; Gartner, L.; Smith, W.

    1994-02-01

    Critical environmental zones are those ecosystems that are so degraded that the health or well-being of human inhabitants is threatened. A conceptual framework is presented for considering criticality and a rationale for a Canadian research project on critical zones. A model of pathways to criticality is outlined and some examples of environmental degradation in Canada are presented, including acid rain and greenhouse gas emissions. Societal response to, and public perception of, critical environmental zones is described. Media, format, and target audiences for output from a Canadian project are considered and some central scientific and policy questions are identified under such categories as environmental stresses, buffering capacity, indicators, human driving forces, and societal responses. An inventory of pertinent international and national activities is included. 53 refs., 8 figs., 3 tabs

  5. TALE-PvuII fusion proteins--novel tools for gene targeting.

    Science.gov (United States)

    Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

    2013-01-01

    Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity.

  6. Processes and effects of targeted online advertising among children

    OpenAIRE

    Reijmersdal, E.A. van; Rozendaal, E.; Smink, N.; Noort, G. van; Buijzen, M.A.

    2017-01-01

    Increasingly, information from children's profile pages on social network sites is being used to target online advertising, a phenomenon known as profile targeting. This practice has raised concerns in society and academia; however, its effects among children remain unstudied. Therefore, we investigated the effects of profile targeting on children's brand responses (i.e., brand attitude and purchase intention). We examined two types of targeting: targeting of product and of form (i.e., color)...

  7. The effect of target and non-target similarity on neural classification performance: A boost from confidence

    Directory of Open Access Journals (Sweden)

    Amar R Marathe

    2015-08-01

    Full Text Available Brain computer interaction (BCI technologies have proven effective in utilizing single-trial classification algorithms to detect target images in rapid serial visualization presentation tasks. While many factors contribute to the accuracy of these algorithms, a critical aspect that is often overlooked concerns the feature similarity between target and non-target images. In most real-world environments there are likely to be many shared features between targets and non-targets resulting in similar neural activity between the two classes. It is unknown how current neural-based target classification algorithms perform when qualitatively similar target and non-target images are presented. This study address this question by comparing behavioral and neural classification performance across two conditions: first, when targets were the only infrequent stimulus presented amongst frequent background distracters; and second when targets were presented together with infrequent non-targets containing similar visual features to the targets. The resulting findings show that behavior is slower and less accurate when targets are presented together with similar non-targets; moreover, single-trial classification yielded high levels of misclassification when infrequent non-targets are included. Furthermore, we present an approach to mitigate the image misclassification. We use confidence measures to assess the quality of single-trial classification, and demonstrate that a system in which low confidence trials are reclassified through a secondary process can result in improved performance.

  8. HomoTarget: a new algorithm for prediction of microRNA targets in Homo sapiens.

    Science.gov (United States)

    Ahmadi, Hamed; Ahmadi, Ali; Azimzadeh-Jamalkandi, Sadegh; Shoorehdeli, Mahdi Aliyari; Salehzadeh-Yazdi, Ali; Bidkhori, Gholamreza; Masoudi-Nejad, Ali

    2013-02-01

    MiRNAs play an essential role in the networks of gene regulation by inhibiting the translation of target mRNAs. Several computational approaches have been proposed for the prediction of miRNA target-genes. Reports reveal a large fraction of under-predicted or falsely predicted target genes. Thus, there is an imperative need to develop a computational method by which the target mRNAs of existing miRNAs can be correctly identified. In this study, combined pattern recognition neural network (PRNN) and principle component analysis (PCA) architecture has been proposed in order to model the complicated relationship between miRNAs and their target mRNAs in humans. The results of several types of intelligent classifiers and our proposed model were compared, showing that our algorithm outperformed them with higher sensitivity and specificity. Using the recent release of the mirBase database to find potential targets of miRNAs, this model incorporated twelve structural, thermodynamic and positional features of miRNA:mRNA binding sites to select target candidates. Copyright © 2012 Elsevier Inc. All rights reserved.

  9. Target cells in internal dosimetry

    Energy Technology Data Exchange (ETDEWEB)

    Goessner, W

    2003-07-01

    Data related to radium induced bone sarcomas in humans are used as a model for defining target cells on bone surfaces and in the bone marrow. The differential distribution of radiation induced bone sarcoma types with a high ratio of non-bone producing, mainly fibroblastic tumours, challenges the ICRP concept that the bone lining cells are target cells. Multipotential mesenchymal stem cells are located within the range of alpha particles, and are the most likely target cells for the fibroblastic type of bone sarcoma. The histogenesis of bone sarcomas after irradiation with alpha emitters shows that their final histopathology is not dependent on a single target cell. Each target cell has a microenvironment, which has to be regarded as a synergistic morpho-functional tissue unit. For this the concept of 'histion', a term used in general pathology, is proposed. Interactions between target cells that have been hit by alpha-particles, leading to lethal, mutational or transformation events with all components of a 'histion', will prove critical to understanding the pathogenesis of both deterministic and stochastic late effects. (author)

  10. Target cells in internal dosimetry

    International Nuclear Information System (INIS)

    Goessner, W.

    2003-01-01

    Data related to radium induced bone sarcomas in humans are used as a model for defining target cells on bone surfaces and in the bone marrow. The differential distribution of radiation induced bone sarcoma types with a high ratio of non-bone producing, mainly fibroblastic tumours, challenges the ICRP concept that the bone lining cells are target cells. Multipotential mesenchymal stem cells are located within the range of alpha particles, and are the most likely target cells for the fibroblastic type of bone sarcoma. The histogenesis of bone sarcomas after irradiation with alpha emitters shows that their final histopathology is not dependent on a single target cell. Each target cell has a microenvironment, which has to be regarded as a synergistic morpho-functional tissue unit. For this the concept of 'histion', a term used in general pathology, is proposed. Interactions between target cells that have been hit by alpha-particles, leading to lethal, mutational or transformation events with all components of a 'histion', will prove critical to understanding the pathogenesis of both deterministic and stochastic late effects. (author)

  11. Altering the spectrum of immunoglobulin V gene somatic hypermutation by modifying the active site of AID.

    Science.gov (United States)

    Wang, Meng; Rada, Cristina; Neuberger, Michael S

    2010-01-18

    High-affinity antibodies are generated by somatic hypermutation with nucleotide substitutions introduced into the IgV in a semirandom fashion, but with intrinsic mutational hotspots strategically located to optimize antibody affinity maturation. The process is dependent on activation-induced deaminase (AID), an enzyme that can deaminate deoxycytidine in DNA in vitro, where its activity is sensitive to the identity of the 5'-flanking nucleotide. As a critical test of whether such DNA deamination activity underpins antibody diversification and to gain insight into the extent to which the antibody mutation spectrum is dependent on the intrinsic substrate specificity of AID, we investigated whether it is possible to change the IgV mutation spectrum by altering AID's active site such that it prefers a pyrimidine (rather than a purine) flanking the targeted deoxycytidine. Consistent with the DNA deamination mechanism, B cells expressing the modified AID proteins yield altered IgV mutation spectra (exhibiting a purine-->pyrimidine shift in flanking nucleotide preference) and altered hotspots. However, AID-catalyzed deamination of IgV targets in vitro does not yield the same degree of hotspot dominance to that observed in vivo, indicating the importance of features beyond AID's active site and DNA local sequence environment in determining in vivo hotspot dominance.

  12. Therapeutic targeting strategies using endogenous cells and proteins.

    Science.gov (United States)

    Parayath, Neha N; Amiji, Mansoor M

    2017-07-28

    Targeted drug delivery has become extremely important in enhancing efficacy and reducing the toxicity of therapeutics in the treatment of various disease conditions. Current approaches include passive targeting, which relies on naturally occurring differences between healthy and diseased tissues, and active targeting, which utilizes various ligands that can recognize targets expressed preferentially at the diseased site. Clinical translation of these mechanisms faces many challenges including the immunogenic and toxic effects of these non-natural systems. Thus, use of endogenous targeting systems is increasingly gaining momentum. This review is focused on strategies for employing endogenous moieties, which could serve as safe and efficient carriers for targeted drug delivery. The first part of the review involves cells and cellular components as endogenous carriers for therapeutics in multiple disease states, while the second part discusses the use of endogenous plasma components as endogenous carriers. Further understanding of the biological tropism with cells and proteins and the newer generation of delivery strategies that exploits these endogenous approaches promises to provide better solutions for site-specific delivery and could further facilitate clinical translations. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. Steady-state critical loads of acidity for forest soils in the Georgia Basin, British Columbia

    Directory of Open Access Journals (Sweden)

    Shaun A. WATMOUGH

    2010-08-01

    Full Text Available There has been growing interest in acid rain research in western Canada where sulphur (S and nitrogen (N emissions are expected to increase during the next two decades. One region of concern is southern British Columbia, specifically the Georgia Basin, where emissions are expected to increase owing to the expansion of industry and urban centres (Vancouver and Victoria. In the current study, weathering rates and critical loads of acidity (S and N for forest soils were estimated at nineteen sites located within the Georgia Basin. A base cation to aluminium ratio of 10 was selected as the critical chemical criterion associated with ecosystem damage. The majority of the sites (58% had low base cation weathering rates (≤50 meq m–2 y–1 based on the PROFILE model. Accordingly, mean critical load for the study sites, estimated using the steady-state mass balance model, ranged between 129–168 meq m–2 y–1. Annual average total (wet and dry S and N deposition during the period 2005–2006 (estimated by the Community Multiscale Air Quality model, exceeded critical load at five–nine of the study sites (mean exceedance = 32–46 meq m–2 y–1. The high-elevation (>1000 m study sites had shallow, acid sensitive, soils with low weathering rates; however, critical loads were predominantly exceeded at sites close to Vancouver under higher modelled deposition loads. The extent of exceedance is similar to other industrial regions in western and eastern Canada.

  14. Magnetic targeting as a strategy to enhance therapeutic effects of mesenchymal stromal cells.

    Science.gov (United States)

    Silva, Luisa H A; Cruz, Fernanda F; Morales, Marcelo M; Weiss, Daniel J; Rocco, Patricia R M

    2017-03-09

    Mesenchymal stromal cells (MSCs) have been extensively investigated in the field of regenerative medicine. It is known that the success of MSC-based therapies depends primarily on effective cell delivery to the target site where they will secrete vesicles and soluble factors with immunomodulatory and potentially reparative properties. However, some lesions are located in sites that are difficult to access, such as the heart, spinal cord, and joints. Additionally, low MSC retention at target sites makes cell therapy short-lasting and, therefore, less effective. In this context, the magnetic targeting technique has emerged as a new strategy to aid delivery, increase retention, and enhance the effects of MSCs. This approach uses magnetic nanoparticles to magnetize MSCs and static magnetic fields to guide them in vivo, thus promoting more focused, effective, and lasting retention of MSCs at the target site. In the present review, we discuss the magnetic targeting technique, its principles, and the materials most commonly used; we also discuss its potential for MSC enhancement, and safety concerns that should be addressed before it can be applied in clinical practice.

  15. Activities of JAERI's health physics department for the criticality accident of JCO

    International Nuclear Information System (INIS)

    Yamamoto, Katsumune; Kitano, Kyoshiro; Murakami, Hiroyuki; Yamaguchi, Takenori; Tsunoda, Masahiko

    2000-01-01

    This report describes early health physics activities from September 30 to October 1 taken by the authors' department after the JCO accident. They firstly knew the accident at around 12:20 (about 2 hr after the criticality). The activities involved the planning of schedule for ending the criticality; calculation of scheduled dose for the work to end it; dose measurement around JCO site; loaning out of devices for measuring neutron and of personal dose-meter; collection and radioactivity measurement of dust and soil, and of drinking water; and examination for contamination of people around the site, of their houses inside and of school gardens and equipments. The dose was scheduled to be firstly 20 mSv and then changed to 50 mSv due to the actual measurement at the accident site. The working time was to be 3 min at the site. The work was on either the dose or time. Radiation monitoring outside the JCO site revealed the presence of Na-24 and Cs-138: neutron dose was 10 times as high as γ-ray dose. The time course of dose rate change was found to be in parallel with the progress of works to end the criticality. (K.H.)

  16. JAERI/KEK target material program overview

    International Nuclear Information System (INIS)

    Kikuchi, Kenji; Kogawa, Hiroyuki; Sasa, Toshinobu

    2001-01-01

    Mercury target was designed for megawatt neutron scattering facility in JAERI/KEK spallation neutron source. The incident proton energy and current are 3 GeV and 333 μA, respectively: the total proton energy is 1 MW in short pulses at a frequency of 25 Hz. Under the guide rule the mercury target was designed: the maximum temperature of target window is 170degC and induced stresses for the type 316 stainless steel are within limits of design guide. In order to demonstrate ADS (Accelerator Driven Systems) transmutation critical and engineering facilities have been designed conceptually. In engineering facility lead-bismuth spallation target station is to be planned. Objective to build the facility is to demonstrate material irradiation. According to neutronics calculation irradiation damage of the target vessel window will be 5 dpa per year. (author)

  17. Federal health web sites: current & future roles.

    Science.gov (United States)

    Cronin, Carol

    2002-09-01

    An examination of the current and possible future roles of federal health Web sites, this paper provides an overview of site categories, functions, target audiences, marketing approaches, knowledge management, and evaluation strategies. It concludes with a look at future opportunities and challenges for the federal government in providing health information online.

  18. Factor XI and XII as antithrombotic targets.

    Science.gov (United States)

    Müller, Felicitas; Gailani, David; Renné, Thomas

    2011-09-01

    Arterial and venous thrombosis are major causes of morbidity and mortality, and the incidence of thromboembolic diseases increases as a population ages. Thrombi are formed by activated platelets and fibrin. The latter is a product of the plasma coagulation system. Currently available anticoagulants such as heparins, vitamin K antagonists and inhibitors of thrombin or factor Xa target enzymes of the coagulation cascade that are critical for fibrin formation. However, fibrin is also necessary for terminating blood loss at sites of vascular injury. As a result, anticoagulants currently in clinical use increase the risk of bleeding, partially offsetting the benefits of reduced thrombosis. This review focuses on new targets for anticoagulation that are associated with minimal or no therapy-associated increased bleeding. Data from experimental models using mice and clinical studies of patients with hereditary deficiencies of coagulation factors XI or XII have shown that both of these clotting factors are important for thrombosis, while having minor or no apparent roles in processes that terminate blood loss (hemostasis). Hereditary deficiency of factor XII (Hageman factor) or factor XI, plasma proteases that initiate the intrinsic pathway of coagulation, impairs thrombus formation and provides protection from vascular occlusive events, while having a minimal impact on hemostasis. As the factor XII-factor XI pathway contributes to thrombus formation to a greater extent than to normal hemostasis, pharmacological inhibition of these coagulation factors may offer the exciting possibility of anticoagulation therapies with minimal or no bleeding risk.

  19. Combined serial analysis of gene expression and transcription factor binding site prediction identifies novel-candidate-target genes of Nr2e1 in neocortex development.

    Science.gov (United States)

    Schmouth, Jean-François; Arenillas, David; Corso-Díaz, Ximena; Xie, Yuan-Yun; Bohacec, Slavita; Banks, Kathleen G; Bonaguro, Russell J; Wong, Siaw H; Jones, Steven J M; Marra, Marco A; Simpson, Elizabeth M; Wasserman, Wyeth W

    2015-07-24

    Nr2e1 (nuclear receptor subfamily 2, group e, member 1) encodes a transcription factor important in neocortex development. Previous work has shown that nuclear receptors can have hundreds of target genes, and bind more than 300 co-interacting proteins. However, recognition of the critical role of Nr2e1 in neural stem cells and neocortex development is relatively recent, thus the molecular mechanisms involved for this nuclear receptor are only beginning to be understood. Serial analysis of gene expression (SAGE), has given researchers both qualitative and quantitative information pertaining to biological processes. Thus, in this work, six LongSAGE mouse libraries were generated from laser microdissected tissue samples of dorsal VZ/SVZ (ventricular zone and subventricular zone) from the telencephalon of wild-type (Wt) and Nr2e1-null embryos at the critical development ages E13.5, E15.5, and E17.5. We then used a novel approach, implementing multiple computational methods followed by biological validation to further our understanding of Nr2e1 in neocortex development. In this work, we have generated a list of 1279 genes that are differentially expressed in response to altered Nr2e1 expression during in vivo neocortex development. We have refined this list to 64 candidate direct-targets of NR2E1. Our data suggested distinct roles for Nr2e1 during different neocortex developmental stages. Most importantly, our results suggest a possible novel pathway by which Nr2e1 regulates neurogenesis, which includes Lhx2 as one of the candidate direct-target genes, and SOX9 as a co-interactor. In conclusion, we have provided new candidate interacting partners and numerous well-developed testable hypotheses for understanding the pathways by which Nr2e1 functions to regulate neocortex development.

  20. The prototype HIV-1 maturation inhibitor, bevirimat, binds to the CA-SP1 cleavage site in immature Gag particles

    Directory of Open Access Journals (Sweden)

    Nguyen Albert T

    2011-12-01

    Full Text Available Abstract Background Bevirimat, the prototype Human Immunodeficiency Virus type 1 (HIV-1 maturation inhibitor, is highly potent in cell culture and efficacious in HIV-1 infected patients. In contrast to inhibitors that target the active site of the viral protease, bevirimat specifically inhibits a single cleavage event, the final processing step for the Gag precursor where p25 (CA-SP1 is cleaved to p24 (CA and SP1. Results In this study, photoaffinity analogs of bevirimat and mass spectrometry were employed to map the binding site of bevirimat to Gag within immature virus-like particles. Bevirimat analogs were found to crosslink to sequences overlapping, or proximal to, the CA-SP1 cleavage site, consistent with previous biochemical data on the effect of bevirimat on Gag processing and with genetic data from resistance mutations, in a region predicted by NMR and mutational studies to have α-helical character. Unexpectedly, a second region of interaction was found within the Major Homology Region (MHR. Extensive prior genetic evidence suggests that the MHR is critical for virus assembly. Conclusions This is the first demonstration of a direct interaction between the maturation inhibitor, bevirimat, and its target, Gag. Information gained from this study sheds light on the mechanisms by which the virus develops resistance to this class of drug and may aid in the design of next-generation maturation inhibitors.

  1. Cleanup around an old waste site

    International Nuclear Information System (INIS)

    Vandergaast, G.; Moffett, D.; Lawrence, B.E.

    1988-01-01

    42,500 m 3 of contaminated soil were removed from off-site areas around an old, low-level radioactive waste site near Port Hope, Ontario. The cleanup was done by means of conventional excavation equipment to criteria developed by Eldorado specific to the land use around the company's waste management facility. These cleanup criteria were based on exposure analyses carried out for critical receptors in two different scenarios. The excavated soils, involving eight different landowners, were placed on the original burial area of the waste management facility. Measures were also undertaken to stabilize the soils brought on-site and to ensure that there would be no subsequent recontamination of the off-site areas

  2. Evaluating and Estimating the WCET Criticality Metric

    DEFF Research Database (Denmark)

    Jordan, Alexander

    2014-01-01

    a programmer (or compiler) from targeting optimizations the right way. A possible resort is to use a metric that targets WCET and which can be efficiently computed for all code parts of a program. Similar to dynamic profiling techniques, which execute code with input that is typically expected...... for the application, based on WCET analysis we can indicate how critical a code fragment is, in relation to the worst-case bound. Computing such a metric on top of static analysis, incurs a certain overhead though, which increases with the complexity of the underlying WCET analysis. We present our approach...... to estimate the Criticality metric, by relaxing the precision of WCET analysis. Through this, we can reduce analysis time by orders of magnitude, while only introducing minor error. To evaluate our estimation approach and share our garnered experience using the metric, we evaluate real-time programs, which...

  3. Criticality safety analysis of Hanford Waste Tank 241-101-SY

    International Nuclear Information System (INIS)

    Perry, R.T.; Sapir, J.L.; Krohn, B.J.

    1993-01-01

    As part of a safety assessment for proposed pump mixing operations to mitigate episodic gas releases in Tank 241-101-SY at the Hanford Site, Richland, Washington, a criticality safety analysis was made using the Sn transport code ONEDANT. The tank contains approximately one million gallons of waste and an estimated 910 G of plutonium. the criticality analysis considers reconfiguration and underestimation of plutonium content. The results indicate that Tank SY-101 does not present a criticality hazard. These methods are also used in criticality analyses of other Hanford tanks

  4. Network Randomization and Dynamic Defense for Critical Infrastructure Systems

    Energy Technology Data Exchange (ETDEWEB)

    Chavez, Adrian R. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Martin, Mitchell Tyler [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Hamlet, Jason [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Stout, William M.S. [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States); Lee, Erik [Sandia National Lab. (SNL-NM), Albuquerque, NM (United States)

    2015-04-01

    Critical Infrastructure control systems continue to foster predictable communication paths, static configurations, and unpatched systems that allow easy access to our nation's most critical assets. This makes them attractive targets for cyber intrusion. We seek to address these attack vectors by automatically randomizing network settings, randomizing applications on the end devices themselves, and dynamically defending these systems against active attacks. Applying these protective measures will convert control systems into moving targets that proactively defend themselves against attack. Sandia National Laboratories has led this effort by gathering operational and technical requirements from Tennessee Valley Authority (TVA) and performing research and development to create a proof-of-concept solution. Our proof-of-concept has been tested in a laboratory environment with over 300 nodes. The vision of this project is to enhance control system security by converting existing control systems into moving targets and building these security measures into future systems while meeting the unique constraints that control systems face.

  5. eMatchSite: sequence order-independent structure alignments of ligand binding pockets in protein models.

    Directory of Open Access Journals (Sweden)

    Michal Brylinski

    2014-09-01

    Full Text Available Detecting similarities between ligand binding sites in the absence of global homology between target proteins has been recognized as one of the critical components of modern drug discovery. Local binding site alignments can be constructed using sequence order-independent techniques, however, to achieve a high accuracy, many current algorithms for binding site comparison require high-quality experimental protein structures, preferably in the bound conformational state. This, in turn, complicates proteome scale applications, where only various quality structure models are available for the majority of gene products. To improve the state-of-the-art, we developed eMatchSite, a new method for constructing sequence order-independent alignments of ligand binding sites in protein models. Large-scale benchmarking calculations using adenine-binding pockets in crystal structures demonstrate that eMatchSite generates accurate alignments for almost three times more protein pairs than SOIPPA. More importantly, eMatchSite offers a high tolerance to structural distortions in ligand binding regions in protein models. For example, the percentage of correctly aligned pairs of adenine-binding sites in weakly homologous protein models is only 4-9% lower than those aligned using crystal structures. This represents a significant improvement over other algorithms, e.g. the performance of eMatchSite in recognizing similar binding sites is 6% and 13% higher than that of SiteEngine using high- and moderate-quality protein models, respectively. Constructing biologically correct alignments using predicted ligand binding sites in protein models opens up the possibility to investigate drug-protein interaction networks for complete proteomes with prospective systems-level applications in polypharmacology and rational drug repositioning. eMatchSite is freely available to the academic community as a web-server and a stand-alone software distribution at http://www.brylinski.org/ematchsite.

  6. Protein and Peptide in Drug Targeting and its Therapeutic Approach

    Directory of Open Access Journals (Sweden)

    Raj K. Keservani

    2015-09-01

    Full Text Available Aim: The main aim of this review article is to provide information like advantages of protein and peptides via different routes of drug administration, targeted to a particular site and its implication in drug delivery system. Methods: To that aim, from the web sites of PubMed, HCAplus, Thomson, and Registry were used as the main sources to perform the search for the most significant research articles published on the subject. The information was then carefully analyzed, highlighting the most important results in the development of protein and peptide drug targeting as well as its therapeutic activity. Results: In recent years many researchers use protein and peptide as a target site of drug by a different delivery system. Proteins and peptides are used as specific and effective therapeutic agents, due to instability and side effects their use is complicated. Protein kinases are important regulators of most, if not all, biological processes. Abnormal activity of proteins and peptides has been implicated in many human diseases, such as diabetes, cancer and neurodegenerative disorders. Conclusions: It is concluded that the protein and peptide were used in drug targeting to specific site and also used in different diseased states like cancer, diabetes, immunomodulating, neurodegenerative effects and antimicrobial activity.

  7. Potential nitrogen critical loads for northern Great Plains grassland vegetation

    Science.gov (United States)

    Symstad, Amy J.; Smith, Anine T.; Newton, Wesley E.; Knapp, Alan K.

    2015-01-01

    The National Park Service is concerned that increasing atmospheric nitrogen deposition caused by fossil fuel combustion and agricultural activities could adversely affect the northern Great Plains (NGP) ecosystems in its trust. The critical load concept facilitates communication between scientists and policy makers or land managers by translating the complex effects of air pollution on ecosystems into concrete numbers that can be used to inform air quality targets. A critical load is the exposure level below which significant harmful effects on sensitive elements of the environment do not occur. A recent review of the literature suggested that the nitrogen critical load for Great Plains vegetation is 10-25 kg N/ha/yr. For comparison, current atmospheric nitrogen deposition in NGP National Park Service (NPS) units ranges from ~4 kg N/ha/yr in the west to ~13 kg N/ha/yr in the east. The suggested critical load, however, was derived from studies far outside of the NGP, and from experiments investigating nitrogen loads substantially higher than current atmospheric deposition in the region.Therefore, to better determine the nitrogen critical load for sensitive elements in NGP parks, we conducted a four-year field experiment in three northern Great Plains vegetation types at Badlands and Wind Cave National Parks. The vegetation types were chosen because of their importance in NGP parks, their expected sensitivity to nitrogen addition, and to span a range of natural fertility. In the experiment, we added nitrogen at rates ranging from below current atmospheric deposition (2.5 kg N/ha/yr) to far above those levels but commensurate with earlier experiments (100 kg N/ha/yr). We measured the response of a variety of vegetation and soil characteristics shown to be sensitive to nitrogen addition in other studies, including plant biomass production, plant tissue nitrogen concentration, plant species richness and composition, non-native species abundance, and soil inorganic

  8. Signatures of RNA binding proteins globally coupled to effective microRNA target sites

    DEFF Research Database (Denmark)

    Jacobsen, Anders; Wen, Jiayu; Marks, Debora S

    2010-01-01

    MicroRNAs (miRNAs) and small interfering RNAs (siRNAs), bound to Argonaute proteins (RISC), destabilize mRNAs through base-pairing with the mRNA. However, the gene expression changes after perturbations of these small RNAs are only partially explained by predicted miRNA/siRNA targeting. Targeting...

  9. Molecular targeted therapy for advanced gastric cancer.

    Science.gov (United States)

    Kim, Jong Gwang

    2013-03-01

    Although medical treatment has been shown to improve quality of life and prolong survival, no significant progress has been made in the treatment of advanced gastric cancer (AGC) within the last two decades. Thus, the optimum standard first-line chemotherapy regimen for AGC remains debatable, and most responses to chemotherapy are partial and of short duration; the median survival is approximately 7 to 11 months, and survival at 2 years is exceptionally > 10%. Recently, remarkable progress in tumor biology has led to the development of new agents that target critical aspects of oncogenic pathways. For AGC, many molecular targeting agents have been evaluated in international randomized studies, and trastuzumab, an anti-HER-2 monoclonal antibody, has shown antitumor activity against HER-2-positive AGC. However, this benefit is limited to only ~20% of patients with AGC (patients with HER-2-positive AGC). Therefore, there remains a critical need for both the development of more effective agents and the identification of molecular predictive and prognostic markers to select those patients who will benefit most from specific chemotherapeutic regimens and targeted therapies.

  10. Computational Characterization of Small Molecules Binding to the Human XPF Active Site and Virtual Screening to Identify Potential New DNA Repair Inhibitors Targeting the ERCC1-XPF Endonuclease

    Directory of Open Access Journals (Sweden)

    Francesco Gentile

    2018-04-01

    Full Text Available The DNA excision repair protein ERCC-1-DNA repair endonuclease XPF (ERCC1-XPF is a heterodimeric endonuclease essential for the nucleotide excision repair (NER DNA repair pathway. Although its activity is required to maintain genome integrity in healthy cells, ERCC1-XPF can counteract the effect of DNA-damaging therapies such as platinum-based chemotherapy in cancer cells. Therefore, a promising approach to enhance the effect of these therapies is to combine their use with small molecules, which can inhibit the repair mechanisms in cancer cells. Currently, there are no structures available for the catalytic site of the human ERCC1-XPF, which performs the metal-mediated cleavage of a DNA damaged strand at 5′. We adopted a homology modeling strategy to build a structural model of the human XPF nuclease domain which contained the active site and to extract dominant conformations of the domain using molecular dynamics simulations followed by clustering of the trajectory. We investigated the binding modes of known small molecule inhibitors targeting the active site to build a pharmacophore model. We then performed a virtual screening of the ZINC Is Not Commercial 15 (ZINC15 database to identify new ERCC1-XPF endonuclease inhibitors. Our work provides structural insights regarding the binding mode of small molecules targeting the ERCC1-XPF active site that can be used to rationally optimize such compounds. We also propose a set of new potential DNA repair inhibitors to be considered for combination cancer therapy strategies.

  11. Targeting the Brain with Nanomedicine.

    Science.gov (United States)

    Rueda, Felix; Cruz, Luis J

    2017-01-01

    Herein, we review innovative nanomedicine-based approaches for treating, preventing and diagnosing neurodegenerative diseases. We focus on nanoscale systems such as polymeric nanoparticles (NPs), liposomes, micelles and other vehicles (e.g. dendrimers, nanogels, nanoemulsions and nanosuspensions) for targeted delivery of bioactive molecules to the brain. To ensure maximum selectivity for optimal therapeutic or diagnostic results, researchers must employ delivery systems that are non-toxic, biodegradable and biocompatible. This entails: (i) use of "safe" materials, such as polymers or lipids; (ii) targeting to the brain and, specifically, to the desired active site within the brain; (iii) controlled release of the loaded agent; and (iv) use of agents that, once released into the brain, will exhibit the desired pharmacologic activity. Here, we explore the design and preclinical use of representative delivery systems that have been proposed to date. We then analyze the principal challenges that have delayed clinical application of these and other approaches. Lastly, we look at future developments in this area, addressing the needs for increased penetration of the blood brain barrier (BBB), enhanced targeting of specific brain sites, improved therapeutic efficacy and lower neurotoxicity. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  12. Artificial Intelligence Support for Landing Site Selection on Mars

    Science.gov (United States)

    Rongier, G.; Pankratius, V.

    2017-12-01

    Mars is a key target for planetary exploration; a better understanding of its evolution and habitability requires roving in situ. Landing site selection is becoming more challenging for scientists as new instruments generate higher data volumes. The involved engineering and scientific constraints make site selection and the anticipation of possible onsite actions into a complex optimization problem: there may be multiple acceptable solutions depending on various goals and assumptions. Solutions must also account for missing data, errors, and potential biases. To address these problems, we propose an AI-informed decision support system that allows scientists, mission designers, engineers, and committees to explore alternative site selection choices based on data. In particular, we demonstrate first results of an exploratory case study using fuzzy logic and a simulation of a rover's mobility map based on the fast marching algorithm. Our system computes favorability maps of the entire planet to facilitate landing site selection and allows a definition of different configurations for rovers, science target priorities, landing ellipses, and other constraints. For a rover similar to NASA's Mars 2020 rover, we present results in form of a site favorability map as well as four derived exploration scenarios that depend on different prioritized scientific targets, all visualizing inherent tradeoffs. Our method uses the NASA PDS Geosciences Node and the NASA/ICA Integrated Database of Planetary Features. Under common assumptions, the data products reveal Eastern Margaritifer Terra and Meridiani Planum to be the most favorable sites due to a high concentration of scientific targets and a flat, easily navigable surface. Our method also allows mission designers to investigate which constraints have the highest impact on the mission exploration potential and to change parameter ranges. Increasing the elevation limit for landing, for example, provides access to many additional

  13. The Research Progress of Targeted Drug Delivery Systems

    Science.gov (United States)

    Zhan, Jiayin; Ting, Xizi Liang; Zhu, Junjie

    2017-06-01

    Targeted drug delivery system (DDS) means to selectively transport drugs to targeted tissues, organs, and cells through a variety of drugs carrier. It is usually designed to improve the pharmacological and therapeutic properties of conventional drugs and to overcome problems such as limited solubility, drug aggregation, poor bio distribution and lack of selectivity, controlling drug release carrier and to reduce normal tissue damage. With the characteristics of nontoxic and biodegradable, it can increase the retention of drug in lesion site and the permeability, improve the concentration of the drug in lesion site. at present, there are some kinds of DDS using at test phase, such as slow controlled release drug delivery system, targeted drug delivery systems, transdermal drug delivery system, adhesion dosing system and so on. This paper makes a review for DDS.

  14. Search for over 2000 current and legacy micropollutants on a wastewater infiltration site with a UPLC-high resolution MS target screening method.

    Science.gov (United States)

    Wode, Florian; van Baar, Patricia; Dünnbier, Uwe; Hecht, Fabian; Taute, Thomas; Jekel, Martin; Reemtsma, Thorsten

    2015-02-01

    A target screening method using ultra high performance liquid chromatography-high resolution mass spectrometry (UPLC-HRMS) was developed. The method was applied to 14 groundwater and 11 surface water samples of a former wastewater infiltration site, where raw wastewater was applied until 1985 and treated wastewater is applied since 2005. The measured data are compared with mass spectrometric data of over 2000 organic micropollutants (OMPs), including pharmaceuticals, personal care products, pesticides, industrial chemicals and metabolites of these classes. A total number of 151 and 159 OMPs were detected in groundwater and surface water, respectively, of which 12 have not been reported before in these matrices. Among these 12 compounds were 11 pharmaceuticals and one personal care product. The identity of 55 of the detected OMPs (35%) was verified by analysis of standard compounds. Based on the distribution in the study area, two groups of OMPs were clearly distinguished: current OMPs introduced with treated municipal wastewater since 2005 and legacy OMPs originating from infiltration of untreated wastewater until 1985. A third group included OMPs contained in historic as well as in current wastewater. During infiltration, OMPs with molecular mass >500 g/mol and log DOW > 3.9 were preferentially removed. Speciation had a strong impact with cationic OMPs showing high, neutral OMPs medium and anionic OMPs lowest elimination during infiltration. This target screening method proved useful to study a wide range of compounds, even in retrospect and at sites with poorly documented history and with a complex and variable hydrological situation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. A mathematical analysis of multiple-target SELEX.

    Science.gov (United States)

    Seo, Yeon-Jung; Chen, Shiliang; Nilsen-Hamilton, Marit; Levine, Howard A

    2010-10-01

    SELEX (Systematic Evolution of Ligands by Exponential Enrichment) is a procedure by which a mixture of nucleic acids can be fractionated with the goal of identifying those with specific biochemical activities. One combines the mixture with a specific target molecule and then separates the target-NA complex from the resulting reactions. The target-NA complex is separated from the unbound NA by mechanical means (such as by filtration), the NA is eluted from the complex, amplified by PCR (polymerase chain reaction), and the process repeated. After several rounds, one should be left with the nucleic acids that best bind to the target. The problem was first formulated mathematically in Irvine et al. (J. Mol. Biol. 222:739-761, 1991). In Levine and Nilsen-Hamilton (Comput. Biol. Chem. 31:11-25, 2007), a mathematical analysis of the process was given. In Vant-Hull et al. (J. Mol. Biol. 278:579-597, 1998), multiple target SELEX was considered. It was assumed that each target has a single nucleic acid binding site that permits occupation by no more than one nucleic acid. Here, we revisit Vant-Hull et al. (J. Mol. Biol. 278:579-597, 1998) using the same assumptions. The iteration scheme is shown to be convergent and a simplified algorithm is given. Our interest here is in the behavior of the multiple target SELEX process as a discrete "time" dynamical system. Our goal is to characterize the limiting states and their dependence on the initial distribution of nucleic acid and target fraction components. (In multiple target SELEX, we vary the target component fractions, but not their concentrations, as fixed and the initial pool of nucleic acids as a variable starting condition). Given N nucleic acids and a target consisting of M subtarget component species, there is an M × N matrix of affinities, the (i,j) entry corresponding to the affinity of the jth nucleic acid for the ith subtarget. We give a structure condition on this matrix that is equivalent to the following

  16. Liposome Delivery Systems for Inhalation: A Critical Review Highlighting Formulation Issues and Anticancer Applications.

    Science.gov (United States)

    Rudokas, Mindaugas; Najlah, Mohammad; Alhnan, Mohamed Albed; Elhissi, Abdelbary

    2016-01-01

    This is a critical review on research conducted in the field of pulmonary delivery of liposomes. Issues relating to the mechanism of nebulisation and liposome composition were appraised and correlated with literature reports of liposome formulations used in clinical trials to understand the role of liposome size and composition on therapeutic outcome. A major highlight was liposome inhalation for the treatment of lung cancers. Many in vivo studies that explored the potential of liposomes as anticancer carrier systems were evaluated, including animal studies and clinical trials. Liposomes can entrap anticancer drugs and localise their action in the lung following pulmonary delivery. The safety of inhaled liposomes incorporating anticancer drugs depends on the anticancer agent used and the amount of drug delivered to the target cancer in the lung. The difficulty of efficient targeting of liposomal anticancer aerosols to the cancerous tissues within the lung may result in low doses reaching the target site. Overall, following the success of liposomes as inhalable carriers in the treatment of lung infections, it is expected that more focus from research and development will be given to designing inhalable liposome carriers for the treatment of other lung diseases, including pulmonary cancers. The successful development of anticancer liposomes for inhalation may depend on the future development of effective aerosolisation devices and better targeted liposomes to maximise the benefit of therapy and reduce the potential for local and systemic adverse effects. © 2016 S. Karger AG, Basel.

  17. A critical appraisal of codes as vehicles for realising on-site quality

    NARCIS (Netherlands)

    Van Breugel, K.

    2014-01-01

    The increasing demand for quality, durability and sustainability requires a critical evaluation of currently used building codes. Although there is no doubt that we need codes, standards, certificates etc., the existence of these documents are no guarantee that the prescribed quality is realized on

  18. Object-based target templates guide attention during visual search

    OpenAIRE

    Berggren, Nick; Eimer, Martin

    2018-01-01

    During visual search, attention is believed to be controlled in a strictly feature-based fashion, without any guidance by object-based target representations. To challenge this received view, we measured electrophysiological markers of attentional selection (N2pc component) and working memory (SPCN) in search tasks where two possible targets were defined by feature conjunctions (e.g., blue circles and green squares). Critically, some search displays also contained nontargets with two target f...

  19. Processes and effects of targeted online advertising among children

    NARCIS (Netherlands)

    van Reijmersdal, E.A.; Rozendaal, E.; Smink, N.; van Noort, G.; Buijzen, M.

    2017-01-01

    Increasingly, information from children's profile pages on social network sites is being used to target online advertising, a phenomenon known as profile targeting. This practice has raised concerns in society and academia; however, its effects among children remain unstudied. Therefore, we

  20. Novel targets for ATM-deficient malignancies

    Science.gov (United States)

    Winkler, Johannes; Hofmann, Kay; Chen, Shuhua

    2014-01-01

    Conventional chemo- and radiotherapies for the treatment of cancer target rapidly dividing cells in both tumor and non-tumor tissues and can exhibit severe cytotoxicity in normal tissue and impair the patient's immune system. Novel targeted strategies aim for higher efficacy and tumor specificity. The role of ATM protein in the DNA damage response is well known and ATM deficiency frequently plays a role in tumorigenesis and development of malignancy. In addition to contributing to disease development, ATM deficiency also renders malignant cells heavily dependent on other pathways that cooperate with the ATM-mediated DNA damage response to ensure tumor cell survival. Disturbing those cooperative pathways by inhibiting critical protein components allows specific targeting of tumors while sparing healthy cells with normal ATM status. We review druggable candidate targets for the treatment of ATM-deficient malignancies and the mechanisms underlying such targeted therapies. PMID:27308314

  1. ICPP criticality event of October 17, 1978. Facts and sequential description of criticality event and precursor events

    International Nuclear Information System (INIS)

    1979-01-01

    On October 17 during the period of approximately 8:15 to 8:40 p.m., a criticality event occurred in the base of IB column, H-100. The inventory of medium short-lived fission products used to determine the number of fissions indicates that the criticality occurred in column H-100 aqueous phase and the sampling of the column wall with counting of the filings clearly indicates that the event occurred in the column base. The events leading up to the accident are described. The event produced no personnel injury, on-or off-site contamination, nor damage to equipment or property

  2. The Nuclear Criticality Information System: An update

    International Nuclear Information System (INIS)

    Koponen, B.L.

    1991-07-01

    The US Department of Energy's Nuclear Criticality Information System (NCIS) has served the criticality community for the past ten years with publications and with an online information system. NCIS provides a mean for widely distributed nuclear criticality specialists to communicate and work together instantly. Users of the system may receive assistance from all members of the NCIS community, which provides a much broader base of support than is available at any single site. When unified by NCIS, these diverse specialists provide a resource that has proven to be very useful in the safe handling of fissile material. NCIS also is a source of current nuclear criticality safety information; the rapid access of such up-to-date information on the handling of fissile materials outside of nuclear reactors is international in scope, extending beyond political and geographical boundaries

  3. A critical assessment of boron target compounds for boron neutron capture therapy.

    Science.gov (United States)

    Hawthorne, M Frederick; Lee, Mark W

    2003-01-01

    Boron neutron capture therapy (BNCT) has undergone dramatic developments since its inception by Locher in 1936 and the development of nuclear energy during World War II. The ensuing Cold War spawned the entirely new field of polyhedral borane chemistry, rapid advances in nuclear reactor technology and a corresponding increase in the number to reactors potentially available for BNCT. This effort has been largely oriented toward the eradication of glioblastoma multiforme (GBM) and melanoma with reduced interest in other types of malignancies. The design and synthesis of boron-10 target compounds needed for BNCT was not channeled to those types of compounds specifically required for GBM or melanoma. Consequently, a number of potentially useful boron agents are known which have not been biologically evaluated beyond a cursory examination and only three boron-10 enriched target species are approved for human use following their Investigational New Drug classification by the US Food and Drug Administration; BSH, BPA and GB-10. All ongoing clinical trials with GBM and melanoma are necessarily conducted with one of these three species and most often with BPA. The further development of BNCT is presently stalled by the absence of strong support for advanced compound evaluation and compound discovery driven by recent advances in biology and chemistry. A rigorous demonstration of BNCT efficacy surpassing that of currently available protocols has yet to be achieved. This article discusses the past history of compound development, contemporary problems such as compound classification and those problems which impede future advances. The latter include means for biological evaluation of new (and existing) boron target candidates at all stages of their development and the large-scale synthesis of boron target species for clinical trials and beyond. The future of BNCT is bright if latitude is given to the choice of clinical disease to be treated and if a recognized study

  4. Hanford Site performance report - December 1998

    International Nuclear Information System (INIS)

    EDER, D.M.

    2001-01-01

    The purpose of the Hanford Site Performance Report is to provide the Department of Energy Richland Operations Office's (DOE-RL's) report of Hanford's performance by: U. S. Department of Energy, Richland Operations Office, Project Hanford Management Contract (PHMC) through Fluor Daniel Hanford, Inc. (FDH) and its subcontractors, Environmental Restoration Contract through Bechtel Hanford, Inc. (BHI), and its subcontractors, and Pacific Northwest National Laboratories (PNNL) for Science and Technology support to the Environmental Management (EM) mission. This report is published monthly with the intent of relating work performance and progress in the context of the Success Indicators and Critical Success Factors as outlined in the Hanford Strategic Plan. Currently, the report focuses on the EM mission, and will be expanded in the future to include non-EM activities. Section A of this report is the Executive Summary, encapsulating high-level data in this report into an overall brief. Summary information provided includes Notable Accomplishments, a tabular performance profile with associated analyses, Critical Issues, Key Integration Activities, a look at Significant Trends, and a ''quick list'' of Upcoming Key Events. Section B of this report, the Site Summary section, provides Environmental Management performance data specifically organized to the pertinent Critical Success Factors and Success Indicators. The Site Summary is a compilation of performance data from all of the Mission Areas and the Projects that comprise these Mission Areas; the information is presented in both narrative and graphical formats. The remaining sections provide performance data relative to each individual mission area (e.g., Waste Management, Spent Nuclear Fuels, etc.). The information provided in the Mission Area sections is at a level of greater detail than is presented in either the Executive Summary or the Site Summary sections. At the end of this report, a glossary of terms is provided

  5. Critical (public) masses: a case study of a radioactive waste site

    International Nuclear Information System (INIS)

    Williams, R.G.; Payne, B.A.

    1985-01-01

    Increasing public sensitivity to radioactive and other hazardous waste issues often results in opposition that ranges from presentations by individuals at various public meetings to organizations initiating legal action in the courts. Organized opposition to proposed plans by the US Department of Energy (DOE) for a Surplus Facilities Management Program site near Weldon Spring, Missouri, has emerged during the two years that DOE has been involved in developing plans for this waste management site. An important aspect in the development of the major interest group in this case was the reliance on extra-local expertise at both the state and national levels. The group received organizational strategies, information on radioactive waste, legal advice, and direction from state and local environmental interest groups and various state agencies. In this paper, the authors present the historical development of organized public response and agency response to DOE's plans for the Weldon Spring site. The role of the interest group has emerged as one of a watchdog, scrutinizing and evaluating data publications, and plans. Other organizations now rely on the group as a clearinghouse for information. This case is of particular importance to other waste management projects because it demonstrates the effective use of networking between various interest groups and agencies from the local to the national level. The authors believe that the emergence of such groups and their ties with a variety of extra-local organizations will be the rule rather than the exception in future waste projects. Agency personnel and project sponsors will find that an interactive, cooperative approach with such groups is an effective way to resolve waste issues. 9 references

  6. Critical (public) masses: a case study of a radioactive waste site

    International Nuclear Information System (INIS)

    Williams, R.G.; Payne, B.A.

    1985-01-01

    Increasing public sensitivity to radioactive and other hazardous waste issues often results in opposition that ranges from presentations by individuals at various public meetings to organizations initiating legal action in the courts. Organized opposition to proposed plans by the US Department of Energy (DOE) for a Surplus Facilities Management Program site near Weldon Spring, Missouri, has emerged during the two years that DOE has been involved in developing plans for this waste management site. An important aspect in the development of the major interest group in this case was the reliance on extra-local expertise at both the state and national levels. The group received organizational strategies, information on radioactive waste, legal advice, and direction from state and local environmental interest groups and various state agencies. In this paper, we present the historical development of organized public response and agency response to DOE's plans for the Weldon Spring site. The role of the interest group has emerged as one of a watchdog, scrutinizing and evaluating data, publications, and plans. Other organizations now rely on the group as a clearinghouse for information. This case is of particular importance to other waste management projects because it demonstrates the effective use of networking between various interest groups and agencies from the local to the national level. We believe that the emergence of such groups and their ties with a variety of extra-local organizations will be the rule rather than the exception in future waste projects. Agency personnel and project sponsors will find that an interactive, cooperative approach with such groups is an effective way to resolve waste issues

  7. Convergent transmission of RNAi guide-target mismatch information across Argonaute internal allosteric network.

    Directory of Open Access Journals (Sweden)

    Thomas T Joseph

    Full Text Available In RNA interference, a guide strand derived from a short dsRNA such as a microRNA (miRNA is loaded into Argonaute, the central protein in the RNA Induced Silencing Complex (RISC that silences messenger RNAs on a sequence-specific basis. The positions of any mismatched base pairs in an miRNA determine which Argonaute subtype is used. Subsequently, the Argonaute-guide complex binds and silences complementary target mRNAs; certain Argonautes cleave the target. Mismatches between guide strand and the target mRNA decrease cleavage efficiency. Thus, loading and silencing both require that signals about the presence of a mismatched base pair are communicated from the mismatch site to effector sites. These effector sites include the active site, to prevent target cleavage; the binding groove, to modify nucleic acid binding affinity; and surface allosteric sites, to control recruitment of additional proteins to form the RISC. To examine how such signals may be propagated, we analyzed the network of internal allosteric pathways in Argonaute exhibited through correlations of residue-residue interactions. The emerging network can be described as a set of pathways emanating from the core of the protein near the active site, distributed into the bulk of the protein, and converging upon a distributed cluster of surface residues. Nucleotides in the guide strand "seed region" have a stronger relationship with the protein than other nucleotides, concordant with their importance in sequence selectivity. Finally, any of several seed region guide-target mismatches cause certain Argonaute residues to have modified correlations with the rest of the protein. This arises from the aggregation of relatively small interaction correlation changes distributed across a large subset of residues. These residues are in effector sites: the active site, binding groove, and surface, implying that direct functional consequences of guide-target mismatches are mediated through the

  8. Dual-band infrared capabilities for imaging buried object sites

    Energy Technology Data Exchange (ETDEWEB)

    Del Grande, N.K.; Durbin, P.F.; Gorvad, M.R.; Perkins, D.E.; Clark, G.A.; Hernandez, J.E.; Sherwood, R.J.

    1993-04-02

    We discuss dual-band infrared (DBIR) capabilities for imaging buried object sizes. We identify physical features affecting thermal contrast needed to distinguish buried object sites from undisturbed sites or surface clutter. Apart from atmospheric transmission and system performance, these features include: object size, shape, and burial depth; ambient soil, disturbed soil and object site thermal diffusivity differences; surface temperature, emissivity, plant-cover, slope, albedo and roughness variations; weather conditions and measurement times. We use good instrumentation to measure the time-varying temperature differences between buried object sites and undisturbed soil sites. We compare near surface soil temperature differences with radiometric infrared (IR) surface temperature differences recorded at 4.7 {plus_minus} 0.4 {mu}m and at 10.6 {plus_minus} 1.0 {mu}m. By producing selective DBIR image ratio maps, we distinguish temperature-difference patterns from surface emissivity effects. We discuss temperature differences between buried object sites, filled hole site (without buried objects), cleared (undisturbed) soil sites, and grass-covered sites (with and without different types of surface clutter). We compare temperature, emissivity-ratio, visible and near-IR reflectance signatures of surface objects, leafy plants and sod. We discuss the physical aspects of environmental, surface and buried target features affecting interpretation of buried targets, surface objects and natural backgrounds.

  9. Nanostructured delivery systems with improved leishmanicidal activity: a critical review.

    Science.gov (United States)

    Bruni, Natascia; Stella, Barbara; Giraudo, Leonardo; Della Pepa, Carlo; Gastaldi, Daniela; Dosio, Franco

    2017-01-01

    Leishmaniasis is a vector-borne zoonotic disease caused by protozoan parasites of the genus Leishmania , which are responsible for numerous clinical manifestations, such as cutaneous, visceral, and mucocutaneous leishmaniasis, depending on the site of infection for particular species. These complexities threaten 350 million people in 98 countries worldwide. Amastigotes living within macrophage phagolysosomes are the principal target of antileishmanial treatment, but these are not an easy target as drugs must overcome major structural barriers. Furthermore, limitations on current therapy are related to efficacy, toxicity, and cost, as well as the length of treatment, which can increase parasitic resistance. Nanotechnology has emerged as an attractive alternative as conventional drugs delivered by nanosized carriers have improved bioavailability and reduced toxicity, together with other characteristics that help to relieve the burden of this disease. The significance of using colloidal carriers loaded with active agents derives from the physiological uptake route of intravenous administered nanosystems (the phagocyte system). Nanosystems are thus able to promote a high drug concentration in intracellular mononuclear phagocyte system (MPS)-infected cells. Moreover, the versatility of nanometric drug delivery systems for the deliberate transport of a range of molecules plays a pivotal role in the design of therapeutic strategies against leishmaniasis. This review discusses studies on nanocarriers that have greatly contributed to improving the efficacy of antileishmaniasis drugs, presenting a critical review and some suggestions for improving drug delivery.

  10. Accelerator-driven sub-critical research facility with low-enriched fuel in lead matrix: Neutron flux calculation

    Directory of Open Access Journals (Sweden)

    Avramović Ivana

    2007-01-01

    Full Text Available The H5B is a concept of an accelerator-driven sub-critical research facility (ADSRF being developed over the last couple of years at the Vinča Institute of Nuclear Sciences, Belgrade, Serbia. Using well-known computer codes, the MCNPX and MCNP, this paper deals with the results of a tar get study and neutron flux calculations in the sub-critical core. The neutron source is generated by an interaction of a proton or deuteron beam with the target placed inside the sub-critical core. The results of the total neutron flux density escaping the target and calculations of neutron yields for different target materials are also given here. Neutrons escaping the target volume with the group spectra (first step are used to specify a neutron source for further numerical simulations of the neutron flux density in the sub-critical core (second step. The results of the calculations of the neutron effective multiplication factor keff and neutron generation time L for the ADSRF model have also been presented. Neutron spectra calculations for an ADSRF with an uranium tar get (highest values of the neutron yield for the selected sub-critical core cells for both beams have also been presented in this paper.

  11. Learning through Social Networking Sites--The Critical Role of the Teacher

    Science.gov (United States)

    Callaghan, Noelene; Bower, Matt

    2012-01-01

    This comparative case study examined factors affecting behaviour and learning in social networking sites (SNS). The behaviour and learning of two classes completing identical SNS based modules of work was observed and compared. All student contributions to the SNS were analysed, with the cognitive process dimension of the Revised Bloom's Taxonomy…

  12. Epitope-Targeting of Tertiary Protein Structure Enables Target-Guided Synthesis of a Potent in Cell Inhibitor of Botulinum Neurotoxin**

    OpenAIRE

    Farrow, Blake; Wong, Michelle; Malette, Jacquie; Lai, Bert; Deyle, Kaycie M.; Das, Samir; Nag, Arundhati; Agnew, Heather D.; Heath, James R.

    2015-01-01

    Botulinum neurotoxin (BoNT) serotype A is the most lethal known toxin and has an occluded structure, which prevents direct inhibition of its active site before it enters the cytosol. Target-guided synthesis by in situ click chemistry is combined with synthetic epitope targeting to exploit the tertiary structure of the BoNT protein as a landscape for assembling a competitive inhibitor. A substrate-mimicking peptide macrocycle is used as a direct inhibitor of BoNT. An epitope-targeting in situ ...

  13. Host-Primed Ebola Virus GP Exposes a Hydrophobic NPC1 Receptor-Binding Pocket, Revealing a Target for Broadly Neutralizing Antibodies.

    Science.gov (United States)

    Bornholdt, Zachary A; Ndungo, Esther; Fusco, Marnie L; Bale, Shridhar; Flyak, Andrew I; Crowe, James E; Chandran, Kartik; Saphire, Erica Ollmann

    2016-02-23

    The filovirus surface glycoprotein (GP) mediates viral entry into host cells. Following viral internalization into endosomes, GP is cleaved by host cysteine proteases to expose a receptor-binding site (RBS) that is otherwise hidden from immune surveillance. Here, we present the crystal structure of proteolytically cleaved Ebola virus GP to a resolution of 3.3 Å. We use this structure in conjunction with functional analysis of a large panel of pseudotyped viruses bearing mutant GP proteins to map the Ebola virus GP endosomal RBS at molecular resolution. Our studies indicate that binding of GP to its endosomal receptor Niemann-Pick C1 occurs in two distinct stages: the initial electrostatic interactions are followed by specific interactions with a hydrophobic trough that is exposed on the endosomally cleaved GP1 subunit. Finally, we demonstrate that monoclonal antibodies targeting the filovirus RBS neutralize all known filovirus GPs, making this conserved pocket a promising target for the development of panfilovirus therapeutics. Ebola virus uses its glycoprotein (GP) to enter new host cells. During entry, GP must be cleaved by human enzymes in order for receptor binding to occur. Here, we provide the crystal structure of the cleaved form of Ebola virus GP. We demonstrate that cleavage exposes a site at the top of GP and that this site binds the critical domain C of the receptor, termed Niemann-Pick C1 (NPC1). We perform mutagenesis to find parts of the site essential for binding NPC1 and map distinct roles for an upper, charged crest and lower, hydrophobic trough in cleaved GP. We find that this 3-dimensional site is conserved across the filovirus family and that antibody directed against this site is able to bind cleaved GP from every filovirus tested and neutralize viruses bearing those GPs. Copyright © 2016 Bornholdt et al.

  14. TALE-PvuII Fusion Proteins – Novel Tools for Gene Targeting

    Science.gov (United States)

    Yanik, Mert; Alzubi, Jamal; Lahaye, Thomas; Cathomen, Toni; Pingoud, Alfred; Wende, Wolfgang

    2013-01-01

    Zinc finger nucleases (ZFNs) consist of zinc fingers as DNA-binding module and the non-specific DNA-cleavage domain of the restriction endonuclease FokI as DNA-cleavage module. This architecture is also used by TALE nucleases (TALENs), in which the DNA-binding modules of the ZFNs have been replaced by DNA-binding domains based on transcription activator like effector (TALE) proteins. Both TALENs and ZFNs are programmable nucleases which rely on the dimerization of FokI to induce double-strand DNA cleavage at the target site after recognition of the target DNA by the respective DNA-binding module. TALENs seem to have an advantage over ZFNs, as the assembly of TALE proteins is easier than that of ZFNs. Here, we present evidence that variant TALENs can be produced by replacing the catalytic domain of FokI with the restriction endonuclease PvuII. These fusion proteins recognize only the composite recognition site consisting of the target site of the TALE protein and the PvuII recognition sequence (addressed site), but not isolated TALE or PvuII recognition sites (unaddressed sites), even at high excess of protein over DNA and long incubation times. In vitro, their preference for an addressed over an unaddressed site is > 34,000-fold. Moreover, TALE-PvuII fusion proteins are active in cellula with minimal cytotoxicity. PMID:24349308

  15. Soil processes and functions in critical zone observatories: hypotheses and experimental design

    NARCIS (Netherlands)

    Banwart, S.; Bernasconi, S.M.; Bloem, J.; Blum, W.; Ruiter, de P.C.; Gaans, van P.; Riemsdijk, van W.H.

    2011-01-01

    European Union policy on soil threats and soil protection has prioritized new research to address global soil threats. This research draws on the methodology of Critical Zone Observatories (CZOs) to focus a critical mass of international, multidisciplinary expertise at specific field sites. These

  16. Target Capture during Mos1 Transposition*

    Science.gov (United States)

    Pflieger, Aude; Jaillet, Jerôme; Petit, Agnès; Augé-Gouillou, Corinne; Renault, Sylvaine

    2014-01-01

    DNA transposition contributes to genomic plasticity. Target capture is a key step in the transposition process, because it contributes to the selection of new insertion sites. Nothing or little is known about how eukaryotic mariner DNA transposons trigger this step. In the case of Mos1, biochemistry and crystallography have deciphered several inverted terminal repeat-transposase complexes that are intermediates during transposition. However, the target capture complex is still unknown. Here, we show that the preintegration complex (i.e., the excised transposon) is the only complex able to capture a target DNA. Mos1 transposase does not support target commitment, which has been proposed to explain Mos1 random genomic integrations within host genomes. We demonstrate that the TA dinucleotide used as the target is crucial both to target recognition and in the chemistry of the strand transfer reaction. Bent DNA molecules are better targets for the capture when the target DNA is nicked two nucleotides apart from the TA. They improve strand transfer when the target DNA contains a mismatch near the TA dinucleotide. PMID:24269942