WorldWideScience

Sample records for randomly-distributed target site

  1. Target sites of anthelmintics.

    Science.gov (United States)

    Martin, R J; Robertson, A P; Bjorn, H

    1997-01-01

    This paper reviews sites of action of anthelmintic drugs including: (1) levamisole and pyrantel, which act as agonists at nicotinic acetylcholine receptors of nematodes; (2) the avermectins, which potentiate or gate the opening of glutamategated chloride channels found only in invertebrates; (3) piperazine, which acts as an agonist at GABA gated chloride channels on nematode muscle; (4) praziquantel, which increases the permeability of trematode tegument to calcium and results in contraction of the parasite muscle; (5) the benzimidazoles, like thiabendazole, which bind selectively to parasite beta-tubulin and prevents microtubule formation; (6) the proton ionophores, like closantel, which uncouple oxidative phosphorylation; (7) diamphenethide and clorsulon, which selectively inhibit glucose metabolism of Fasciola and; (8) diethylcarbamazine, which appears to interfere with arachidonic acid metabolism of filarial parasites and host. The review concludes with brief comments on the development of anthelmintics in the future.

  2. Non-Random Distribution of 5S rDNA Sites and Its Association with 45S rDNA in Plant Chromosomes.

    Science.gov (United States)

    Roa, Fernando; Guerra, Marcelo

    2015-01-01

    5S and 45S rDNA sites are the best mapped chromosome regions in eukaryotic chromosomes. In this work, a database was built gathering information about the position and number of 5S rDNA sites in 784 plant species, aiming to identify patterns of distribution along the chromosomes and its correlation with the position of 45S rDNA sites. Data revealed that in most karyotypes (54.5%, including polyploids) two 5S rDNA sites (a single pair) are present, with 58.7% of all sites occurring in the short arm, mainly in the proximal region. In karyotypes of angiosperms with only 1 pair of sites (single sites) they are mostly found in the proximal region (52.0%), whereas in karyotypes with multiple sites the location varies according to the average chromosome size. Karyotypes with multiple sites and small chromosomes (sites, while medium-sized (between 3 and 6 µm) and large chromosomes (>6 µm) more commonly show terminal or interstitial sites. In species with holokinetic chromosomes, the modal value of sites per karyotype was also 2, but they were found mainly in a terminal position. Adjacent 5S and 45S rDNA sites were often found in the short arm, reflecting the preferential distribution of both sites in this arm. The high frequency of genera with at least 1 species with adjacent 5S and 45S sites reveals that this association appeared several times during angiosperm evolution, but it has been maintained only rarely as the dominant array in plant genera. © 2015 S. Karger AG, Basel.

  3. Process of random distributions : classification and prediction ...

    African Journals Online (AJOL)

    Dirichlet random distribution. The parameter of this process can be the distribution of any usual such as the (multifractional) Brownian motion. We also extend Kraft random distribution to the continuous time case. We give an application in ...

  4. Non-random distribution of instability-associated chromosomal rearrangement breakpoints in human lymphoblastoid cells

    Energy Technology Data Exchange (ETDEWEB)

    Moore, Stephen R. [Environmental Toxicology Graduate Program, Department of Cell Biology and Neuroscience, University of California, Riverside, CA (United States); Radiation and Genome Stability Unit, Medical Research Council, Harwell, Oxfordshire (United Kingdom); Papworth, David [Radiation and Genome Stability Unit, Medical Research Council, Harwell, Oxfordshire (United Kingdom); Grosovsky, Andrew J. [Environmental Toxicology Graduate Program, Department of Cell Biology and Neuroscience, University of California, Riverside, CA (United States)]. E-mail: Grosovsky@ucr.edu

    2006-08-30

    Genomic instability is observed in tumors and in a large fraction of the progeny surviving irradiation. One of the best-characterized phenotypic manifestations of genomic instability is delayed chromosome aberrations. Our working hypothesis for the current study was that if genomic instability is in part attributable to cis mechanisms, we should observe a non-random distribution of chromosomes or sites involved in instability-associated rearrangements, regardless of radiation quality, dose, or trans factor expression. We report here the karyotypic examination of 296 instability-associated chromosomal rearrangement breaksites (IACRB) from 118 unstable TK6 human B lymphoblast, and isogenic derivative, clones. When we tested whether IACRB were distributed across the chromosomes based on target size, a significant non-random distribution was evident (p < 0.00001), and three IACRB hotspots (chromosomes 11, 12, and 22) and one IACRB coldspot (chromosome 2) were identified. Statistical analysis at the chromosomal band-level identified four IACRB hotspots accounting for 20% of all instability-associated breaks, two of which account for over 14% of all IACRB. Further, analysis of independent clones provided evidence within 14 individual clones of IACRB clustering at the chromosomal band level, suggesting a predisposition for further breaks after an initial break at some chromosomal bands. All of these events, independently, or when taken together, were highly unlikely to have occurred by chance (p < 0.000001). These IACRB band-level cluster hotspots were observed independent of radiation quality, dose, or cellular p53 status. The non-random distribution of instability-associated chromosomal rearrangements described here significantly differs from the distribution that was observed in a first-division post-irradiation metaphase analysis (p = 0.0004). Taken together, these results suggest that genomic instability may be in part driven by chromosomal cis mechanisms.

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

    Science.gov (United States)

    2015-10-01

    targeted therapy on the efficacy of cabazitaxel in men with metastatic castration-resistant prostate cancer R. Van Soest1, A. Nieuweboer2, E. De...AWARD NUMBER: W81XWH-14-2-0159 TITLE: Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies PRINCIPAL INVESTIGATOR...Sep 2015 4. TITLE AND SUBTITLE 5a. CONTRACT NUMBER Prostate Cancer Clinical Consortium Clinical Research Site: Targeted Therapies 5b. GRANT NUMBER

  6. 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…

  7. Non-target-site herbicide resistance: a family business.

    Science.gov (United States)

    Yuan, Joshua S; Tranel, Patrick J; Stewart, C Neal

    2007-01-01

    We have witnessed a dramatic increase in the frequency and diversity of herbicide-resistant weed biotypes over the past two decades, which poses a threat to the sustainability of agriculture at both local and global levels. In addition, non-target-site mechanisms of herbicide resistance seem to be increasingly implicated. Non-target-site herbicide resistance normally involves the biochemical modification of the herbicide and/or the compartmentation of the herbicide (and its metabolites). In contrast to herbicide target site mutations, fewer non-target mechanisms have been elucidated at the molecular level because of the inherently complicated biochemical processes and the limited genomic information available for weedy species. To further understand the mechanisms of non-target-site resistance, we propose an integrated genomics approach to dissect systematically the functional genomics of four gene families in economically important weed species.

  8. 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.

  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. Integrin-Targeting Fluorescent Proteins: Exploration of RGD Insertion Sites.

    Science.gov (United States)

    Sonntag, Michael H; Schill, Jurgen; Brunsveld, Luc

    2017-03-02

    The potential of the fluorescent protein scaffold to control peptide sequence functionality is illustrated by an exploration of fluorescent proteins as novel probes for targeting integrins. A library of fluorescent mCitrine proteins with RGD motifs incorporated at several positions in loops within the protein main chain was generated and characterized. Amino acid mutations to RGD as well as RGD insertions were evaluated: both led to constructs with typical mCitrine fluorescent properties. Screening experiments against four human integrin receptors revealed two strong-binding constructs and two selective integrin binders. The effect of the site of RGD incorporation illustrates the importance of the protein scaffold on RGD sequence functionality, leading to fluorescent protein constructs with the potential for selective integrin targeting. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  11. 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.

  12. 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.

  13. 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.

  14. Graphene materials having randomly distributed two-dimensional structural defects

    Science.gov (United States)

    Kung, Harold H; Zhao, Xin; Hayner, Cary M; Kung, Mayfair C

    2013-10-08

    Graphene-based storage materials for high-power battery applications are provided. The storage materials are composed of vertical stacks of graphene sheets and have reduced resistance for Li ion transport. This reduced resistance is achieved by incorporating a random distribution of structural defects into the stacked graphene sheets, whereby the structural defects facilitate the diffusion of Li ions into the interior of the storage materials.

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

    Science.gov (United States)

    2016-10-01

    a multi-institutional infrastructure incorporating 5 leading prostate cancer clinical sites, 2 sequencing and computational analysis sites, linked...unacceptable toxicity. Radiological assesment were defined according PCWG2 criteria and RECIST 1.1. Results: 64 pts were identified, 47 met all criteria

  16. 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.

  17. 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.

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

    Science.gov (United States)

    Luo, Yumei; Zhang, Zhizhuo; Chen, Yaoyong; Sun, Xiaofang

    2015-01-01

    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. PMID:25918715

  19. Enzyme-triggered Gelation: Targeting Proteases with Internal Cleavage Sites

    Science.gov (United States)

    Bremmer, Steven C.

    2014-01-01

    A generalizable method for detecting protease activity via gelation is described. A recognition sequence is used to target the protease of interest while a second protease is used to remove the residual residues from the gelator scaffold. Using this approach, selective assays for both MMP-9 and PSA are demonstrated. PMID:24394494

  20. Runoff production on a slope with randomly distributed infiltrabilities

    Science.gov (United States)

    Mouche, E.; Harel, M.

    2013-12-01

    Runoff generated on one- and two-dimensional slopes with randomly distributed infiltrability is studied in the queuing theory and connectivity frameworks. The equivalence between the runoff-runon equation and the customers waiting time in a single server queue provides a theoretical link between the statistical descriptions of infiltrability and that of runoff flow rate. Different distributions of infiltrability, representing soil heterogeneities at different scales, are considered. Numerical simulations validate these results and improve our understanding of runoff-runon process. All of the quantities describing the generation of runoff (runoff one-point statistics) and its organization into patterns (patterns statistics and connectivity) are studied as functions of rainfall rate and runoff dimensionality.

  1. The rising power of random distributed feedback fiber laser

    Science.gov (United States)

    Zhou, Pu; Ye, Jun; Xu, Jiangming; Zhang, Hanwei; Huang, Long; Wu, Jian; Xiao, Hu; Leng, Jinyong

    2018-01-01

    Random distributed feedback fiber lasers (RDFFL) are now attracting more and more attentions for their unique cavity-free, mode-free and structural simplicity features and broadband application potentials in many fields, such as long distance sensing, speck free imaging, nonlinear frequency conversion as well as new pump source. In this talk, we will review the recent research progresses on high power RDFFLs. We have achieved (1) More than 400 W RDFFL with nearly Gaussian beam profile based on crucial employment of fiber mismatching architecture. (2) High power RDFFL with specialized optical property that include: high power narrow-band RDFFL, hundred-watt level linearly-polarized RDFFL, hundred-watt level high-order RDFFL. (3) Power enhancements of RDFFL to record kilowatt level are demonstrated with the aid of fiber master oscillator power amplifier (MOPA) with different pump schemes.

  2. Ultrathin wide bandwidth metamaterial absorber using randomly distributed scatterers

    Science.gov (United States)

    Ahmadi, Farzad; Ida, Nathan

    2017-02-01

    In this paper, a broadband, ultrathin metamaterial absorber (MA) using randomly distributed scatterers is presented. Each scattering element consists of two parallel strips. These elements can either be isolated or they may overlap with nearby elements. Three different randomly positioned structures are investigated for normal incident angle as well as oblique incident angles showing that these MAs can provide broadband absorption for all cases. The results presented here coincide with some previous works. Each structure obviously has different absorption spectrum and FWHM since the coupling between the randomly positioned scatterers is different in each case. The coupling between neighboring isolated and clustered scatterers form many resonating modes resulting in broadband absorption. The distribution of the electromagnetic fields are analyzed to obtain the physical behavior of the absorber. This shows that promising results can still be obtained for MAs when there is a significant tolerance distance between scatterers due to fabrication errors in micro and nanoscale metadevices.

  3. The impact of miRNA target sites in coding sequences and in 3'UTRs.

    Directory of Open Access Journals (Sweden)

    Zhuo Fang

    Full Text Available Animal miRNAs are a large class of small regulatory RNAs that are known to directly and negatively regulate the expression of a large fraction of all protein encoding genes. The identification and characterization of miRNA targets is thus a fundamental problem in biology. miRNAs regulate target genes by binding to 3' untranslated regions (3'UTRs of target mRNAs, and multiple binding sites for the same miRNA in 3'UTRs can strongly enhance the degree of regulation. Recent experiments have demonstrated that a large fraction of miRNA binding sites reside in coding sequences. Overall, miRNA binding sites in coding regions were shown to mediate smaller regulation than 3'UTR binding. However, possible interactions between target sites in coding sequences and 3'UTRs have not been studied. Using transcriptomics and proteomics data of ten miRNA mis-expression experiments as well as transcriptome-wide experimentally identified miRNA target sites, we found that mRNA and protein expression of genes containing target sites both in coding regions and 3'UTRs were in general mildly but significantly more regulated than those containing target sites in 3'UTRs only. These effects were stronger for conserved target sites of length 7-8 nt in coding regions compared to non-conserved sites. Combined with our other finding that miRNA target sites in coding regions are under negative selection, our results shed light on the functional importance of miRNA targeting in coding regions.

  4. Target and Non-target Site Mechanisms Developed by Glyphosate-Resistant Hairy beggarticks (Bidens pilosa L.) Populations from Mexico

    OpenAIRE

    Alcántara de la Cruz, Ricardo; Fernández-Moreno, Pablo T.; Ozuna, Carmen; Rojano-Delgado, Antonia María; Cruz-Hipólito, Hugo Enrique; Domínguez Valenzuela, José A; Barro Losada, Francisco; Prado, R. del

    2016-01-01

    In 2014 hairy beggarticks (Bidens pilosa L.) has been identified as being glyphosate-resistant in citrus orchards from Mexico. The target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (R1 and R2) and one susceptible (S) were studied. Experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) gene sequencing were carried out in each population. The ...

  5. Development of a target-site based regional frequency model using historical information

    Science.gov (United States)

    Hamdi, Yasser; Bardet, Lise; Duluc, Claire-Marie; Rebour, Vincent

    2016-04-01

    Nuclear power facilities in France were designed to withstand extreme environmental conditions with a very low probability of failure. Nevertheless, some exceptional surges considered as outliers are not properly addressed by classical frequency analysis models. If available data at the site of interest (target-site) is sufficiently complete on a long period and not characterized by the presence of an outlier, at-site frequency analysis can be used to estimate quantiles with acceptable uncertainties. Otherwise, regional and historical information (HI) may be used to mitigate the lack of data and the influence of the outlier by increasing its representativeness in the sample. several models have been proposed over the last years for regional extreme surges frequency analysis in France to take into account these outliers in the frequency analysis. However, these models do not give a specific weight to the target site and cannot take into account HI. The objective of the present work is to develop a regional frequency model (RFM) centered on a target-site and using HI. The neighborhood between sites is measured by a degree of physical and statistical dependence between observations (with a prior confidence level). Unlike existing models, the obtained region around the target site (and constituting the neighboring sites) is sliding from a target-site to another. In other words, the developed model assigns a region for each target site. The idea behind the construction of a frequency model favoring target sites and the principle of moving regions around these target-sites is the original key point of the developed model. A related issue regards the estimation of missed and/or ungauged surges at target-sites from those of gauged potential neighboring sites, a multiple linear regression (MLR) is used and it can be extended to other reconstitutions models. MLR analysis can be considered conclusive only if available observations at neighboring sites are informative enough

  6. Target-site and non-target-site based resistance to the herbicide tribenuron-methyl in flixweed (Descurainia sophia L.).

    Science.gov (United States)

    Yang, Qian; Deng, Wei; Li, Xuefeng; Yu, Qin; Bai, Lianyang; Zheng, Mingqi

    2016-08-05

    Flixweed (Descurainia sophia L.) is a troublesome and widespread broadleaf weed in winter fields in China, and has evolved high level resistance to acetolactate synthase (ALS)-inhibiting sulfonylurea herbicide tribenuron-methyl. We identified a resistant flixweed population (N11) exhibiting 116.3-fold resistance to tribenuron-methyl relative to the susceptible population (SD8). Target-site ALS gene mutation Pro-197-Thr was identified in resistant plants. Moreover, the resistance can be reversed to 28.7-fold by the cytochrome P450 inhibitor malathion. The RNA-Sequencing was employed to identify candidate genes involved in non-target-site metabolic resistance in this population. Total 26 differentially expressed contigs were identified and eight of them (four P450s, one ABC transporter, three glycosyltransferase) verified by qRT-PCR. Consistent over-expression of the two contigs homology to CYP96A13 and ABCC1 transporter, respectively, were further qRT-PCR validated using additional plants from the resistant and susceptible populations. Tribenuron-methyl resistance in flixweed is controlled by target-site ALS mutation and non-target-site based mechanisms. Two genes, CYP96A13 and ABCC1 transporter, could play an important role in metabolic resistance to tribenuron-methyl in the resistant flixweed population and justify further functional studies.

  7. Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae

    National Research Council Canada - National Science Library

    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

    .... 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...

  8. 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

  9. 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.

  10. 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

  11. Evaluating the Use of Random Distribution Theory to Introduce Statistical Inference Concepts to Business Students

    Science.gov (United States)

    Larwin, Karen H.; Larwin, David A.

    2011-01-01

    Bootstrapping methods and random distribution methods are increasingly recommended as better approaches for teaching students about statistical inference in introductory-level statistics courses. The authors examined the effect of teaching undergraduate business statistics students using random distribution and bootstrapping simulations. It is the…

  12. Near surface swimming of Salmonella Typhimurium explains target-site selection and cooperative invasion.

    Directory of Open Access Journals (Sweden)

    Benjamin Misselwitz

    Full Text Available Targeting of permissive entry sites is crucial for bacterial infection. The targeting mechanisms are incompletely understood. We have analyzed target-site selection by S. Typhimurium. This enteropathogenic bacterium employs adhesins (e.g. fim and the type III secretion system 1 (TTSS-1 for host cell binding, the triggering of ruffles and invasion. Typically, S. Typhimurium invasion is focused on a subset of cells and multiple bacteria invade via the same ruffle. It has remained unclear how this is achieved. We have studied target-site selection in tissue culture by time lapse microscopy, movement pattern analysis and modeling. Flagellar motility (but not chemotaxis was required for reaching the host cell surface in vitro. Subsequently, physical forces trapped the pathogen for ∼1.5-3 s in "near surface swimming". This increased the local pathogen density and facilitated "scanning" of the host surface topology. We observed transient TTSS-1 and fim-independent "stopping" and irreversible TTSS-1-mediated docking, in particular at sites of prominent topology, i.e. the base of rounded-up cells and membrane ruffles. Our data indicate that target site selection and the cooperative infection of membrane ruffles are attributable to near surface swimming. This mechanism might be of general importance for understanding infection by flagellated bacteria.

  13. Rapid identification of ubiquitination and SUMOylation target sites by microfluidic peptide array

    Directory of Open Access Journals (Sweden)

    Bing Zhu

    2016-03-01

    Full Text Available SUMOylation and ubiquitination are two essential post translational modifications (PTMs involved in the regulation of important biological processes in eukaryotic cells. Identification of ubiquitin (Ub and small ubiquitin-related modifier (SUMO-conjugated lysine residues in proteins is critical for understanding the role of ubiquitination and SUMOylation, but remains experimentally challenging. We have developed a powerful in vitro Ub/SUMO assay using a novel high density peptide array incorporated within a microfluidic device that allows rapid identification of ubiquitination and SUMOylation sites on target proteins. We performed the assay with a panel of human proteins and a microbial effector with known target sites for Ub or SUMO modifications, and determined that 80% of these proteins were modified by Ub or specific SUMO isoforms at the sites previously determined using conventional methods. Our results confirm the specificity for both SUMO isoform and individual target proteins at the peptide level. In summary, this microfluidic high density peptide array approach is a rapid screening assay to determine sites of Ub and SUMO modification of target substrates, which will provide new insights into the composition, selectivity and specificity of these PTM target sites.

  14. 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.

  15. CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites.

    Science.gov (United States)

    Naito, Yuki; Hino, Kimihiro; Bono, Hidemasa; Ui-Tei, Kumiko

    2015-04-01

    CRISPRdirect is a simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ∼ 20 nt targeted sequence. The target sequence requirements are twofold. First, the 5'-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast. Freely available at http://crispr.dbcls.jp/. Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

  16. 177-lu labeled peptide for site-specific uPAR-targeting

    DEFF Research Database (Denmark)

    2015-01-01

    There is provided a 177-Lu labelled peptide for site-specific targeting of the Urokinase Plasminogen Activator Receptor (uPAR) thereby enabling treatment of a cancer disease associated with high uPAR expression; e.g. treatment of colorectal cancer by administering to a patient an effective amount...... of the 177-Lu labelled peptide....

  17. Coactivation of GR and NFKB alters the repertoire of their binding sites and target genes

    Science.gov (United States)

    Rao, Nagesha A.S.; McCalman, Melysia T.; Moulos, Panagiotis; Francoijs, Kees-Jan; Chatziioannou, Aristotelis; Kolisis, Fragiskos N.; Alexis, Michael N.; Mitsiou, Dimitra J.; Stunnenberg, Hendrik G.

    2011-01-01

    Glucocorticoid receptor (GR) exerts anti-inflammatory action in part by antagonizing proinflammatory transcription factors such as the nuclear factor kappa-b (NFKB). Here, we assess the crosstalk of activated GR and RELA (p65, major NFKB component) by global identification of their binding sites and target genes. We show that coactivation of GR and p65 alters the repertoire of regulated genes and results in their association with novel sites in a mutually dependent manner. These novel sites predominantly cluster with p65 target genes that are antagonized by activated GR and vice versa. Our data show that coactivation of GR and NFKB alters signaling pathways that are regulated by each factor separately and provide insight into the networks underlying the GR and NFKB crosstalk. PMID:21750107

  18. 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.

  19. Electrospun dye-doped fiber networks: lasing emission from randomly distributed cavities

    DEFF Research Database (Denmark)

    Krammer, Sarah; Vannahme, Christoph; Smith, Cameron

    2015-01-01

    Dye-doped polymer fiber networks fabricated with electrospinning exhibit comb-like laser emission. We identify randomly distributed ring resonators being responsible for lasing emission by making use of spatially resolved spectroscopy. Numerical simulations confirm this result quantitatively....

  20. 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.

  1. Target and Non-Target Site Mechanisms Developed by Glyphosate-Resistant Hairy beggarticks (Bidens pilosa L. Populations from Mexico

    Directory of Open Access Journals (Sweden)

    Ricardo Alcántara-de la Cruz

    2016-10-01

    Full Text Available In 2014 hairy beggarticks (Bidens pilosa L. has been identified as being glyphosate-resistant in citrus orchards from Mexico. The target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (R1 and R2 and one susceptible (S were studied. Experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and EPSPS gene sequencing were carried out in each population. The R1 and R2 populations were 20.4 and 2.8-fold less glyphosate sensitive, respectively, than the S population. The resistant populations showed a lesser shikimic acid accumulation than the S population. In the latter one, 24.9% of 14C-glyphosate was translocated to the roots at 96 h after treatment; in the R1 and R2 populations only 12.9 and 15.5%, respectively, was translocated. Qualitative results confirmed the reduced 14C-glyphosate translocation in the resistant populations. The EPSPS enzyme activity of the S population was 128.4 and 8.5-fold higher than the R1 and R2 populations of glyphosate-treated plants, respectively. A single (Pro-106-Ser, and a double (Thr-102-Ile followed by Pro-106-Ser mutations were identified in the EPSPS2 gene conferred high resistance in R1 population. Target-site mutations associated with a reduced translocation were responsible for the higher glyphosate resistance in the R1 population. The low-intermediate resistance of the R2 population was mediated by reduced translocation. This is the first glyphosate resistance case confirmed in hairy beggarticks in the world.

  2. Target and Non-target Site Mechanisms Developed by Glyphosate-Resistant Hairy beggarticks (Bidens pilosa L.) Populations from Mexico.

    Science.gov (United States)

    Alcántara-de la Cruz, Ricardo; Fernández-Moreno, Pablo T; Ozuna, Carmen V; Rojano-Delgado, Antonia M; Cruz-Hipolito, Hugo E; Domínguez-Valenzuela, José A; Barro, Francisco; De Prado, Rafael

    2016-01-01

    In 2014 hairy beggarticks (Bidens pilosa L.) has been identified as being glyphosate-resistant in citrus orchards from Mexico. The target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (R1 and R2) and one susceptible (S) were studied. Experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and 5-enolpyruvyl shikimate-3-phosphate synthase (EPSPS) gene sequencing were carried out in each population. The R1 and R2 populations were 20.4 and 2.8-fold less glyphosate sensitive, respectively, than the S population. The resistant populations showed a lesser shikimic acid accumulation than the S population. In the latter one, 24.9% of 14C-glyphosate was translocated to the roots at 96 h after treatment; in the R1 and R2 populations only 12.9 and 15.5%, respectively, was translocated. Qualitative results confirmed the reduced 14C-glyphosate translocation in the resistant populations. The EPSPS enzyme activity of the S population was 128.4 and 8.5-fold higher than the R1 and R2 populations of glyphosate-treated plants, respectively. A single (Pro-106-Ser), and a double (Thr-102-Ile followed by Pro-106-Ser) mutations were identified in the EPSPS2 gene conferred high resistance in R1 population. Target-site mutations associated with a reduced translocation were responsible for the higher glyphosate resistance in the R1 population. The low-intermediate resistance of the R2 population was mediated by reduced translocation. This is the first glyphosate resistance case confirmed in hairy beggarticks in the world.

  3. 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.

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

    OpenAIRE

    Mitchell, SN; Rigden, DJ; Dowd, AJ; Lu, F.; Wilding, CS; Weetman, D.; Dadzie, S.; Jenkins, AM; Regna, K; Boko, P.; Djogbenou, L.; Muskavitch, MAT.; Ranson, H; Paine, MJI; Mayans, O

    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 ...

  5. 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.

  6. 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.

  7. 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.

  8. Programmable Site-Specific Nucleases for Targeted Genome Engineering in Higher Eukaryotes.

    Science.gov (United States)

    Govindan, Ganesan; Ramalingam, Sivaprakash

    2016-11-01

    Recent advances in the targeted genome engineering enable molecular biologists to generate sequence specific modifications with greater efficiency and higher specificity in complex eukaryotic genomes. Programmable site-specific DNA cleavage reagents and cellular DNA repair mechanisms have made this possible. These reagents have become powerful tools for delivering a site-specific genomic double-strand break (DSB) at the desired chromosomal locus, which produces sequence alterations through error-prone non-homologous end joining (NHEJ) resulting in gene inactivations/knockouts. Alternatively, the DSB can be repaired through homology-directed repair (HDR) using a donor DNA template, which leads to the introduction of desired sequence modifications at the predetermined site. Here, we summarize the role of three classes of nucleases; zinc finger nucleases (ZFNs), transcription activator like effector nucleases (TALENs), and clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system in achieving targeted genome modifications. Further, we discuss the progress towards the applications of programmable site-specific nucleases (SSNs) in treating human diseases and other biological applications in economically important higher eukaryotic organisms such as plants and livestock. J. Cell. Physiol. 231: 2380-2392, 2016. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  9. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants.

    Science.gov (United States)

    Hehle, Verena K; Paul, Matthew J; Roberts, Victoria A; van Dolleweerd, Craig J; Ma, Julian K-C

    2016-04-01

    This study examined the degradation pattern of a murine IgG1κ monoclonal antibody expressed in and extracted from transformedNicotiana tabacum Gel electrophoresis of leaf extracts revealed a consistent pattern of recombinant immunoglobulin bands, including intact and full-length antibody, as well as smaller antibody fragments. N-terminal sequencing revealed these smaller fragments to be proteolytic cleavage products and identified a limited number of protease-sensitive sites in the antibody light and heavy chain sequences. No strictly conserved target sequence was evident, although the peptide bonds that were susceptible to proteolysis were predominantly and consistently located within or near to the interdomain or solvent-exposed regions in the antibody structure. Amino acids surrounding identified cleavage sites were mutated in an attempt to increase resistance. Different Guy's 13 antibody heavy and light chain mutant combinations were expressed transiently inN. tabacumand demonstrated intensity shifts in the fragmentation pattern, resulting in alterations to the full-length antibody-to-fragment ratio. The work strengthens the understanding of proteolytic cleavage of antibodies expressed in plants and presents a novel approach to stabilize full-length antibody by site-directed mutagenesis.-Hehle, V. K., Paul, M. J., Roberts, V. A., van Dolleweerd, C. J., Ma, J. K.-C. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants. © The Author(s).

  10. Comprehensive identification and modified-site mapping of S-nitrosylated targets in prostate epithelial cells.

    Directory of Open Access Journals (Sweden)

    Ying Wai Lam

    2010-02-01

    Full Text Available Although overexpression of nitric oxide synthases (NOSs has been found associated with prostate diseases, the underlying mechanisms for NOS-related prostatic diseases remain unclear. One proposed mechanism is related to the S-nitrosylation of key regulatory proteins in cell-signaling pathways due to elevated levels of NO in the prostate. Thus, our primary objective was to identify S-nitrosylated targets in an immortalized normal prostate epithelial cell line, NPrEC.We treated NPrEC with nitroso-cysteine and used the biotin switch technique followed by gel-based separation and mass spectrometry protein identification (using the LTQ-Orbitrap to discover S-nitrosylated (SNO proteins in the treated cells. In parallel, we adapted a peptide pull-down methodology to locate the site(s of S-nitrosylation on the protein SNO targets identified by the first technique. This combined approach identified 116 SNO proteins and determined the sites of modification for 82 of them. Over 60% of these proteins belong to four functional groups: cell structure/cell motility/protein trafficking, protein folding/protein response/protein assembly, mRNA splicing/processing/transcriptional regulation, and metabolism. Western blot analysis validated a subset of targets related to disease development (proliferating cell nuclear antigen, maspin, integrin beta4, alpha-catenin, karyopherin [importin] beta1, and elongation factor 1A1. We analyzed the SNO sequences for their primary and secondary structures, solvent accessibility, and three-dimensional structural context. We found that about 80% of the SNO sites that can be mapped into resolved structures are buried, of which approximately half have charged amino acids in their three-dimensional neighborhood, and the other half residing within primarily hydrophobic pockets.We here identified 116 potential SNO targets and mapped their putative SNO sites in NPrEC. Elucidation of how this post-translational modification alters the

  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. High-power random distributed feedback fiber laser: From science to application

    Energy Technology Data Exchange (ETDEWEB)

    Du, Xueyuan [College of Optoelectronic Science and Engineering, National University of Defense Technology, Changsha 410073 (China); Naval Academy of Armament, Beijing 100161 (China); Zhang, Hanwei; Xiao, Hu; Ma, Pengfei; Wang, Xiaolin; Zhou, Pu; Liu, Zejin [College of Optoelectronic Science and Engineering, National University of Defense Technology, Changsha 410073 (China)

    2016-10-15

    A fiber laser based on random distributed feedback has attracted increasing attention in recent years, as it has become an important photonic device and has found wide applications in fiber communications or sensing. In this article, recent advances in high-power random distributed feedback fiber laser are reviewed, including the theoretical analyses, experimental approaches, discussion on the practical applications and outlook. It is found that a random distributed feedback fiber laser can not only act as an information photonics device, but also has the feasibility for high-efficiency/high-power generation, which makes it competitive with conventional high-power laser sources. In addition, high-power random distributed feedback fiber laser has been successfully applied for midinfrared lasing, frequency doubling to the visible and high-quality imaging. It is believed that the high-power random distributed feedback fiber laser could become a promising light source with simple and economic configurations. (copyright 2016 by WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  13. 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.

  14. Nucleosomes Selectively Inhibit Cas9 Off-target Activity at a Site Located at the Nucleosome Edge.

    Science.gov (United States)

    Hinz, John M; Laughery, Marian F; Wyrick, John J

    2016-11-25

    Nucleosomes affect Cas9 binding and activity at on-target sites, but their impact at off-target sites is unknown. To investigate how nucleosomes affect Cas9 cleavage at off-target sites in vitro, we used a single guide RNA (sgRNA) that has been previously shown to efficiently direct Cas9 cleavage at the edge of the strongly positioned 601 nucleosome. Our data indicate that single mismatches between the sgRNA and DNA target have relatively little effect on Cas9 cleavage of naked DNA substrates, but strongly inhibit cleavage of nucleosome substrates, particularly when the mismatch is in the sgRNA "seed" region. These findings indicate that nucleosomes may enhance Cas9 specificity by inhibiting cleavage of off-target sites at the nucleosome edge. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

  15. 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.

  16. The BET Family of Proteins Targets Moloney Murine Leukemia Virus Integration near Transcription Start Sites

    Directory of Open Access Journals (Sweden)

    Jan De Rijck

    2013-11-01

    Full Text Available A hallmark of retroviral replication is integration of the viral genome into host cell DNA. This characteristic makes retrovirus-based vectors attractive delivery vehicles for gene therapy. However, adverse events in gene therapeutic trials, caused by activation of proto-oncogenes due to murine leukemia virus (MLV-derived vector integration, hamper their application. Here, we show that bromodomain and extraterminal (BET proteins (BRD2, BRD3, and BRD4 and MLV integrase specifically interact and colocalize within the nucleus of the cell. Inhibition of the BET proteins’ chromatin interaction via specific bromodomain inhibitors blocks MLV virus replication at the integration step. MLV integration site distribution parallels the chromatin binding profile of BET proteins, and expression of an artificial fusion protein of the BET integrase binding domain with the chromatin interaction domain of the lentiviral targeting factor LEDGF/p75 retargets MLV integration away from transcription start sites and into the body of actively transcribed genes, conforming to the HIV integration pattern. Together, these data validate BET proteins as MLV integration targeting factors.

  17. Site-targeted acoustic contrast agent detects molecular expression of tissue factor after balloon angioplasty

    Science.gov (United States)

    Hall, Christopher S.; Abendschein, Dana R.; Scherrer, David E.; Scott, Michael J.; Marsh, Jon N.; Wickline, Samuel A.; Lanza, Gregory M.

    2000-04-01

    Complex molecular signaling heralds the early stages of pathologies such as angiogenesis, inflammation, and cellular responses to mechanically damaged coronary arteries after balloon angioplasty. In previous studies, we have demonstrated acoustic enhancement of blood clot morphology with the use of a nongaseous, ligand-targeted acoustic nanoparticle emulsion delivered to areas of thrombosis both in vitro and in vivo. In this paper, we characterize the early expression of tissue factor which contributes to subsequent arterial restenosis. Tissue factor is a 42kd glycoprotein responsible for blood coagulation but also plays a well-described role in cancer metastasis, angiogenesis, and vascular restenosis. This study was designed to determine whether the targeted contrast agent could localize tissue factor expressed within the wall of balloon-injured arteries. Both carotid arteries of five pigs (20 kg) were injured using an 8 X 20 mm angioplasty balloon. The carotids were treated in situ with a perfluorocarbon nanoparticle emulsion covalently complexed to either specific anti-tissue factor polyclonal F(ab) fragments (treatment) or non-specific IgG F(ab) fragments (control). Intravascular ultrasound (30 MHz) images of the arteries were obtained before and after exposure to the emulsions. Tissue- factor targeted ultrasonic contrast agent acoustically enhanced the subintima and media at the site of balloon- induced injury compared with control contrast arteries (p less than 0.05). Immunohistochemical staining confirmed the presence of increased tissue factor at the sites of acoustic enhancement. Binding of the targeted agents was demonstrated in vitro by scanning electron microscope images of cultured smooth muscle cells that constitutively express tissue factor. This study demonstrates the concept of molecular imaging and localization of carotid arteries' tissue factor in vivo using a new, nanoparticulate emulsion. Enhancement of the visualization of the molecular

  18. Targeted Mutagenesis, Precise Gene Editing, and Site-Specific Gene Insertion in Maize Using Cas9 and Guide RNA

    National Research Council Canada - National Science Library

    Svitashev, Sergei; Young, Joshua K; Schwartz, Christine; Gao, Huirong; Falco, S Carl; Cigan, A Mark

    2015-01-01

    Targeted mutagenesis, editing of endogenous maize (Zea mays) genes, and site-specific insertion of a trait gene using clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas...

  19. Identification of several potential chromatin binding sites of HOXB7 and its downstream target genes in breast cancer.

    Science.gov (United States)

    Heinonen, Henna; Lepikhova, Tatiana; Sahu, Biswajyoti; Pehkonen, Henna; Pihlajamaa, Päivi; Louhimo, Riku; Gao, Ping; Wei, Gong-Hong; Hautaniemi, Sampsa; Jänne, Olli A; Monni, Outi

    2015-11-15

    HOXB7 encodes a transcription factor that is overexpressed in a number of cancers and encompasses many oncogenic functions. Previous results have shown it to promote cell proliferation, angiogenesis, epithelial-mesenchymal transition, DNA repair and cell survival. Because of its role in many cancers and tumorigenic processes, HOXB7 has been suggested to be a potential drug target. However, HOXB7 binding sites on chromatin and its targets are poorly known. The aim of our study was to identify HOXB7 binding sites on breast cancer cell chromatin and to delineate direct target genes located nearby these binding sites. We found 1,504 HOXB7 chromatin binding sites in BT-474 breast cancer cell line that overexpresses HOXB7. Seventeen selected binding sites were validated by ChIP-qPCR in several breast cancer cell lines. Furthermore, we analyzed expression of a large number of genes located nearby HOXB7 binding sites and found several new direct targets, such as CTNND2 and SCGB1D2. Identification of HOXB7 chromatin binding sites and target genes is essential to understand better the role of HOXB7 in breast cancer and mechanisms by which it regulates tumorigenic processes. © 2015 The Authors. Published by Wiley Periodicals, Inc. on behalf of UICC.

  20. 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.

  1. Metabolic and target-site mechanisms combine to confer strong DDT resistance in Anopheles gambiae.

    Directory of Open Access Journals (Sweden)

    Sara N Mitchell

    Full Text Available 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.

  2. 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

  3. Glyphosate resistance in Ambrosia trifida: Part 2. Rapid response physiology and non-target-site resistance.

    Science.gov (United States)

    Moretti, Marcelo L; Van Horn, Christopher R; Robertson, Renae; Segobye, Kabelo; Weller, Stephen C; Young, Bryan G; Johnson, William G; Douglas Sammons, R; Wang, Dafu; Ge, Xia; d' Avignon, André; Gaines, Todd A; Westra, Philip; Green, Amanda C; Jeffery, Taylor; Lespérance, Mackenzie A; Tardif, François J; Sikkema, Peter H; Christopher Hall, J; McLean, Michael D; Lawton, Mark B; Schulz, Burkhard

    2017-03-08

    The glyphosate-resistant rapid response (GR RR) resistance mechanism in Ambrosia trifida is not due to target-site resistance (TSR) mechanisms. This study explores the physiology of the rapid response and the possibility of reduced translocation and vacuolar sequestration as non-target-site resistance (NTSR) mechanisms. GR RR leaf discs accumulated hydrogen peroxide within minutes of glyphosate exposure, but only in mature leaf tissue. The rapid response required energy either as light or exogenous sucrose. The combination of phenylalanine and tyrosine inhibited the rapid response in a dose-dependent manner. Reduced glyphosate translocation was observed in GR RR, but only when associated with tissue death caused by the rapid response. Nuclear magnetic resonance studies indicated that glyphosate enters the cytoplasm and reaches chloroplasts, and it is not moved into the vacuole of GR RR, GR non-rapid response or glyphosate-susceptible A. trifida. The GR RR mechanism of resistance is not associated with vacuole sequestration of glyphosate, and the observed reduced translocation is likely a consequence of rapid tissue death. Rapid cell death was inhibited by exogenous application of aromatic amino acids phenylalanine and tyrosine. The mechanism by which these amino acids inhibit rapid cell death in the GR RR phenotype remains unknown, and it could involve glyphosate phytotoxicity or other agents generating reactive oxygen species. Implications of these findings are discussed. The GR RR mechanism is distinct from the currently described glyphosate TSR or NTSR mechanisms in other species. © 2017 Society of Chemical Industry. © 2017 Society of Chemical Industry.

  4. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site.

    Science.gov (United States)

    Kanekiyo, Masaru; Bu, Wei; Joyce, M Gordon; Meng, Geng; Whittle, James R R; Baxa, Ulrich; Yamamoto, Takuya; Narpala, Sandeep; Todd, John-Paul; Rao, Srinivas S; McDermott, Adrian B; Koup, Richard A; Rossmann, Michael G; Mascola, John R; Graham, Barney S; Cohen, Jeffrey I; Nabel, Gary J

    2015-08-27

    Epstein-Barr virus (EBV) represents a major global health problem. Though it is associated with infectious mononucleosis and ∼200,000 cancers annually worldwide, a vaccine is not available. The major target of immunity is EBV glycoprotein 350/220 (gp350) that mediates attachment to B cells through complement receptor 2 (CR2/CD21). Here, we created self-assembling nanoparticles that displayed different domains of gp350 in a symmetric array. By focusing presentation of the CR2-binding domain on nanoparticles, potent neutralizing antibodies were elicited in mice and non-human primates. The structurally designed nanoparticle vaccine increased neutralization 10- to 100-fold compared to soluble gp350 by targeting a functionally conserved site of vulnerability, improving vaccine-induced protection in a mouse model. This rational approach to EBV vaccine design elicited potent neutralizing antibody responses by arrayed presentation of a conserved viral entry domain, a strategy that can be applied to other viruses. Copyright © 2015 Elsevier Inc. All rights reserved.

  5. Prediction of TF target sites based on atomistic models of protein-DNA complexes

    Directory of Open Access Journals (Sweden)

    Collado-Vides Julio

    2008-10-01

    Full Text Available Abstract Background The specific recognition of genomic cis-regulatory elements by transcription factors (TFs plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding specificity in protein-DNA interactions is thus an important goal. Most current approaches for modeling TF specific recognition rely on the knowledge of large sets of cognate target sites and consider only the information contained in their primary sequence. Results Here we describe a structure-based methodology for predicting sequence motifs starting from the coordinates of a TF-DNA complex. Our algorithm combines information regarding the direct and indirect readout of DNA into an atomistic statistical model, which is used to estimate the interaction potential. We first measure the ability of our method to correctly estimate the binding specificities of eight prokaryotic and eukaryotic TFs that belong to different structural superfamilies. Secondly, the method is applied to two homology models, finding that sampling of interface side-chain rotamers remarkably improves the results. Thirdly, the algorithm is compared with a reference structural method based on contact counts, obtaining comparable predictions for the experimental complexes and more accurate sequence motifs for the homology models. Conclusion Our results demonstrate that atomic-detail structural information can be feasibly used to predict TF binding sites. The computational method presented here is universal and might be applied to other systems involving protein-DNA recognition.

  6. 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.

  7. Shear elastic modulus of magnetic gels with random distribution of magnetizable particles

    Science.gov (United States)

    Iskakova, L. Yu; Zubarev, A. Yu

    2017-04-01

    Magnetic gels present new type of composite materials with rich set of uniquie physical properties, which find active applications in many industrial and bio-medical technologies. We present results of mathematically strict theoretical study of elastic modulus of these systems with randomly distributed magnetizable particles in an elastic medium. The results show that an external magnetic field can pronouncedly increase the shear modulus of these composites.

  8. Splice-site A choice targets plasma-membrane Ca2+-ATPase isoform 2 to hair bundles.

    Science.gov (United States)

    Hill, Jennifer K; Williams, Diane E; LeMasurier, Meredith; Dumont, Rachel A; Strehler, Emanuel E; Gillespie, Peter G

    2006-06-07

    Localization of mechanotransduction in sensory hair cells to hair bundles requires selective targeting of essential proteins to specific locations. Isoform 2 of the plasma-membrane Ca2+-ATPase (PMCA2), required for hearing and balance, is found exclusively in hair bundles. We determined the contribution of splicing at the two major splicing sites (A and C) to hair-cell targeting of PMCA2. When PMCA2 isoforms were immunoprecipitated from purified hair bundles of rat utricle, 2w was the only site A variant detected; moreover, immunocytochemistry for 2w in rat vestibular and cochlear tissues indicated that this splice form was located solely in bundles. To demonstrate the necessity of the 2w sequence, we transfected hair cells with PMCA2 containing different variants at splice sites A and C. Although native hair bundles exclusively use the 2a form at splice-site C, epitope-tagged PMCA2w/a and PMCA2w/b were both concentrated in bundles, indicating that site C is not involved in bundle targeting. In contrast, PMCA2z/a was excluded from bundles and was instead targeted to the basolateral plasma membrane. Bundle-specific targeting of PMCA2w/a tagged with green fluorescent protein (GFP) was diminished, suggesting that GFP interfered with splice-site A. Together, these data demonstrate that PMCA2w/a is the hair-bundle isoform of PMCA in rat hair cells and that 2w targets PMCA2 to bundles. The 2w sequence is thus the first targeting signal identified for a hair-bundle membrane protein; moreover, the striking distribution of inner-ear PMCA isoforms dictated by selective targeting suggests a critical functional role for segregated pathways of Ca2+ transport.

  9. Generation mechanism of nonlinear ultrasonic Lamb waves in thin plates with randomly distributed micro-cracks.

    Science.gov (United States)

    Zhao, Youxuan; Li, Feilong; Cao, Peng; Liu, Yaolu; Zhang, Jianyu; Fu, Shaoyun; Zhang, Jun; Hu, Ning

    2017-08-01

    Since the identification of micro-cracks in engineering materials is very valuable in understanding the initial and slight changes in mechanical properties of materials under complex working environments, numerical simulations on the propagation of the low frequency S 0 Lamb wave in thin plates with randomly distributed micro-cracks were performed to study the behavior of nonlinear Lamb waves. The results showed that while the influence of the randomly distributed micro-cracks on the phase velocity of the low frequency S 0 fundamental waves could be neglected, significant ultrasonic nonlinear effects caused by the randomly distributed micro-cracks was discovered, which mainly presented as a second harmonic generation. By using a Monte Carlo simulation method, we found that the acoustic nonlinear parameter increased linearly with the micro-crack density and the size of micro-crack zone, and it was also related to the excitation frequency and friction coefficient of the micro-crack surfaces. In addition, it was found that the nonlinear effect of waves reflected by the micro-cracks was more noticeable than that of the transmitted waves. This study theoretically reveals that the low frequency S 0 mode of Lamb waves can be used as the fundamental waves to quantitatively identify micro-cracks in thin plates. Copyright © 2017 Elsevier B.V. All rights reserved.

  10. Quantum tunneling recombination in a system of randomly distributed trapped electrons and positive ions.

    Science.gov (United States)

    Pagonis, Vasilis; Kulp, Christopher; Chaney, Charity-Grace; Tachiya, M

    2017-09-13

    During the past 10 years, quantum tunneling has been established as one of the dominant mechanisms for recombination in random distributions of electrons and positive ions, and in many dosimetric materials. Specifically quantum tunneling has been shown to be closely associated with two important effects in luminescence materials, namely long term afterglow luminescence and anomalous fading. Two of the common assumptions of quantum tunneling models based on random distributions of electrons and positive ions are: (a) An electron tunnels from a donor to the nearest acceptor, and (b) the concentration of electrons is much lower than that of positive ions at all times during the tunneling process. This paper presents theoretical studies for arbitrary relative concentrations of electrons and positive ions in the solid. Two new differential equations are derived which describe the loss of charge in the solid by tunneling, and they are solved analytically. The analytical solution compares well with the results of Monte Carlo simulations carried out in a random distribution of electrons and positive ions. Possible experimental implications of the model are discussed for tunneling phenomena in long term afterglow signals, and also for anomalous fading studies in feldspars and apatite samples.

  11. The effect of local anatomy on the electric field induced by TMS: evaluation at 14 different target sites.

    Science.gov (United States)

    Janssen, Arno M; Oostendorp, Thom F; Stegeman, Dick F

    2014-10-01

    Many human cortical regions are targeted with transcranial magnetic stimulation (TMS). The stimulus intensity used for a certain region is generally based on the motor threshold stimulation intensity determined over the motor cortex (M1). However, it is well known that differences exist in coil-target distance and target site anatomy between cortical regions. These differences may well make the stimulation intensity derived from M1 sub-optimal for other regions. Our goal was to determine in what way the induced electric fields differ between cortical target regions. We used finite element method modeling to calculate the induced electric field for multiple target sites in a realistic head model. The effects on the electric field due to coil-target distance and target site anatomy have been quantified. The results show that a correction based on the distance alone does not correctly adjust the induced electric field for regions other than M1. In addition, a correction based solely on the TMS-induced electric field (primary field) does not suffice. A precise adjustment should include coil-target distance, the secondary field caused by charge accumulation at conductivity discontinuities and the direction of the field relative to the local cerebrospinal fluid-grey matter boundary.

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

    Science.gov (United States)

    Adams, Marc-Oliver; Fiedler, Konrad

    2016-01-01

    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.

  13. 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.

  14. 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.

  15. Broadband supercontinuum light source seeded by random distributed feedback fiber laser

    Science.gov (United States)

    Ma, R.; Rao, Y. J.; Zhang, W. L.; Wu, H.; Zeng, X.

    2017-04-01

    A novel broadband light source based on supercontinuum (SC) generation seeded by random distributed feedback fiber laser (RFL) is proposed and demonstrated for the first time. A half-opened fiber cavity formed by FBG and TrueWave fiber is used to generate random lasing and SC simultaneously. Experimental results indicate that RFL can be used as an effective pump for generation of SC. SC with 20-dB bandwidth of >250 nm was obtained. Such a broadband SC light source seeded by RFL may pave a way to generate high power broadband RFLs for use in optical sensing and measurement.

  16. Resonant Scattering of Acoustic Phonons by Randomly Distributed Two-Level Systems

    Science.gov (United States)

    Kayanuma, Yosuke; Yamada, Hiroshi; Tanaka, Satoshi

    1985-07-01

    A Green function formalism is developed for the resonant scattering of acoustic phonons by randomly distributed two-level systems. The randomness is treated by the coherent potential approximation. The theory reproduces the Jacobsen-Stevens dispersion law in the dense limit of the concentration of the two-level system and the results obtained so far by the average t-matrix approximation in the dilute limit. The gradual change of the character of the resonantly scattered phonons as the concentration is varied is investigated through the calculation of various quantities such as the phonon density of states, the neutron scattering cross sections and the sound velocity.

  17. Electromagnetic wave propagation in a random distribution of C{sub 60} molecules

    Energy Technology Data Exchange (ETDEWEB)

    Moradi, Afshin, E-mail: a.moradi@kut.ac.ir [Department of Engineering Physics, Kermanshah University of Technology, Kermanshah, Iran and Department of Nano Sciences, Institute for Studies in Theoretical Physics and Mathematics (IPM), Tehran (Iran, Islamic Republic of)

    2014-10-15

    Propagation of electromagnetic waves in a random distribution of C{sub 60} molecules are investigated, within the framework of the classical electrodynamics. Electronic excitations over the each C{sub 60} molecule surface are modeled by a spherical layer of electron gas represented by two interacting fluids, which takes into account the different nature of the π and σ electrons. It is found that the present medium supports four modes of electromagnetic waves, where they can be divided into two groups: one group with shorter wavelength than the light waves of the same frequency and the other with longer wavelength than the free-space radiation.

  18. The Geology of the Hellas Basin Region: Possible Mars Express HRSC Target Sites

    Science.gov (United States)

    Kostama, V.-P.; Aittola, M.; Raitala, J.; Öhman, T.

    2001-11-01

    This study was done from the two quadrangles of the Hellas impact basin, the MC-27 (Noachis) and MC-28 (Hellas). The Hellas region is very versatile area and offers good possibilities to research several geological structures and events as well as interactions between them: Hellas impact basin and its central parts and boundaries, highland patera formations, and several large outflow channels. The comparison of all highland paterae around the Hellas basin and studying their relations with the outflow channels may provide evidence of volcanic activity-permafrost interaction as well as information on the old post-impact volcanism and catastrophic outflow processes. Eolian activity is also very interesting within the region, based on the fact that Hellas is thought to represent a major source region for regional dust storms on Mars. The region provides possible evidence for glacial activity on Mars. It has been proposed that the interior of the Hellas basin held ice-covered lakes early in Mars history. There are morphologic, stratigraphic, and topographic evidence implying that first water-laid, then later ice-rich, sediments dominated the geology of the Hellas interior. On Mars, there are also a variety of features that have been attributed to the presence of local ground ice and permafrost. These features include lobate debris aprons and rampart craters, which are abundant in the Hellas region. We also have several larger craters with interaction by post-impact fluvial activity. This may be indication for lacustrine deposits of some craters with smooth basin floors. Several proposed target sites include also parts of the Hellespontus Montes, which is supposed to represent the oldest material in the region, and the system of grabens, which is more or less parallel to Hellas rim. This system occurs at radial distances between 1900-2500 km to west and and north-west from the basin center.

  19. Global distribution and origin of target site insecticide resistance mutations in Tetranychus urticae.

    Science.gov (United States)

    Ilias, A; Vontas, J; Tsagkarakou, A

    2014-05-01

    The control of Tetranychus urticae, a worldwide agricultural pest, is largely dependent on pesticides. However, their efficacy is often compromised by the development of resistance. Recent molecular studies identified a number of target site resistance mutations, such as G119S, A201S, T280A, G328A, F331W in the acetylcholinesterase gene, L1024V, A1215D, F1538I in the voltage-gated sodium channel gene, G314D and G326E in glutamate-gated chloride channel genes, G126S, I136T, S141F, D161G, P262T in the cytochrome b and the I1017F in the chitin synthase 1 gene. We examined their distribution, by sequencing the relevant gene fragments in a large number of T. urticae collections from a wide geographic range. Our study revealed that most of the resistance mutations are spread worldwide, with remarkably variable frequencies. Furthermore, we analyzed the variability of the ace locus, which has been subjected to longer periods of selection pressure historically, to investigate the evolutionary origin of ace resistant alleles and determine whether they resulted from single or multiple mutation events. By sequencing a 1540 bp ace fragment, encompassing the resistance mutations and downstream introns in 139 T. urticae individuals from 27 countries, we identified 6 susceptible and 31 resistant alleles which have arisen from at least three independent mutation events. The frequency and distribution of these ace haplotypes varied geographically, suggesting an interplay between different mutational events, gene flow and local selection. Copyright © 2014 Elsevier Ltd. All rights reserved.

  20. Transportation risk assessment for the shipment of irradiated FFTF tritium target assemblies from the Hanford Site to the Savannah River Site

    Energy Technology Data Exchange (ETDEWEB)

    Nielsen, D. L.

    1997-11-19

    A Draft Technical Information Document (HNF-1855) is being prepared to evaluate proposed interim tritium and medical isotope production at the Fast Flux Test Facility (FFTF). This report examines the potential health and safety impacts associated with transportation of irradiated tritium targets from FFTF to the Savannah River Site for processing at the Tritium Extraction Facility. Potential risks to workers and members of the public during normal transportation and accident conditions are assessed.

  1. Detecting the presence of target-site resistance to neonicotinoids and pyrethroids in Italian populations of Myzus persicae.

    Science.gov (United States)

    Panini, Michela; Dradi, Davide; Marani, Gabriele; Butturini, Alda; Mazzoni, Emanuele

    2014-06-01

    Myzus persicae is a key pest of peach, which in commercial orchards is mainly controlled by chemical treatments. Neonicotinoids represent the main control strategy, but resistance monitoring programmes in Southern Europe have shown the widespread presence of populations highly resistant to this insecticide class in peach orchards. Moreover, in Italy reports of neonicotinoid application failures are increasing. This work describes the status of the main target-site mutations associated with neonicotinoid and pyrethroid resistance in Italian populations collected in 2012. R81T mutation linked with neonicotinoid resistance was found in 65% of analysed aphids (35.5% with a homozygous resistant genotype). For the first time, R81T was found in samples collected from herbaceous hosts. Bioassays on a few genotyped populations also revealed the involvement of P450-based metabolic resistance. Only a few individuals without kdr (L1014F) and s-kdr (M918T) target-site mutations were collected. A new single nucleotide polymorphism in the s-kdr locus producing M918L substitution was found. Target-site resistance to neonicotinoids is common in specialised peach-growing areas, and it is spreading in other Italian regions and on herbaceous hosts. The high frequency of target-site mutations and data obtained from bioassays confirm the presence of multiple resistance mechanisms and suggest the importance of coordinated control strategies. © 2013 Society of Chemical Industry.

  2. Targeting of angiogenic endothelial cells at sites of inflammation by dexamethasone phosphate-containing RGD peptide liposomes inhibits experimental arthritis

    NARCIS (Netherlands)

    Koning, Gerben A.; Wauben, MHM; Kok, Robert J.; Mastrobattista, E; Molema, Grietje; ten Hagen, TLM; Storm, G

    Objective. To investigate whether RGD peptide-exposing long circulating polyethylene glycol (PEG) liposomes (RGD-PEG-L) targeted to alpha v beta 3 integrins expressed on angiogenic vascular endothelial cells (VECs) are able to bind VECs at sites of inflammation and whether such liposomes containing

  3. 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.

  4. TISs-ST: a web server to evaluate polymorphic translation initiation sites and their reflections on the secretory targets

    Directory of Open Access Journals (Sweden)

    Menossi Marcelo

    2007-05-01

    Full Text Available Abstract Background The nucleotide sequence flanking the translation initiation codon (start codon context affects the translational efficiency of eukaryotic mRNAs, and may indicate the presence of an alternative translation initiation site (TIS to produce proteins with different properties. Multi-targeting may reflect the translational variability of these other protein forms. In this paper we present a web server that performs computations to investigate the usage of alternative translation initiation sites for the synthesis of new protein variants that might have different functions. Results An efficient web-based tool entitled TISs-ST (Translation Initiation Sites and Secretory Targets evaluates putative translation initiation sites and indicates the prediction of a signal peptide of the protein encoded from this site. The TISs-ST web server is freely available to both academic and commercial users and can be accessed at http://ipe.cbmeg.unicamp.br/pub/TISs-ST. Conclusion The program can be used to evaluate alternative translation initiation site consensus with user-specified sequences, based on their composition or on many position weight matrix models. TISs-ST provides analytical and visualization tools for evaluating the periodic frequency, the consensus pattern and the total information content of a sequence data set. A search option allows for the identification of signal peptides from predicted proteins using the PrediSi software.

  5. Accurate microRNA target prediction using detailed binding site accessibility and machine learning on proteomics data

    Directory of Open Access Journals (Sweden)

    Martin eReczko

    2012-01-01

    Full Text Available MicroRNAs (miRNAs are a class of small regulatory genes regulating gene expression by targetingmessenger RNA. Though computational methods for miRNA target prediction are the prevailingmeans to analyze their function, they still miss a large fraction of the targeted genes and additionallypredict a large number of false positives. Here we introduce a novel algorithm called DIANAmicroT-ANN which combines multiple novel target site features through an artificial neural network(ANN and is trained using recently published high-throughput data measuring the change of proteinlevels after miRNA overexpression, providing positive and negative targeting examples. The featurescharacterizing each miRNA recognition element include binding structure, conservation level and aspecific profile of structural accessibility. The ANN is trained to integrate the features of eachrecognition element along the 3’ untranslated region into a targeting score, reproducing the relativerepression fold change of the protein. Tested on two different sets the algorithm outperforms otherwidely used algorithms and also predicts a significant number of unique and reliable targets notpredicted by the other methods. For 542 human miRNAs DIANA-microT-ANN predicts 120,000targets not provided by TargetScan 5.0. The algorithm is freely available athttp://microrna.gr/microT-ANN.

  6. 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...

  7. Non-target-site glyphosate resistance in Conyza bonariensis is based on modified subcellular distribution of the herbicide.

    Science.gov (United States)

    Kleinman, Ziv; Rubin, Baruch

    2017-01-01

    Conyza spp. were the first broadleaf weeds reported to have evolved glyphosate resistance. Several mechanisms have been proposed for glyphosate resistance. In an effort to elucidate the mechanism of this resistance in Conyza bonariensis, possible target-site and non-target-site mechanisms were investigated in glyphosate-resistant (GR) C. bonariensis biotypes. Using differential glyphosate applications and analyses of shikimate accumulation, we followed the herbicide effect in different plant organs and monitored the herbicide's apparent mobility. We found high shikimate levels in the roots and young leaves of glyphosate-sensitive (GS) plants, regardless of the site of application, whereas in GR plants, shikimate accumulated mainly in treated young leaves. (14) C-glyphosate studies, however, revealed the expected source-to-sink translocation pattern in both GS and GR plants. Sequencing of the appropriate EPSPS DNA fragments of GR and GS plants revealed no alteration at the Pro106 position. These data support the hypothesis that the glyphosate resistance of our C. bonariensis GR biotypes is associated with altered subcellular distribution of glyphosate, which keeps the herbicide sequestered away from the EPSPS target site in the chloroplast. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

  8. 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

    2017-03-16

    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.

  9. 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.

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

    DEFF Research Database (Denmark)

    Butchart, Stuart H. M.; Scharlemann, Jörn P.W.; Evans, Mike I.

    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......, 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...

  11. 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.

  12. The compaction of a random distribution of metal cylinders by the discrete element method

    DEFF Research Database (Denmark)

    Redanz, Pia; Fleck, N. A.

    2001-01-01

    The cold compaction of a 2D random distribution of metal circular cylinders has been investigated numerically by the discrete element method. Each cylindrical particle is located by a node at its centre and the plastic indentation of the contacts between neighbouring particles is represented by non...... takes place. leading to yield surfaces of similar shape but about half the size of that found for affine motion, as reported in [J. Mech. Phys. Solids 40 (1992) 1139 43 (1995) 1409; 47 (1999) 785]. An increase in the level of inter-particle friction leads to a reduction in the degree of local particle...... rearrangement: the relative displacement of particle centres in the network is more closely represented by affine motion for the case of sticking contacts than frictionless contacts. The discrete element calculations suggest that the yield surfaces for sticking contacts are similar in shape to those...

  13. Targeting Alpha5 Beta1 Integrin to Prevent Metastatic Breast Cancer Cell Invasion: PhScN Target Site Definition and Plasma Stability

    Science.gov (United States)

    2015-11-01

    termini, and/or cysteine side chain to determine the initial spatial constraints of the binding pocket of the ligand to its target site. This will...invasion, extravasation, and lung colony formation. Clin Exp Metastasis, 2010. 27(3): p. 173-84. PMID: 20339907 14. Woods Ignatoski, K.M., N.K. Grewal, S...Neoplasia, 2003. 5(2): p. 128-34. PMID: 12659685 20 15. Woods Ignatoski, K.M., D.L. Livant, S. Markwart, N.K. Grewal, and S.P. Ethier, The role of

  14. 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.

  15. 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.

  16. Differential recruitment of nuclear receptor coactivators may determine alternative RNA splice site choice in target genes

    Science.gov (United States)

    Auboeuf, Didier; Dowhan, Dennis H.; Kang, Yun Kyoung; Larkin, Kimberly; Lee, Jae Woon; Berget, Susan M.; O'Malley, Bert W.

    2004-01-01

    The biological consequences of steroid hormone-mediated transcriptional activation of target genes might be difficult to predict because alternative splicing of a single neosynthesized precursor RNA can result in production of different protein isoforms with opposite biological activities. Therefore, an important question to address is the manner in which steroid hormones affect the splicing of their target gene transcripts. In this report, we demonstrate that individual steroid hormones had different and opposite effects on alternative splicing decisions, stimulating the production of different spliced variants produced from genes driven by steroid hormone-dependent promoters. Steroid hormone transcriptional effects are mediated by steroid hormone receptor coregulators that also modify alternative splicing decisions. Our data suggest that activated steroid hormone receptors recruit coregulators to the target promoter that participate in both the production and the splicing of the target gene transcripts. Because different coregulators activating transcription can have opposite effects on alternative splicing decisions, we conclude that the precise nature of the transcriptional coregulators recruited by activated steroid receptors, depending on the promoter and cellular contexts, may play a major role in regulating the nature of the spliced variants produced from certain target genes in response to steroid hormones. PMID:14982999

  17. 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.

  18. Time- and Cost-Efficient Identification of T-DNA Insertion Sites through Targeted Genomic Sequencing

    Science.gov (United States)

    Lepage, Étienne; Zampini, Éric; Boyle, Brian; Brisson, Normand

    2013-01-01

    Forward genetic screens enable the unbiased identification of genes involved in biological processes. In Arabidopsis, several mutant collections are publicly available, which greatly facilitates such practice. Most of these collections were generated by agrotransformation of a T-DNA at random sites in the plant genome. However, precise mapping of T-DNA insertion sites in mutants isolated from such screens is a laborious and time-consuming task. Here we report a simple, low-cost and time efficient approach to precisely map T-DNA insertions simultaneously in many different mutants. By combining sequence capture, next-generation sequencing and 2D-PCR pooling, we developed a new method that allowed the rapid localization of T-DNA insertion sites in 55 out of 64 mutant plants isolated in a screen for gyrase inhibition hypersensitivity. PMID:23951038

  19. GHB receptor targets in the CNS: Focus on high-affinity binding sites

    DEFF Research Database (Denmark)

    Bay, Tina; Eghorn, Laura Friis; Klein, Anders Bue

    2014-01-01

    γ-Hydroxybutyric acid (GHB) is an endogenous compound in the mammalian brain with both low- and high-affinity receptor targets. GHB is used clinically in the treatment of symptoms of narcolepsy and alcoholism, but also illicitly abused as the recreational drug Fantasy. Major pharmacological effects...... effects. In this research update, a description of the various reported receptors for GHB is provided, including GABAB receptors, certain GABAA receptor subtypes and other reported GHB receptors. The main focus will thus be on the high-affinity binding targets for GHB and their potential functional roles...

  20. Rational Design of an Epstein-Barr Virus Vaccine Targeting the Receptor-Binding Site

    National Research Council Canada - National Science Library

    Kanekiyo, Masaru; Bu, Wei; Joyce, M. Gordon; Meng, Geng; Whittle, James R.R; Baxa, Ulrich; Yamamoto, Takuya; Narpala, Sandeep; Todd, John-Paul; Rao, Srinivas S; McDermott, Adrian B; Koup, Richard A; Rossmann, Michael G; Mascola, John R; Graham, Barney S; Cohen, Jeffrey I; Nabel, Gary J

    2015-01-01

    ... a vaccine have focused on the viral major envelope glycoprotein 350/220 (gp350), because it represents a principal target of neutralizing antibodies in naturally infected individuals ( Hoffman et al., 1980; Thorley-Lawson and Geilinger, 1980; Thorley-Lawson and Poodry, 1982 ). Prototype gp350-based vaccines have induced protective immunity a...

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

    DEFF Research Database (Denmark)

    Dugal, Cherie; van Beest, Floris; Vander Wal, Eric

    2013-01-01

    , 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...

  2. Identification of thyroid hormone receptor binding sites and target genes using ChIP-on-chip in developing mouse cerebellum.

    Directory of Open Access Journals (Sweden)

    Hongyan Dong

    Full Text Available Thyroid hormone (TH is critical to normal brain development, but the mechanisms operating in this process are poorly understood. We used chromatin immunoprecipitation to enrich regions of DNA bound to thyroid receptor beta (TRbeta of mouse cerebellum sampled on post natal day 15. Enriched target was hybridized to promoter microarrays (ChIP-on-chip spanning -8 kb to +2 kb of the transcription start site (TSS of 5000 genes. We identified 91 genes with TR binding sites. Roughly half of the sites were located in introns, while 30% were located within 1 kb upstream (5' of the TSS. Of these genes, 83 with known function included genes involved in apoptosis, neurodevelopment, metabolism and signal transduction. Two genes, MBP and CD44, are known to contain TREs, providing validation of the system. This is the first report of TR binding for 81 of these genes. ChIP-on-chip results were confirmed for 10 of the 13 binding fragments using ChIP-PCR. The expression of 4 novel TH target genes was found to be correlated with TH levels in hyper/hypothyroid animals providing further support for TR binding. A TRbeta binding site upstream of the coding region of myelin associated glycoprotein was demonstrated to be TH-responsive using a luciferase expression system. Motif searches did not identify any classic binding elements, indicating that not all TR binding sites conform to variations of the classic form. These findings provide mechanistic insight into impaired neurodevelopment resulting from TH deficiency and a rich bioinformatics resource for developing a better understanding of TR binding.

  3. Site-targeted mutagenesis for stabilization of recombinant monoclonal antibody expressed in tobacco (Nicotiana tabacum) plants.

    OpenAIRE

    Hehle, VK; Paul, MJ; Roberts, VA; van Dolleweerd, CJ; Ma, JK

    2015-01-01

    This study examined the degradation pattern of a murine IgG1? monoclonal antibody expressed in and extracted from transformed Nicotiana tabacum. Gel electrophoresis of leaf extracts revealed a consistent pattern of recombinant immunoglobulin bands, including intact and full-length antibody, as well as smaller antibody fragments. N-terminal sequencing revealed these smaller fragments to be proteolytic cleavage products and identified a limited number of protease-sensitive sites in the antibody...

  4. LIM domains target actin regulators paxillin and zyxin to sites of stress fiber strain.

    Directory of Open Access Journals (Sweden)

    Mark A Smith

    Full Text Available Contractile actomyosin stress fibers are critical for maintaining the force balance between the interior of the cell and its environment. Consequently, the actin cytoskeleton undergoes dynamic mechanical loading. This results in spontaneous, stochastic, highly localized strain events, characterized by thinning and elongation within a discrete region of stress fiber. Previous work showed the LIM-domain adaptor protein, zyxin, is essential for repair and stabilization of these sites. Using live imaging, we show paxillin, another LIM-domain adaptor protein, is also recruited to stress fiber strain sites. Paxillin recruitment to stress fiber strain sites precedes zyxin recruitment. Zyxin and paxillin are each recruited independently of the other. In cells lacking paxillin, actin recovery is abrogated, resulting in slowed actin recovery and increased incidence of catastrophic stress fiber breaks. For both paxillin and zyxin, the LIM domains are necessary and sufficient for recruitment. This work provides further evidence of the critical role of LIM-domain proteins in responding to mechanical stress in the actin cytoskeleton.

  5. Analysis of a polymorphic microRNA target site in the purinergic receptor P2RX7 gene.

    Science.gov (United States)

    Rahman, Omar Abdul; Sasvari-Szekely, Maria; Szekely, Anna; Faludi, Gabor; Guttman, Andras; Nemoda, Zsofia

    2010-06-01

    The recent discovery of post-transcriptional regulation by microRNAs (miRNAs) drew our attention to SNPs of putative miRNA target sites in candidate genes of depression-related psychiatric disorders. The P2RX7 (purinergic receptor P2X, ligand-gated ion channel, 7) gene has been suggested as a candidate for major depressive and bipolar disorder, because of repeated associations with the rs2230912 (Gln460Arg) polymorphism. As this polymorphism is located at the end of the coding region, we considered a possible linkage with SNP(s) in putative miRNA target sites of the 3' untranslated region. Based on our in silico search, the rs1653625 fulfilled this criterion. This SNP, however, is surrounded with polycytosine and polyadenine tracts, which hindered its analysis until now. In this study, we describe a readily applicable genotyping method for rs1653625 by applying a primer that introduces mismatched nucleotides to create a restriction enzyme cleavage site. The resulting allele-specific products with 19 base pair difference were separated by both traditional horizontal agarose gel electrophoresis and multicapillary gel electrophoresis. The developed genotyping method was applied in our depression-related association study.

  6. 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.

  7. Parameters controlling the gene-targeting frequency at the Sphingomonas species rrn site and expression of the methyl parathion hydrolase gene.

    Science.gov (United States)

    Jiang, J; Zhang, R; Cui, Z; He, J; Gu, L; Li, S

    2007-06-01

    To investigate the key parameters controlling the exogenous methyl parathion hydrolase (MPH) gene mpd-targeting frequency at the ribosomal RNA operon (rrn) site of Sphingomonas species which has a wide range of biotechnological applications. Targeting vectors with different homology lengths and recipient target DNA with different homology identities were used to investigate the parameters controlling the targeting frequency at the Sphingomonas species rrn site. Targeting frequency decreased with the reduction of homology length, and the minimal size for normal homologous recombination was >100 bp. Homologous recombination could succeed even if there were 3-4% mismatches; however, targeting frequency decreased with increasing sequence divergence. The Red recombination system could increase the targeting frequency to some extent. Targeting of the mpd gene to the rrn site did not affect cell viability and resulted in an increase of MPH-specific activity in recombinants. Targeting frequency was affected by homology length, identity and the Red recombination system. The rrn site is a good target site for the expression of exogenous genes. This work is useful as a foundation for a better understanding of recombination events involving homologous sequences and for the improved manipulation of Sphingomonas genes in biotechnological applications.

  8. Diffusion of dilute gas in arrays of randomly distributed, vertically aligned, high-aspect-ratio cylinders.

    Science.gov (United States)

    Szmyt, Wojciech; Guerra, Carlos; Utke, Ivo

    2017-01-01

    In this work we modelled the diffusive transport of a dilute gas along arrays of randomly distributed, vertically aligned nanocylinders (nanotubes or nanowires) as opposed to gas diffusion in long pores, which is described by the well-known Knudsen theory. Analytical expressions for (i) the gas diffusion coefficient inside such arrays, (ii) the time between collisions of molecules with the nanocylinder walls (mean time of flight), (iii) the surface impingement rate, and (iv) the Knudsen number of such a system were rigidly derived based on a random-walk model of a molecule that undergoes memoryless, diffusive reflections from nanocylinder walls assuming the molecular regime of gas transport. It can be specifically shown that the gas diffusion coefficient inside such arrays is inversely proportional to the areal density of cylinders and their mean diameter. An example calculation of a diffusion coefficient is delivered for a system of titanium isopropoxide molecules diffusing between vertically aligned carbon nanotubes. Our findings are important for the correct modelling and optimisation of gas-based deposition techniques, such as atomic layer deposition or chemical vapour deposition, frequently used for surface functionalisation of high-aspect-ratio nanocylinder arrays in solar cells and energy storage applications. Furthermore, gas sensing devices with high-aspect-ratio nanocylinder arrays and the growth of vertically aligned carbon nanotubes need the fundamental understanding and precise modelling of gas transport to optimise such processes.

  9. Internal wave generation by tidal flow over periodically and randomly distributed seamounts

    Science.gov (United States)

    Zhang, Likun; Buijsman, Maarten C.; Comino, Eva; Swinney, Harry L.

    2017-06-01

    We examine numerically the conversion of barotropic tidal energy into internal waves by flow over an isolated seamount and over systems of periodically and randomly distributed 1100 m tall seamounts with Gaussian profiles. The simulations use the Massachusetts Institute of Technology general circulation model (MITgcm) to calculate for an infinitely deep ocean the dependence of the energy conversion on seamount slope, seamount separation, tidal direction, and the size and aspect ratio of the simulation domain. For neighboring seamounts with a slope greater than the internal wave beam slope, wave interference reduces the conversion relative to that calculated for an isolated seamount, and relative to that predicted by linear theory for a seamount of slope less than the beam slope. The conversion by an individual seamount in a system of random seamounts separated by an average distance of 18 km is found to be suppressed by 16% relative to the conversion by an isolated seamount. This study provides insight into tidal conversion by ocean seamounts modeled as Gaussian mountains with slopes both smaller and larger than the beam slope. We conclude that the total energy conversion by all seamounts (peak height ≥1000 m) and knolls (peak height 500-1000 m), taking into account interference affects, is of the order of 1% of the total barotropic to baroclinic energy conversion in the oceans, which is about twice as large as previous estimates.

  10. Common-cavity ytterbium/Raman random distributed feedback fiber laser

    Science.gov (United States)

    Wu, Han; Wang, Zinan; He, Qiheng; Sun, Wei; Rao, Yunjiang

    2017-06-01

    In this letter, a common-cavity random distributed feedback fiber laser which can generate both 1064 nm ytterbium-doped random lasing and 1115 nm ytterbium-Raman random lasing is proposed and experimentally demonstrated for the first time. The common cavity is based on the combination of the double-cladding ytterbium-doped fiber and the standard single mode fiber (SMF); a 1064 nm high-reflectivity fiber Bragg grating and the fiber flat-end are connected to the signal port of the pump combiner as the point reflectors. The generated 1064 nm random lasing can serve as the Raman pump in the SMF, thus 1115 nm random lasing could be stimulated with the hybrid ytterbium-Raman gain. The feedback for 1115 nm random lasing is the combination of flat-end fiber and random Rayleigh feedback. By controlling the value of flat-end fiber’s reflectivity to 0.002, stable 1.91 W of 1064 nm ytterbium-doped random lasing and 3.72 W of 1115 nm ytterbium-Raman random lasing are generated successively. This work could provide a simple and cost-effective way to generate high-power random lasing.

  11. Deviations from the Gutenberg–Richter law on account of a random distribution of block sizes

    Energy Technology Data Exchange (ETDEWEB)

    Sibiryakov, B. P., E-mail: sibiryakovbp@ipgg.sbras.ru [Trofimuk Institute of Oil and Gas Geology and Geophysics SB RAS, Novosibirsk, 630090 (Russian Federation); Novosibirsk State University, Novosibirsk, 630090 (Russian Federation)

    2015-10-27

    This paper studies properties of a continuum with structure. The characteristic size of the structure governs the fact that difference relations are nonautomatically transformed into differential ones. It is impossible to consider an infinitesimal volume of a body, to which the major conservation laws could be applied, because the minimum representative volume of the body must contain at least a few elementary microstructures. The corresponding equations of motion are equations of infinite order, solutions of which include, along with usual sound waves, unusual waves with abnormally low velocities without a lower limit. It is shown that in such media weak perturbations can increase or decrease outside the limits. The number of complex roots of the corresponding dispersion equation, which can be interpreted as the number of unstable solutions, depends on the specific surface of cracks and is an almost linear dependence on a logarithmic scale, as in the seismological Gutenberg–Richter law. If the distance between one pore (crack) to another one is a random value with some distribution, we must write another dispersion equation and examine different scenarios depending on the statistical characteristics of the random distribution. In this case, there are sufficient deviations from the Gutenberg–Richter law and this theoretical result corresponds to some field and laboratory observations.

  12. Diffusion of dilute gas in arrays of randomly distributed, vertically aligned, high-aspect-ratio cylinders

    Directory of Open Access Journals (Sweden)

    Wojciech Szmyt

    2017-01-01

    Full Text Available In this work we modelled the diffusive transport of a dilute gas along arrays of randomly distributed, vertically aligned nanocylinders (nanotubes or nanowires as opposed to gas diffusion in long pores, which is described by the well-known Knudsen theory. Analytical expressions for (i the gas diffusion coefficient inside such arrays, (ii the time between collisions of molecules with the nanocylinder walls (mean time of flight, (iii the surface impingement rate, and (iv the Knudsen number of such a system were rigidly derived based on a random-walk model of a molecule that undergoes memoryless, diffusive reflections from nanocylinder walls assuming the molecular regime of gas transport. It can be specifically shown that the gas diffusion coefficient inside such arrays is inversely proportional to the areal density of cylinders and their mean diameter. An example calculation of a diffusion coefficient is delivered for a system of titanium isopropoxide molecules diffusing between vertically aligned carbon nanotubes. Our findings are important for the correct modelling and optimisation of gas-based deposition techniques, such as atomic layer deposition or chemical vapour deposition, frequently used for surface functionalisation of high-aspect-ratio nanocylinder arrays in solar cells and energy storage applications. Furthermore, gas sensing devices with high-aspect-ratio nanocylinder arrays and the growth of vertically aligned carbon nanotubes need the fundamental understanding and precise modelling of gas transport to optimise such processes.

  13. Numerical simulation of fibrous biomaterials with randomly distributed fiber network structure.

    Science.gov (United States)

    Jin, Tao; Stanciulescu, Ilinca

    2016-08-01

    This paper presents a computational framework to simulate the mechanical behavior of fibrous biomaterials with randomly distributed fiber networks. A random walk algorithm is implemented to generate the synthetic fiber network in 2D used in simulations. The embedded fiber approach is then adopted to model the fibers as embedded truss elements in the ground matrix, which is essentially equivalent to the affine fiber kinematics. The fiber-matrix interaction is partially considered in the sense that the two material components deform together, but no relative movement is considered. A variational approach is carried out to derive the element residual and stiffness matrices for finite element method (FEM), in which material and geometric nonlinearities are both included. Using a data structure proposed to record the network geometric information, the fiber network is directly incorporated into the FEM simulation without significantly increasing the computational cost. A mesh sensitivity analysis is conducted to show the influence of mesh size on various simulation results. The proposed method can be easily combined with Monte Carlo (MC) simulations to include the influence of the stochastic nature of the network and capture the material behavior in an average sense. The computational framework proposed in this work goes midway between homogenizing the fiber network into the surrounding matrix and accounting for the fully coupled fiber-matrix interaction at the segment length scale, and can be used to study the connection between the microscopic structure and the macro-mechanical behavior of fibrous biomaterials with a reasonable computational cost.

  14. 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.

  15. Site Targeted Press Coated Delivery of Methylprednisolone Using Eudragit RS 100 and Chitosan for Treatment of Colitis.

    Science.gov (United States)

    Jagdale, Swati; Chandekar, Apoorva

    2016-01-01

    Inflammatory bowel disease (IBD) is one of the five most prevalent gastrointestinal disease burdens which commonly require lifetime care. Worldwide incidence rate of ulcerative colitis and Crohn's disease is about 16.8% and 13.4% respectively. Colitis is an inflammation of the colon. Colon targeted drug delivery will direct the drug to the colon. The drug will reach at the site of action and hence its side effects as well as dose can be reduced. Recent patent describes treatment of ulcerative colitis using anti CD3 antibodies, with nicotine and anti-depressant drugs, budesonide foam etc. Present study deals with optimization of site targeted methylprednisolone delivery for treatment of colitis. Chitosan and Eudragit RS 100 were used as coating polymers. Tablets were prepared by press coated technology. The core tablets contain drug, avicel as binder, croscarmellose sodium as super disintegrant and dicalcium phosphate as diluent. Drug excipient compatibility was carried out using FTIR, UV and DSC. Design of experiment was used to optimize the formulation. Tablets were evaluated for thickness, weight variation, hardness, swelling index, in-vitro drug release and release of drug in simulated media. Optimized batch (B2) contained chitosan 40% and eudragit RS 100 17.5%. B2 showed in-vitro drug release 85.65 ± 7.6% in 6.8 pH phosphate buffer and 96.7 ±9.1% in simulated media after 7.5 hours. In-vivo x-ray placebo study for formulation B2 had shown that the tablet reached to the ascending colon after 5 hours. This indicated a potential site targeted delivery of optimized batch B2.

  16. 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.

  17. Risk analysis applied to a contaminant industrial site. Determination of risk based remedial targets

    Energy Technology Data Exchange (ETDEWEB)

    Carlon, C.; Norbiato, M.; Critto, A.; Marcomini, A. [Venice Univ., Venice (Italy). Dept. of Environmental Sciences

    2000-06-01

    In this work a dismissed industrial site has been the object of a risk analysis (RA) in order to define site-specific remediation objectives. A screening risk analysis is proposed, by employing conservative and default area. A second level analysis, characterised by site specific input data, is proposed as well. The RA involves modeling the heavy metal transport in soil, which is very sensitive to the metal soil-water distribution coefficient (K{sub d}). For the first tier analysis, K{sub d} has been evaluated on the basis of published results of studies on the relationship between K{sub d}, soil pH and total metal concentration, while for the second tier analysis the K{sub d} value has been experimentally determined by two leaching tests. At the end, a comparison has been performed between the second tier RA results (SSTL) and the first tier results (RBSL) and the generic threshold concentration established by the Italian national and regional authorities for the soil remediation. [Italian] Nel presente lavoro e' stato sottoposto ad analisi di rischio un sito industriale dismesso per la definizione di obiettivi di bonifica sito-specifici: e' stata svolta un'analisi di rischio di screening, con l'impiego di dati conservativi e di default, ed un'analisi di secondo livello, caratterizzata dall'uso di input sito-specifici. L'analisi di rischio comporta l'impiego di modelli di trasporto dei metalli pesanti nel suolo che sono molto sensibili al coefficiente di distribuzione suolo-acqua dei metalli (K{sub d}). Per l'analisi di primo livello il K{sub d} e'stato stimato sulla base di risultati pubblicati di studi sulle relazioni tra K{sub d}, pH e contenuto totale di metalli nel suolo, mentre per l'analisi di secondo livello il K{sub d} e' stato determinato sperimentalmente con due tests di leaching. Alla fine e' stato fatto un confronto tra i risultati dell'analisi di rischio di secondo livello, i

  18. Site selection and directional models of deserts used for ERBE validation targets

    Science.gov (United States)

    Staylor, W. F.

    1986-01-01

    Broadband shortwave and longwave radiance measurements obtained from the Nimbus 7 Earth Radiation Budget scanner were used to develop reflectance and emittance models for the Sahara, Gibson, and Saudi Deserts. These deserts will serve as in-flight validation targets for the Earth Radiation Budget Experiment being flown on the Earth Radiation Budget Satellite and two National Oceanic and Atmospheric Administration polar satellites. The directional reflectance model derived for the deserts was a function of the sum and product of the cosines of the solar and viewing zenith angles, and thus reciprocity existed between these zenith angles. The emittance model was related by a power law of the cosine of the viewing zenith angle.

  19. Targeting proteins to RNA transcription and processing sites within the nucleus.

    Science.gov (United States)

    Sánchez-Hernández, Noemí; Prieto-Sánchez, Silvia; Moreno-Castro, Cristina; Muñoz-Cobo, Juan Pablo; El Yousfi, Younes; Boyero-Corral, Sofía; Suñé-Pou, Marc; Hernández-Munain, Cristina; Suñé, Carlos

    2017-10-01

    Studies of the spatial organization of the highly compartmentalized eukaryotic nucleus and dynamics of transcription and RNA processing within it are fundamental for fully understanding how gene expression is regulated in the cell. Although some progress has been made in deciphering the functional consequences of this complex network of interacting molecules in the context of nuclear organization, how proteins and RNA move in the nucleus and how the transcription and RNA processing machineries find their targets are important questions that remain largely unexplored. Here, we review major hallmarks and novel insights regarding the movement of RNA and proteins in the context of nuclear organization as well as the mechanisms by which the proteins involved in RNA processing localize to specific nuclear compartments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  20. Association of impulsivity and polymorphic microRNA-641 target sites in the SNAP-25 gene.

    Directory of Open Access Journals (Sweden)

    Nóra Németh

    Full Text Available Impulsivity is a personality trait of high impact and is connected with several types of maladaptive behavior and psychiatric diseases, such as attention deficit hyperactivity disorder, alcohol and drug abuse, as well as pathological gambling and mood disorders. Polymorphic variants of the SNAP-25 gene emerged as putative genetic components of impulsivity, as SNAP-25 protein plays an important role in the central nervous system, and its SNPs are associated with several psychiatric disorders. In this study we aimed to investigate if polymorphisms in the regulatory regions of the SNAP-25 gene are in association with normal variability of impulsivity. Genotypes and haplotypes of two polymorphisms in the promoter (rs6077690 and rs6039769 and two SNPs in the 3' UTR (rs3746544 and rs1051312 of the SNAP-25 gene were determined in a healthy Hungarian population (N = 901 using PCR-RFLP or real-time PCR in combination with sequence specific probes. Significant association was found between the T-T 3' UTR haplotype and impulsivity, whereas no association could be detected with genotypes or haplotypes of the promoter loci. According to sequence alignment, the polymorphisms in the 3' UTR of the gene alter the binding site of microRNA-641, which was analyzed by luciferase reporter system. It was observed that haplotypes altering one or two nucleotides in the binding site of the seed region of microRNA-641 significantly increased the amount of generated protein in vitro. These findings support the role of polymorphic SNAP-25 variants both at psychogenetic and molecular biological levels.

  1. CID Aircraft in practice flight above target impact site with wing cutters

    Science.gov (United States)

    1984-01-01

    In this photograph the B-720 is seen making a practice close approach over the prepared impact site. The wing openers, designed to tear open the wings and spill the fuel, are clearly seen on the ground just at the start of the bed of rocks. In a typical aircraft crash, fuel spilled from ruptured fuel tanks forms a fine mist that can be ignited by a number of sources at the crash site. In 1984 the NASA Dryden Flight Research Facility (after 1994 a full-fledged Center again) and the Federal Aviation Administration (FAA) teamed-up in a unique flight experiment called the Controlled Impact Demonstration (CID), to test crash a Boeing 720 aircraft using standard fuel with an additive designed to supress fire. The additive, FM-9, a high-molecular-weight long-chain polymer, when blended with Jet-A fuel had demonstrated the capability to inhibit ignition and flame propagation of the released fuel in simulated crash tests. This anti-misting kerosene (AMK) cannot be introduced directly into a gas turbine engine due to several possible problems such as clogging of filters. The AMK must be restored to almost Jet-A before being introduced into the engine for burning. This restoration is called 'degradation' and was accomplished on the B-720 using a device called a 'degrader.' Each of the four Pratt & Whitney JT3C-7 engines had a 'degrader' built and installed by General Electric (GE) to break down and return the AMK to near Jet-A quality. In addition to the AMK research the NASA Langley Research Center was involved in a structural loads measurement experiment, which included having instrumented dummies filling the seats in the passenger compartment. Before the final flight on December 1, 1984, more than four years of effort passed trying to set-up final impact conditions considered survivable by the FAA. During those years while 14 flights with crews were flown the following major efforts were underway: NASA Dryden developed the remote piloting techniques necessary for the B-720

  2. Tailoring structure-function and targeting properties of ceramides by site-specific cationization.

    Science.gov (United States)

    Szulc, Zdzislaw M; Bielawski, Jacek; Gracz, Hanna; Gustilo, Marietta; Mayroo, Nalini; Hannun, Yusuf A; Obeid, Lina M; Bielawska, Alicja

    2006-11-01

    In the course of our studies on compartment-specific lipid-mediated cell regulation, we identified an intimate connection between ceramides (Cers) and the mitochondria-dependent death-signaling pathways. Here, we report on a new class of cationic Cer mimics, dubbed ceramidoids, designed to act as organelle-targeted sphingolipids (SPLs), based on conjugates of Cer and dihydroceramide (dhCer) with pyridinium salts (CCPS and dhCCPS, respectively). Ceramidoids having the pyridinium salt unit (PSU) placed internally (alpha and gamma- CCPS) or as a tether (omega-CCPS) in the N-acyl moiety were prepared by N-acylation of sphingoid bases with different omega-bromo acids or pyridine carboxylic acid chlorides following capping with respective pyridines or alkyl bromides. Consistent with their design, these analogs, showed a significantly improved solubility in water, well-resolved NMR spectra in D(2)O, broadly modified hydrophobicity, fast cellular uptake, and higher anticancer activities in cells in comparison to uncharged counterparts. Structure-activity relationship (SAR) studies in MCF-7 breast carcinoma cells revealed that the location of the PSU and its overall chain length affected markedly the cytotoxic effects of these ceramidoids. All omega-CCPSs were more potent (IC(50/48 h): 0.6-8.0 microM) than their alpha/gamma-CCPS (IC(50/48 h): 8-20 microM) or D-erythro-C6-Cer (IC(50/48 h): 15 microM) analogs. omega-DhCCPSs were also moderately potent (IC(50/48 h): 2.5-12.5 microM). Long-chain omega-dhCCPSs were rapidly and efficiently oxidized in cells to the corresponding omega-CCPSs, as established by LC-MS analysis. CCPS analogs also induced acute changes in the levels and composition of endogenous Cers (upregulation of C16-, C14-, and C18-Cers, and downregulation of C24:0- and C24:1-Cers). These novel ceramidoids illustrate the feasibility of compartment-targeted lipids, and they should be useful in cell-based studies as well as potential novel therapeutics.

  3. Optimization of Time Controlled 6-mercaptopurine Delivery for Site- Specific Targeting to Colon Diseases.

    Science.gov (United States)

    Hude, Rahul U; Jagdale, Swati C

    2016-01-01

    6-MP has short elimination time (croscarmellose sodium were found to be optimum concentration for the core tablet. The outer coat of optimized batch (ED) contains 21.05% w/w Eudragit RS 100 and 78.95% w/w HPMC K100 of total polymer weight. In-vitro dissolution study indicated that combination of polymer retards the drug release in gastric region and releases ≥95% of drug in colonic region after ≥7 h. Whereas in case of in-vivo placebo x-ray imaging study had shown that the tablet reaches colonic part after 5±0.5 h providing the proof of arrival in the colon. Stability study indicated that the optimized formulation were physically and chemically stable. Present research work concluded that compression coating by Eudragit RS 100 and HPMC K100 to 6-MP core provides potential colon targeted system with advantages of reduced gastric exposure and enhanced bioavailability. Formulation can be considered as potential and promising candidate for the treatment of colon diseases.

  4. Quantification of Mesenchymal Stem Cell (MSC delivery to a target site using in vivo confocal microscopy.

    Directory of Open Access Journals (Sweden)

    Luke J Mortensen

    Full Text Available The ability to deliver cells to appropriate target tissues is a prerequisite for successful cell-based therapy. To optimize cell therapy it is therefore necessary to develop a robust method of in vivo cell delivery quantification. Here we examine Mesenchymal Stem Cells (MSCs labeled with a series of 4 membrane dyes from which we select the optimal dye combination for pair-wise comparisons of delivery to inflamed tissue in the mouse ear using confocal fluorescence imaging. The use of an optimized dye pair for simultaneous tracking of two cell populations in the same animal enables quantification of a test population that is referenced to an internal control population, thereby eliminating intra-subject variations and variations in injected cell numbers. Consistent results were obtained even when the administered cell number varied by more than an order of magnitude, demonstrating an ability to neutralize one of the largest sources of in vivo experimental error and to greatly reduce the number of cells required to evaluate cell delivery. With this method, we are able to show a small but significant increase in the delivery of cytokine pre-treated MSCs (TNF-α & IFN-γ compared to control MSCs. Our results suggest future directions for screening cell strategies using our in vivo cell delivery assay, which may be useful to develop methods to maximize cell therapeutic potential.

  5. Targeted Deletion of a Plasmodium Site-2 Protease Impairs Life Cycle Progression in the Mammalian Host.

    Science.gov (United States)

    Koussis, Konstantinos; Goulielmaki, Evi; Chalari, Anna; Withers-Martinez, Chrislaine; Siden-Kiamos, Inga; Matuschewski, Kai; Loukeris, Thanasis G

    2017-01-01

    Site-2 proteases (S2P) belong to the M50 family of metalloproteases, which typically perform essential roles by mediating activation of membrane-bound transcription factors through regulated intramembrane proteolysis (RIP). Protease-dependent liberation of dormant transcription factors triggers diverse cellular responses, such as sterol regulation, Notch signalling and the unfolded protein response. Plasmodium parasites rely on regulated proteolysis for controlling essential pathways throughout the life cycle. In this study we examine the Plasmodium-encoded S2P in a murine malaria model and show that it is expressed in all stages of Plasmodium development. Localisation studies by endogenous gene tagging revealed that in all invasive stages the protein is in close proximity to the nucleus. Ablation of PbS2P by reverse genetics leads to reduced growth rates during liver and blood infection and, hence, virulence attenuation. Strikingly, absence of PbS2P was compatible with parasite life cycle progression in the mosquito and mammalian hosts under physiological conditions, suggesting redundant or dispensable roles in vivo.

  6. Linking oviposition site choice to offspring fitness in Aedes aegypti: consequences for targeted larval control of dengue vectors.

    Directory of Open Access Journals (Sweden)

    Jacklyn Wong

    Full Text Available Current Aedes aegypti larval control methods are often insufficient for preventing dengue epidemics. To improve control efficiency and cost-effectiveness, some advocate eliminating or treating only highly productive containers. The population-level outcome of this strategy, however, will depend on details of Ae. aegypti oviposition behavior.We simultaneously monitored female oviposition and juvenile development in 80 experimental containers located across 20 houses in Iquitos, Peru, to test the hypothesis that Ae. aegypti oviposit preferentially in sites with the greatest potential for maximizing offspring fitness. Females consistently laid more eggs in large vs. small containers (β = 9.18, p<0.001, and in unmanaged vs. manually filled containers (β = 5.33, p<0.001. Using microsatellites to track the development of immature Ae. aegypti, we found a negative correlation between oviposition preference and pupation probability (β = -3.37, p<0.001. Body size of emerging adults was also negatively associated with the preferred oviposition site characteristics of large size (females: β = -0.19, p<0.001; males: β = -0.11, p = 0.002 and non-management (females: β = -0.17, p<0.001; males: β = -0.11, p<0.001. Inside a semi-field enclosure, we simulated a container elimination campaign targeting the most productive oviposition sites. Compared to the two post-intervention trials, egg batches were more clumped during the first pre-intervention trial (β = -0.17, P<0.001, but not the second (β = 0.01, p = 0.900. Overall, when preferred containers were unavailable, the probability that any given container received eggs increased (β = 1.36, p<0.001.Ae. aegypti oviposition site choice can contribute to population regulation by limiting the production and size of adults. Targeted larval control strategies may unintentionally lead to dispersion of eggs among suitable, but previously unoccupied or under

  7. The Groucho co-repressor is primarily recruited to local target sites in active chromatin to attenuate transcription.

    Directory of Open Access Journals (Sweden)

    Aamna Kaul

    2014-08-01

    Full Text Available Gene expression is regulated by the complex interaction between transcriptional activators and repressors, which function in part by recruiting histone-modifying enzymes to control accessibility of DNA to RNA polymerase. The evolutionarily conserved family of Groucho/Transducin-Like Enhancer of split (Gro/TLE proteins act as co-repressors for numerous transcription factors. Gro/TLE proteins act in several key pathways during development (including Notch and Wnt signaling, and are implicated in the pathogenesis of several human cancers. Gro/TLE proteins form oligomers and it has been proposed that their ability to exert long-range repression on target genes involves oligomerization over broad regions of chromatin. However, analysis of an endogenous gro mutation in Drosophila revealed that oligomerization of Gro is not always obligatory for repression in vivo. We have used chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq to profile Gro recruitment in two Drosophila cell lines. We find that Gro predominantly binds at discrete peaks (<1 kilobase. We also demonstrate that blocking Gro oligomerization does not reduce peak width as would be expected if Gro oligomerization induced spreading along the chromatin from the site of recruitment. Gro recruitment is enriched in "active" chromatin containing developmentally regulated genes. However, Gro binding is associated with local regions containing hypoacetylated histones H3 and H4, which is indicative of chromatin that is not fully open for efficient transcription. We also find that peaks of Gro binding frequently overlap the transcription start sites of expressed genes that exhibit strong RNA polymerase pausing and that depletion of Gro leads to release of polymerase pausing and increased transcription at a bona fide target gene. Our results demonstrate that Gro is recruited to local sites by transcription factors to attenuate rather than silence gene expression by promoting histone

  8. Multiple-site mutations of phage Bp7 endolysin improves its activities against target bacteria.

    Science.gov (United States)

    Zhang, Can; Wang, Yuanchao; Sun, Huzhi; Ren, Huiying

    2015-10-01

    The widespread use of antibiotics has caused serious drug resistance. Bacteria that were once easily treatable are now extremely difficult to treat. Endolysin can be used as an alternative to antibiotics for the treatment of drug-resistant bacteria. To analyze the antibacterial activity of the endolysin of phage Bp7 (Bp7e), a 489-bp DNA fragment of endolysin Bp7e was PCR-amplified from a phage Bp7 genome and cloned, and then a pET28a-Bp7e prokaryotic expression vector was constructed. Two amino acids were mutated (L99A, M102E) to construct pET28a-Bp7Δe, with pET28a-Bp7e as a template. Phylogenetic analysis suggested that BP7e belongs to a T4-like phage endolysin group. Bp7e and its mutant Bp7Δe were expressed in Escherichia coli BL21(DE3) as soluble proteins. They were purified by affinity chromatography, and then their antibacterial activities were analyzed. The results demonstrated that the recombinant proteins Bp7e and Bp7Δe showed obvious antibacterial activity against Micrococcus lysodeikticus but no activity against Staphylococcus aureus. In the presence of malic acid, Bp7e and Bp7Δe exhibited an effect on most E. coli strains which could be lysed by phage Bp7, but no effect on Salmonella paratyphi or Pseudomonas aeruginosa. Moreover, Bp7Δe with double-site mutations showed stronger antibacterial activity and a broader lysis range than Bp7e.

  9. Internal Ribosome Entry Site-Based Bicistronic In Situ Reporter Assays for Discovery of Transcription-Targeted Lead Compounds.

    Science.gov (United States)

    Lang, Liwei; Ding, Han-Fei; Chen, Xiaoguang; Sun, Shi-Yong; Liu, Gang; Yan, Chunhong

    2015-07-23

    Although transgene-based reporter gene assays have been used to discover small molecules targeting expression of cancer-driving genes, the success is limited due to the fact that reporter gene expression regulated by incomplete cis-acting elements and foreign epigenetic environments does not faithfully reproduce chemical responses of endogenous genes. Here, we present an internal ribosome entry site-based strategy for bicistronically co-expressing reporter genes with an endogenous gene in the native gene locus, yielding an in situ reporter assay closely mimicking endogenous gene expression without disintegrating its function. This strategy combines the CRISPR-Cas9-mediated genome-editing tool with the recombinase-mediated cassette-exchange technology, and allows for rapid development of orthogonal assays for excluding false hits generated from primary screens. We validated this strategy by developing a screening platform for identifying compounds targeting oncogenic eIF4E, and demonstrated that the novel reporter assays are powerful in searching for transcription-targeted lead compounds with high confidence. Copyright © 2015 Elsevier Ltd. All rights reserved.

  10. The DNA-binding box of human SPARTAN contributes to the targeting of Polη to DNA damage sites.

    Science.gov (United States)

    Toth, Agnes; Hegedus, Lili; Juhasz, Szilvia; Haracska, Lajos; Burkovics, Peter

    2017-01-01

    Inappropriate repair of UV-induced DNA damage results in human diseases such as Xeroderma pigmentosum (XP), which is associated with an extremely high risk of skin cancer. A variant form of XP is caused by the absence of Polη, which is normally able to bypass UV-induced DNA lesions in an error-free manner. However, Polη is highly error prone when replicating undamaged DNA and, thus, the regulation of the proper targeting of Polη is crucial for the prevention of mutagenesis and UV-induced cancer formation. Spartan is a novel regulator of the damage tolerance pathway, and its association with Ub-PCNA has a role in Polη targeting; however, our knowledge about its function is only rudimentary. Here, we describe a new biochemical property of purified human SPARTAN by showing that it is a DNA-binding protein. Using a DNA binding mutant, we provide in vivo evidence that DNA binding by SPARTAN regulates the targeting of Polη to damage sites after UV exposure, and this function contributes highly to its DNA-damage tolerance function. Copyright © 2016 Elsevier B.V. All rights reserved.

  11. Contact Bioassays with Phenoxybenzyl and Tetrafluorobenzyl Pyrethroids against Target-Site and Metabolic Resistant Mosquitoes.

    Directory of Open Access Journals (Sweden)

    Sebastian Horstmann

    Full Text Available Mosquito strains that exhibit increased tolerance to the chemical class of compounds with a sodium channel modulator mode of action (pyrethroids and pyrethrins are typically described as "pyrethroid resistant". Resistance to pyrethroids is an increasingly important challenge in the control of mosquito-borne diseases, such as malaria or dengue, because one of the main interventions (the distribution of large numbers of long-lasting insecticide-treated bed nets currently relies entirely on long-lasting pyrethroids. Increasing tolerance of target insects against this class of insecticides lowers their impact in vector control. The current study suggests that the level of metabolic resistance depends on the structure of the molecule and that structurally different compounds may still be effective because detoxifying enzymes are unable to bind to these uncommon structures.Treated surface contact bioassays were performed on susceptible Aedes aegypti, East African knockdown resistance (kdr Anopheles gambiae (strain RSP-H and metabolically resistant Anopheles funestus (strain FUMOZ-R with different pyrethroids, such as cypermethrin, ß-cyfluthrin, deltamethrin, permethrin and transfluthrin (alone and in combination with the synergist piperonyl butoxide. The nonfluorinated form of transfluthrin was also assessed as a single agent and in combination with piperonyl butoxide.Although the dosages for pyrethroids containing a phenoxybenzyl moiety have exhibited differences in terms of effectiveness among the three tested mosquito species, the structurally different transfluthrin with a polyfluorobenzyl moiety remained active in mosquitoes with upregulated P450 levels. In trials with transfluthrin mixed with piperonyl butoxide, the added synergist exhibited no efficacy-enhancing effect.The results of this study suggest that transfluthrin has the potential to control P450-mediated metabolically resistant mosquitoes because the structural formula of

  12. Geology and MER target site characteristics along the southern rim of Isidis Planitia, Mars

    Science.gov (United States)

    Crumpler, L.S.; Tanaka, K.L.

    2003-01-01

    crustal materials, in the form of rocks within the debris fans, and the weathered condition of the rocky material are potential sources for mineralogical evidence of climatic conditions in earliest Martian geologic history. The absence of alteration within rocks would, on the other hand, support the hypothesis that fluvial runoff during the earliest history of Mars was geologically brief rather than long-term and that long-term saturated groundwater flow was not present. Determination of the presence or absence of alteration would have corresponding implications for hypotheses requiring the long-term presence of aqueous solutions (i.e., complex organic compounds and life). A proposed MER site along the margin addresses realistic field science objectives of the Mars Exploration Rover mission and the current goals of the Mars Exploration Program. In situ measurements may be important in deriving estimates of the longevity and intensity of past wetter climates. Copyright 2003 by the American Geophysical Union.

  13. Properties of thermoluminescence glow curves from tunneling recombination processes in random distributions of defects

    Energy Technology Data Exchange (ETDEWEB)

    Kitis, George [Nuclear Physics Laboratory, Aristotle University of Thessaloniki, 54124 Thessaloniki (Greece); Pagonis, Vasilis, E-mail: vpagonis@mcdaniel.edu [Physics Department, McDaniel College, Westminster, MD 21157 (United States)

    2014-09-15

    Localized electronic recombination processes in donor–acceptor pairs of luminescent materials have been recently modeled using a new kinetic model based on tunneling. Within this model, recombination is assumed to take place via the excited state of the donor, and nearest-neighbor recombinations take place within a random distribution of centers. An approximate semi-analytical version of the model has been shown to simulate successfully thermally and optically stimulated luminescence (TL and OSL), linearly modulated OSL (LM-OSL) and isothermal TL processes. This paper presents a detailed analysis of the geometrical properties of the TL glow curves obtained within three different published versions of the model. The dependence of the shape of the TL glow curves on the kinetic parameters of the model is examined by allowing simultaneous random variations of the parameters, within wide ranges of physically reasonable values covering several orders of magnitude. It is found that the TL glow curves can be characterized according to their shape factors μ{sub g}, as commonly done in TL theory of delocalized transitions. The values of the shape factor are found to depend rather weakly on the activation energy E and the frequency factor s, but they have a strong dependence on the parameter ρ′ which characterizes the concentration of acceptors in the model. It is also shown by simulation that both the variable heating rate and initial rise methods are applicable in this type of model and can yield the correct value of the activation energy E. However, the initial rise method of analysis for the semianalytical version of the model fails to yield the correct E value, since it underestimates the low temperature part of the TL glow curves. Two analytical expressions are given for the TL intensity, which can be used on an empirical basis for computerized glow curve deconvolution analysis (CGCD). - Highlights: • Detailed study of TL glow curves in a tunneling model for

  14. 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

  15. An illegitimate microRNA target site within the 3' UTR of MDM4 affects ovarian cancer progression and chemosensitivity

    DEFF Research Database (Denmark)

    Wynendaele, Jessika; Böhnke, Anja; Leucci, Eleonora

    2010-01-01

    4 gene in a series of ovarian cancer cell lines and carcinomas to identify mutations and/or single nucleotide polymorphisms (SNPs). We identified an SNP (SNP34091) in the 3'-UTR of MDM4 that creates a putative target site for hsa-miR-191, a microRNA that is highly expressed in normal and tumor...... tissues. Biochemical evidence supports specific miR-191-dependent regulation of the MDM4-C, but not MDM4-A, variant. Consistently, the A-allele was associated with statistically significant increased expression of MDM4 mRNA and protein levels in ovarian carcinomas. Importantly, the wild-type genotype (A...... downregulation of MDM4 expression, thereby significantly delaying ovarian carcinoma progression and tumor-related death. Importantly, these effects appear to be, at least partly, independent of p53....

  16. RNA interference as a method for target-site screening in the Western corn rootworm, Diabrotica virgifera virgifera.

    Science.gov (United States)

    Alves, Analiza P; Lorenzen, Marcé D; Beeman, Richard W; Foster, John E; Siegfried, Blair D

    2010-01-01

    To test the efficacy of RNA interference (RNAi) as a method for target-site screening in Diabrotica virgifera virgifera LeConte (Coleptera: Chrysomelidae) larvae, genes were identified and tested for which clear RNAi phenotypes had been identified in the Coleopteran model, Tribolium castaneum. Here the cloning of the D. v. vergifera orthologs of laccase 2 (DvvLac2) and chitin synthase 2 (DvvCHS2) is reported. Injection of DvvLac2-specific double-stranded RNA resulted in prevention of post-molt cuticular tanning, while injection of DvvCHS2-specific dsRNA reduced chitin levels in midguts. Silencing of both DvvLac2 and DvvCHS2 was confirmed by RT-PCR and quantitative RT-PCR. As in T. castaneum, RNAi-mediated gene silencing is systemic in Diabrotica. The results indicate that RNAi-induced silencing of D. v. vergifera genes provides a powerful tool for identifying potential insecticide targets.

  17. p38α MAPK and Type I Inhibitors: Binding Site Analysis and Use of Target Ensembles in Virtual Screening

    Directory of Open Access Journals (Sweden)

    Andrea Astolfi

    2015-08-01

    Full Text Available Mitogen-activated protein kinase p38α plays an essential role in the regulation of pro-inflammatory signaling, and selective blockade of this kinase could be efficacious in many pathological processes. Despite considerable research efforts focused on the discovery and development of p38α MAPK inhibitors, no drug targeting this protein has been approved for clinical use so far. We herein analyze the available crystal structures of p38α MAPK in complex with ATP competitive type I inhibitors, getting insights into ATP binding site conformation and its influence on automated molecular docking results. The use of target ensembles, rather than single conformations, resulted in a performance improvement in both the ability to reproduce experimental bound conformations and the capability of mining active molecules from compound libraries. The information gathered from this study can be exploited in structure-based drug discovery programs having as the ultimate aim the identification of novel p38α MAPK type I inhibitors.

  18. Structure-based prediction of RNA-binding domains and RNA-binding sites and application to structural genomics targets.

    Science.gov (United States)

    Zhao, Huiying; Yang, Yuedong; Zhou, Yaoqi

    2011-04-01

    Mechanistic understanding of many key cellular processes often involves identification of RNA binding proteins (RBPs) and RNA binding sites in two separate steps. Here, they are predicted simultaneously by structural alignment to known protein-RNA complex structures followed by binding assessment with a DFIRE-based statistical energy function. This method achieves 98% accuracy and 91% precision for predicting RBPs and 93% accuracy and 78% precision for predicting RNA-binding amino-acid residues for a large benchmark of 212 RNA binding and 6761 non-RNA binding domains (leave-one-out cross-validation). Additional tests revealed that the method makes no false positive prediction from 311 DNA binding domains but correctly detects six domains binding with both DNA and RNA. In addition, it correctly identified 31 of 75 unbound RNA-binding domains with 92% accuracy and 65% precision for predicted binding residues and achieved 86% success rate in its application to SCOP RNA binding domain superfamily (Structural Classification Of Proteins). It further predicts 25 targets as RBPs in 2076 structural genomics targets: 20 of 25 predicted ones (80%) are putatively RNA binding. The superior performance over existing methods indicates the importance of dividing structures into domains, using a Z-score to measure relative structural similarity, and a statistical energy function to measure protein-RNA binding affinity.

  19. A FluoPol-ABPP PAD2 high-throughput screen identifies the first calcium site inhibitor targeting the PADs.

    Science.gov (United States)

    Lewallen, Daniel M; Bicker, Kevin L; Madoux, Franck; Chase, Peter; Anguish, Lynne; Coonrod, Scott; Hodder, Peter; Thompson, Paul R

    2014-04-18

    The protein arginine deiminases (PADs) catalyze the post-translational hydrolysis of peptidyl-arginine to form peptidyl-citrulline in a process termed deimination or citrullination. PADs likely play a role in the progression of a range of disease states because dysregulated PAD activity is observed in a host of inflammatory diseases and cancer. For example, recent studies have shown that PAD2 activates ERα target gene expression in breast cancer cells by citrullinating histone H3 at ER target promoters. To date, all known PAD inhibitors bind directly to the enzyme active site. PADs, however, also require calcium ions to drive a conformational change between the inactive apo-state and the fully active calcium bound holoenzyme, suggesting that it would be possible to identify inhibitors that bind the apoenzyme and prevent this conformational change. As such, we set out to develop a screen that can identify PAD2 inhibitors that bind to either the apo or calcium bound form of PAD2. Herein, we provide definitive proof of concept for this approach and report the first PAD inhibitor, ruthenium red (Ki of 17 μM), to preferentially bind the apoenzyme.

  20. The TTSMI database: a catalog of triplex target DNA sites associated with genes and regulatory elements in the human genome

    Science.gov (United States)

    Jenjaroenpun, Piroon; Chew, Chee Siang; Yong, Tai Pang; Choowongkomon, Kiattawee; Thammasorn, Wimada; Kuznetsov, Vladimir A.

    2015-01-01

    A triplex target DNA site (TTS), a stretch of DNA that is composed of polypurines, is able to form a triple-helix (triplex) structure with triplex-forming oligonucleotides (TFOs) and is able to influence the site-specific modulation of gene expression and/or the modification of genomic DNA. The co-localization of a genomic TTS with gene regulatory signals and functional genome structures suggests that TFOs could potentially be exploited in antigene strategies for the therapy of cancers and other genetic diseases. Here, we present the TTS Mapping and Integration (TTSMI; http://ttsmi.bii.a-star.edu.sg) database, which provides a catalog of unique TTS locations in the human genome and tools for analyzing the co-localization of TTSs with genomic regulatory sequences and signals that were identified using next-generation sequencing techniques and/or predicted by computational models. TTSMI was designed as a user-friendly tool that facilitates (i) fast searching/filtering of TTSs using several search terms and criteria associated with sequence stability and specificity, (ii) interactive filtering of TTSs that co-localize with gene regulatory signals and non-B DNA structures, (iii) exploration of dynamic combinations of the biological signals of specific TTSs and (iv) visualization of a TTS simultaneously with diverse annotation tracks via the UCSC genome browser. PMID:25324314

  1. 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 H2O2 on PSCKM (muscle type creatine kinase from Pelodiscus sinensis) by the integrating method between enzyme kinetics and docking simulations. We found that H2O2 strongly inactivated PSCKM (IC50=0.25mM) in a first-order kinetic process, and targeted the active site cysteine directly. A conformational study showed that H2O2 did not induce the tertiary structural changes in PSCKM with no extensive exposure of hydrophobic surfaces. Sequential docking simulations between PSCKM and H2O2 indicated that H2O2 interacts with the ADP binding region of the active site, consistent with experimental results that demonstrated H2O2-induced inactivation. Our study demonstrates the effect of H2O2 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.

  2. Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations.

    Science.gov (United States)

    Roberts, Gareth A; Houston, Patrick J; White, John H; Chen, Kai; Stephanou, Augoustinos S; Cooper, Laurie P; Dryden, David T F; Lindsay, Jodi A

    2013-08-01

    A limited number of Methicillin-resistant Staphylococcus aureus (MRSA) clones are responsible for MRSA infections worldwide, and those of different lineages carry unique Type I restriction-modification (RM) variants. We have identified the specific DNA sequence targets for the dominant MRSA lineages CC1, CC5, CC8 and ST239. We experimentally demonstrate that this RM system is sufficient to block horizontal gene transfer between clinically important MRSA, confirming the bioinformatic evidence that each lineage is evolving independently. Target sites are distributed randomly in S. aureus genomes, except in a set of large conjugative plasmids encoding resistance genes that show evidence of spreading between two successful MRSA lineages. This analysis of the identification and distribution of target sites explains evolutionary patterns in a pathogenic bacterium. We show that a lack of specific target sites enables plasmids to evade the Type I RM system thereby contributing to the evolution of increasingly resistant community and hospital MRSA.

  3. 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

    2017-11-03

    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.

  4. Small RNAs targeting transcription start site induce heparanase silencing through interference with transcription initiation in human cancer cells.

    Directory of Open Access Journals (Sweden)

    Guosong Jiang

    Full Text Available Heparanase (HPA, an endo-h-D-glucuronidase that cleaves the heparan sulfate chain of heparan sulfate proteoglycans, is overexpressed in majority of human cancers. Recent evidence suggests that small interfering RNA (siRNA induces transcriptional gene silencing (TGS in human cells. In this study, transfection of siRNA against -9/+10 bp (siH3, but not -174/-155 bp (siH1 or -134/-115 bp (siH2 region relative to transcription start site (TSS locating at 101 bp upstream of the translation start site, resulted in TGS of heparanase in human prostate cancer, bladder cancer, and gastric cancer cells in a sequence-specific manner. Methylation-specific PCR and bisulfite sequencing revealed no DNA methylation of CpG islands within heparanase promoter in siH3-transfected cells. The TGS of heparanase did not involve changes of epigenetic markers histone H3 lysine 9 dimethylation (H3K9me2, histone H3 lysine 27 trimethylation (H3K27me3 or active chromatin marker acetylated histone H3 (AcH3. The regulation of alternative splicing was not involved in siH3-mediated TGS. Instead, siH3 interfered with transcription initiation via decreasing the binding of both RNA polymerase II and transcription factor II B (TFIIB, but not the binding of transcription factors Sp1 or early growth response 1, on the heparanase promoter. Moreover, Argonaute 1 and Argonaute 2 facilitated the decreased binding of RNA polymerase II and TFIIB on heparanase promoter, and were necessary in siH3-induced TGS of heparanase. Stable transfection of the short hairpin RNA construct targeting heparanase TSS (-9/+10 bp into cancer cells, resulted in decreased proliferation, invasion, metastasis and angiogenesis of cancer cells in vitro and in athymic mice models. These results suggest that small RNAs targeting TSS can induce TGS of heparanase via interference with transcription initiation, and significantly suppress the tumor growth, invasion, metastasis and angiogenesis of cancer cells.

  5. Evolutionary Origin and Conserved Structural Building Blocks of Riboswitches and Ribosomal RNAs: Riboswitches as Probable Target Sites for Aminoglycosides Interaction

    Directory of Open Access Journals (Sweden)

    Elnaz Mehdizadeh Aghdam

    2014-05-01

    Full Text Available Purpose: Riboswitches, as noncoding RNA sequences, control gene expression through direct ligand binding. Sporadic reports on the structural relation of riboswitches with ribosomal RNAs (rRNA, raises an interest in possible similarity between riboswitches and rRNAs evolutionary origins. Since aminoglycoside antibiotics affect microbial cells through binding to functional sites of the bacterial rRNA, finding any conformational and functional relation between riboswitches/rRNAs is utmost important in both of medicinal and basic research. Methods: Analysis of the riboswitches structures were carried out using bioinformatics and computational tools. The possible functional similarity of riboswitches with rRNAs was evaluated based on the affinity of paromomycin antibiotic (targeting “A site” of 16S rRNA to riboswitches via docking method. Results: There was high structural similarity between riboswitches and rRNAs, but not any particular sequence based similarity between them was found. The building blocks including "hairpin loop containing UUU", "peptidyl transferase center conserved hairpin A loop"," helix 45" and "S2 (G8 hairpin" as high identical rRNA motifs were detected in all kinds of riboswitches. Surprisingly, binding energies of paromomycin with different riboswitches are considerably better than the binding energy of paromomycin with “16S rRNA A site”. Therefore the high affinity of paromomycin to bind riboswitches in comparison with rRNA “A site” suggests a new insight about riboswitches as possible targets for aminoglycoside antibiotics. Conclusion: These findings are considered as a possible supporting evidence for evolutionary origin of riboswitches/rRNAs and also their role in the exertion of antibiotics effects to design new drugs based on the concomitant effects via rRNA/riboswitches.

  6. Selective inhibition of the human tie-1 promoter with triplex-forming oligonucleotides targeted to Ets binding sites.

    Science.gov (United States)

    Hewett, Peter W; Daft, Emma L; Laughton, Charles A; Ahmad, Shakil; Ahmed, Asif; Murray, J Clifford

    2006-01-01

    The Tie receptors (Tie-1 and Tie-2/Tek) are essential for angiogenesis and vascular remodeling/integrity. Tie receptors are up-regulated in tumor-associated endothelium, and their inhibition disrupts angiogenesis and can prevent tumor growth as a consequence. To investigate the potential of anti-gene approaches to inhibit tie gene expression for anti-angiogenic therapy, we have examined triple-helical (triplex) DNA formation at 2 tandem Ets transcription factor binding motifs (designated E-1 and E-2) in the human tie-1 promoter. Various tie-1 promoter deletion/mutation luciferase reporter constructs were generated and transfected into endothelial cells to examine the relative activities of E-1 and E-2. The binding of antiparallel and parallel (control) purine motif oligonucleotides (21-22 bp) targeted to E-1 and E-2 was assessed by plasmid DNA fragment binding and electrophoretic mobility shift assays. Triplex-forming oligonucleotides were incubated with tie-1 reporter constructs and transfected into endothelial cells to determine their activity. The Ets binding motifs in the E-1 sequence were essential for human tie-1 promoter activity in endothelial cells, whereas the deletion of E-2 had no effect. Antiparallel purine motif oligonucleotides targeted at E-1 or E-2 selectively formed strong triplex DNA (K(d) approximately 10(-7) M) at 37 degrees C. Transfection of tie-1 reporter constructs with triplex DNA at E-1, but not E-2, specifically inhibited tie-1 promoter activity by up to 75% compared with control oligonucleotides in endothelial cells. As similar multiple Ets binding sites are important for the regulation of several endothelial-restricted genes, this approach may have broad therapeutic potential for cancer and other pathologies involving endothelial proliferation/dysfunction.

  7. Final work plan : targeted groundwater sampling and monitoring well installation for potential site reclassification at Barnes, Kansas.

    Energy Technology Data Exchange (ETDEWEB)

    LaFreniere, L. M.

    2006-07-11

    This ''Work Plan'' outlines the scope of work for a targeted groundwater sampling investigation and monitoring well installation at Barnes, Kansas. This activity is being conducted at the request of the Kansas Department of Health and Environment (KDHE), in accordance with the intergovernmental agreement between the KDHE and the Commodity Credit Corporation (CCC), an agency of the U.S. Department of Agriculture (USDA). Data resulting from the proposed work will be used to determine the hydraulic gradient near the former CCC/USDA facility, delineate the downgradient carbon tetrachloride plume, and determine additional monitoring requirements at Barnes. The overall goal is to establish criteria for monitoring leading to potential site reclassification. The proposed work will be performed on behalf of the CCC/USDA by the Environmental Science Division of Argonne National Laboratory. Argonne is a nonprofit, multidisciplinary research center operated by the University of Chicago for the U.S. Department of Energy (DOE). The Farm Service Agency of the USDA has entered into an interagency agreement with DOE, under which Argonne provides technical assistance with environmental site characterization and remediation at former CCC/USDA grain storage facilities. Argonne issued a ''Master Work Plan'' (Argonne 2002) to provide general guidance for all investigations at former CCC/USDA facilities in Kansas. The ''Master Work Plan'', approved by the KDHE, contains the materials common to investigations at all locations in Kansas. This document must be consulted for the complete details of plans for this work associated with the former CCC/USDA facility at Barnes.

  8. Small molecules targeted to a non-catalytic "RVxF" binding site of protein phosphatase-1 inhibit HIV-1.

    Directory of Open Access Journals (Sweden)

    Tatiana Ammosova

    Full Text Available HIV-1 Tat protein recruits host cell factors including CDK9/cyclin T1 to HIV-1 TAR RNA and thereby induces HIV-1 transcription. An interaction with host Ser/Thr protein phosphatase-1 (PP1 is critical for this function of Tat. PP1 binds to a Tat sequence, Q(35VCF(38, which resembles the PP1-binding "RVxF" motif present on PP1-binding regulatory subunits. We showed that expression of PP1 binding peptide, a central domain of Nuclear Inhibitor of PP1, disrupted the interaction of HIV-1 Tat with PP1 and inhibited HIV-1 transcription and replication. Here, we report small molecule compounds that target the "RVxF"-binding cavity of PP1 to disrupt the interaction of PP1 with Tat and inhibit HIV-1 replication. Using the crystal structure of PP1, we virtually screened 300,000 compounds and identified 262 small molecules that were predicted to bind the "RVxF"-accommodating cavity of PP1. These compounds were then assayed for inhibition of HIV-1 transcription in CEM T cells. One of the compounds, 1H4, inhibited HIV-1 transcription and replication at non-cytotoxic concentrations. 1H4 prevented PP1-mediated dephosphorylation of a substrate peptide containing an RVxF sequence in vitro. 1H4 also disrupted the association of PP1 with Tat in cultured cells without having an effect on the interaction of PP1 with the cellular regulators, NIPP1 and PNUTS, or on the cellular proteome. Finally, 1H4 prevented the translocation of PP1 to the nucleus. Taken together, our study shows that HIV- inhibition can be achieved through using small molecules to target a non-catalytic site of PP1. This proof-of-principle study can serve as a starting point for the development of novel antiviral drugs that target the interface of HIV-1 viral proteins with their host partners.

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

    Science.gov (United States)

    Yamamoto, Yumi; Välitalo, 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

    2017-02-01

    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 brain disposition. A mathematical model consisting of several physiological brain compartments in the rat was developed using rich concentration-time profiles from nine structurally diverse drugs in plasma, brain extracellular fluid, and two cerebrospinal fluid compartments. The effect of active drug transporters was also accounted for. Subsequently, the model was translated to predict human concentration-time profiles for acetaminophen and morphine, by scaling or replacing system- and drug-specific parameters in the model. A common model structure was identified that adequately described the rat pharmacokinetic profiles for each of the nine drugs across brain compartments, with good precision of structural model parameters (relative standard error human concentration-time profiles in different brain compartments well (symmetric mean absolute percentage error brain pharmacokinetic model was developed and its structure could adequately describe data across nine different drugs. The model could be successfully translated to predict human brain concentrations.

  10. Target site mutation and reduced translocation are present in a glyphosate-resistant Lolium multiflorum Lam. biotype from Spain.

    Science.gov (United States)

    González-Torralva, Fidel; Gil-Humanes, Javier; Barro, Francisco; Brants, Ivo; De Prado, Rafael

    2012-09-01

    The resistance mechanism of a glyphosate-resistant Lolium multiflorum Lam. biotype collected in Córdoba (Southern Spain) was examined. Resistance Factor values at three different growth stages ranged between 4.77 and 4.91. At 96 hours after treatment (HAT) the S biotype had accumulated seven times more shikimic acid than the R biotype. There were significant differences in translocation of (14)C-glyphosate between biotypes, i.e. at 96 HAT, the R biotype accumulated in the treated leaf more than 70% of the absorbed herbicide, in comparison with 59.21% of the S biotype; the R biotype translocated only 14.79% of the absorbed (14)C-glyphosate to roots, while in the S population this value was 24.79%. Visualization of (14)C-glyphosate by phosphor imaging showed a reduced distribution in the R biotype compared with the S. Glyphosate metabolism was not involved in the resistance mechanism due to both biotypes showing similar values of glyphosate at 96 HAT. Comparison of the EPSPS gene sequences between biotypes indicated that the R biotype has a proline 182 to serine amino acid substitution. In short, the resistance mechanism of the L. multiflorum Lam. biotype is due to an impaired translocation of the herbicide and an altered target site. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

  11. A systematic review of social networking sites: innovative platforms for health research targeting adolescents and young adults.

    Science.gov (United States)

    Park, Bu Kyung; Calamaro, Christina

    2013-09-01

    To review the evidence to determine if social networking sites (SNS) are effective tools for health research in the adolescent and young adult populations. Systematic review of published research articles focused on use of SNS for youth health research. Seventeen articles were selected that met the following criteria: used SNS at any stage of study, participants between 13 and 25 years of age, English language, and both international and national studies. Reviewers categorized selected studies based on the way SNS were used. Utilization of SNS for effectively implementing research with adolescents and young adults include (a) recruitment, (b) intervention, and (c) measurement. Four findings about advantages of using SNS apparent in this review are (a) ease of access to youth, (b) cost effectiveness in recruitment, (c) ease of intervention, and (d) reliable screening venue of mental status and high-risk behaviors. Although this literature review showed relatively minimal research to date on the use of SNS for research targeting adolescents and young adults, the impact of using SNS for health research is of considerable importance for researchers as well as participants. With careful focus, SNS can become a valuable platform to access, recruit, and deliver health interventions in a cost-effective manner to youth populations as well as hard-to-reach minority or underserved populations. The evidence demonstrates the usefulness of SNS as innovative platforms for health promotion among adolescents and young adults. © 2013 Sigma Theta Tau International.

  12. Detection of canonical A-to-G editing events at 3' UTRs and microRNA target sites in human lungs using next-generation sequencing.

    Science.gov (United States)

    Soundararajan, Ramani; Stearns, Timothy M; Griswold, Anthony L; Mehta, Arpit; Czachor, Alexander; Fukumoto, Jutaro; Lockey, Richard F; King, Benjamin L; Kolliputi, Narasaiah

    2015-11-03

    RNA editing is a post-transcriptional modification of RNA. The majority of these changes result from adenosine deaminase acting on RNA (ADARs) catalyzing the conversion of adenosine residues to inosine in double-stranded RNAs (dsRNAs). Massively parallel sequencing has enabled the identification of RNA editing sites in human transcriptomes. In this study, we sequenced DNA and RNA from human lungs and identified RNA editing sites with high confidence via a computational pipeline utilizing stringent analysis thresholds. We identified a total of 3,447 editing sites that overlapped in three human lung samples, and with 50% of these sites having canonical A-to-G base changes. Approximately 27% of the edited sites overlapped with Alu repeats, and showed A-to-G clustering (>3 clusters in 100 bp). The majority of edited sites mapped to either 3' untranslated regions (UTRs) or introns close to splice sites; whereas, only few sites were in exons resulting in non-synonymous amino acid changes. Interestingly, we identified 652 A-to-G editing events in the 3' UTR of 205 target genes that mapped to 932 potential miRNA target binding sites. Several of these miRNA edited sites were validated in silico. Additionally, we validated several A-to-G edited sites by Sanger sequencing. Altogether, our study suggests a role for RNA editing in miRNA-mediated gene regulation and splicing in human lungs. In this study, we have generated a RNA editome of human lung tissue that can be compared with other RNA editomes across different lung tissues to delineate a role for RNA editing in normal and diseased states.

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

    Science.gov (United States)

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

    2012-02-01

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

  14. Multiple insecticide resistance mechanisms involving metabolic changes and insensitive target sites selected in anopheline vectors of malaria in Sri Lanka

    Directory of Open Access Journals (Sweden)

    Karunaratne SHP Parakrama

    2008-08-01

    Full Text Available Abstract Background The current status of insecticide resistance and the underlying resistance mechanisms were studied in the major vector of malaria, Anopheles culicifacies, and the secondary vector, Anopheles subpictus in five districts (Anuradhapura, Kurunegala, Moneragala, Puttalam and Trincomalee of Sri Lanka. Eight other anophelines, Anopheles annularis, Anopheles barbirostris, Anopheles jamesii, Anopheles nigerrimus, Anopheles peditaeniatus, Anopheles tessellatus, Anopheles vagus and Anopheles varuna from Anuradhapura district were also tested. Methods Adult females were exposed to the WHO discriminating dosages of DDT, malathion, fenitrothion, propoxur, λ-cyhalothrin, cyfluthrin, cypermethrin, deltamethrin, permethrin and etofenprox. The presence of metabolic resistance by esterase, glutathione S-transferase (GST and monooxygenase-based mechanisms, and the sensitivity of the acetylcholinesterase target site were assessed using synergists, and biochemical, and metabolic techniques. Results All the anopheline species had high DDT resistance. All An. culicifacies and An. subpictus populations were resistant to malathion, except An. culicifacies from Kurunegala, where there was no malathion carboxylesterase activity. Kurunegala and Puttalam populations of An. culicifacies were susceptible to fenitrothion. All the An. culicifacies populations were susceptible to carbamates. Both species were susceptible to the discriminating dosages of cypermethrin and cyfluthrin, but had different levels of resistance to other pyrethroids. Of the 8 other anophelines, only An. nigerrimus and An. peditaeniatus were resistant to all the insecticides tested, probably due to their high exposure to the insecticides used in agriculture. An. vagus showed some resistance to permethrin. Esterases, GSTs and monooxygenases were elevated in both An. culicifacies and An. subpictus. AChE was most sensitive to insecticides in Kurunegala and Trincomalee An. culicifacies

  15. 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

  16. CRISPR/Cas9-Mediated Insertion of loxP Sites in the Mouse Dock7 Gene Provides an Effective Alternative to Use of Targeted Embryonic Stem Cells

    Directory of Open Access Journals (Sweden)

    Kathleen A. Bishop

    2016-07-01

    Full Text Available Targeted gene mutation in the mouse is a primary strategy to understand gene function and relation to phenotype. The Knockout Mouse Project (KOMP had an initial goal to develop a public resource of mouse embryonic stem (ES cell clones that carry null mutations in all genes. Indeed, many useful novel mouse models have been generated from publically accessible targeted mouse ES cell lines. However, there are limitations, including incorrect targeting or cassette structure, and difficulties with germline transmission of the allele from chimeric mice. In our experience, using a small sample of targeted ES cell clones, we were successful ∼50% of the time in generating germline transmission of a correctly targeted allele. With the advent of CRISPR/Cas9 as a mouse genome modification tool, we assessed the efficiency of creating a conditional targeted allele in one gene, dedicator of cytokinesis 7 (Dock7, for which we were unsuccessful in generating a null allele using a KOMP targeted ES cell clone. The strategy was to insert loxP sites to flank either exons 3 and 4, or exons 3 through 7. By coinjecting Cas9 mRNA, validated sgRNAs, and oligonucleotide donors into fertilized eggs from C57BL/6J mice, we obtained a variety of alleles, including mice homozygous for the null alleles mediated by nonhomologous end joining, alleles with one of the two desired loxP sites, and correctly targeted alleles with both loxP sites. We also found frequent mutations in the inserted loxP sequence, which is partly attributable to the heterogeneity in the original oligonucleotide preparation.

  17. Imidazole- and Benzimidazole-Based Inhibitors of the Kinase IspE : Targeting the Substrate-Binding Site and the Triphosphate-Binding Loop of the ATP Site

    NARCIS (Netherlands)

    Mombelli, Paolo; Le Chapelain, Camille; Munzinger, Noah; Joliat, Evelyne; Illarionov, Boris; Schweizer, W. Bernd; Hirsch, Anna K. H.; Fischer, Markus; Bacher, Adelbert; Diederich, Francois

    The enzymes of the mevalonate-independent biosynthetic pathway to isoprenoids are attractive targets for the development of new drug candidates, in particular against malaria and tuberculosis, because they are present in major human pathogens but not in humans. Herein, the structure-based design,

  18. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-01-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state–dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites. PMID:24448449

  19. Improved design of hammerhead ribozyme for selective digestion of target RNA through recognition of site-specific adenosine-to-inosine RNA editing.

    Science.gov (United States)

    Fukuda, Masatora; Kurihara, Kei; Yamaguchi, Shota; Oyama, Yui; Deshimaru, Masanobu

    2014-03-01

    Adenosine-to-inosine (A-to-I) RNA editing is an endogenous regulatory mechanism involved in various biological processes. Site-specific, editing-state-dependent degradation of target RNA may be a powerful tool both for analyzing the mechanism of RNA editing and for regulating biological processes. Previously, we designed an artificial hammerhead ribozyme (HHR) for selective, site-specific RNA cleavage dependent on the A-to-I RNA editing state. In the present work, we developed an improved strategy for constructing a trans-acting HHR that specifically cleaves target editing sites in the adenosine but not the inosine state. Specificity for unedited sites was achieved by utilizing a sequence encoding the intrinsic cleavage specificity of a natural HHR. We used in vitro selection methods in an HHR library to select for an extended HHR containing a tertiary stabilization motif that facilitates HHR folding into an active conformation. By using this method, we successfully constructed highly active HHRs with unedited-specific cleavage. Moreover, using HHR cleavage followed by direct sequencing, we demonstrated that this ribozyme could cleave serotonin 2C receptor (HTR2C) mRNA extracted from mouse brain, depending on the site-specific editing state. This unedited-specific cleavage also enabled us to analyze the effect of editing state at the E and C sites on editing at other sites by using direct sequencing for the simultaneous quantification of the editing ratio at multiple sites. Our approach has the potential to elucidate the mechanism underlying the interdependencies of different editing states in substrate RNA with multiple editing sites.

  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. The effect of the random distribution of electronic components in the output characteristics of the Howland current source

    Science.gov (United States)

    Bertemes-Filho, P.; Felipe, A.

    2013-04-01

    When a Howland source is designed, the components are chosen so that the designed source has the desired characteristics. However, the operational amplifier limitations and resistor tolerances causes undesired behaviours. This work proposes to take in account the influence of the random distribution of the commercial resistors in the Howland circuit over the frequency range of 10 Hz to 10 MHz. The probability density function due to small changes over the resistors was calculated by using an analytical model. Results show that both output current and impedance are very sensitive to the resistor tolerances. It is shown that the output impedance is very dependent on the open-loop gain of the Opamp rather than the resistor tolerances, especially at higher frequencies. This might improve the implementations of real current source used in electrical bioimpedance.

  2. Targeting and design methodology for reduction of fuel, power and CO{sub 2} on total sites

    Energy Technology Data Exchange (ETDEWEB)

    Klemes, J.; Dhole, V.R.; Raissi, K.; Perry, S.J. [University of Manchester Institute of Science and Technology, Manchester (United Kingdom); Puigjaner, L. [Universitat de Catalunya, Barcelona (Spain)

    1997-08-01

    Simultaneous optimisation of production processes and total site utility systems provides a novel methodology that can reduce energy demands and emission on a total factory site whilst simultaneously avoiding loss of cogeneration efficiency. This paper reports on the results of total sites where the application of the methodology has achieved savings in fuel of up to 20%, along with improvements in global CO{sub 2} levels and other emissions levels of at least 50% when compared to those achieved by application to individual processes. The novel methodology took into account the specific features of semi-continuous and batch operations and also the opportunities offered by the multi-objective optimisation of the design strategy for the total site. The environmental costs and potential for regulatory action were also incorporated. Software tools were developed to support total site approach which was subsequently tested and its capabilities validated by successfully solving various case studies from different industrial sectors. (author)

  3. Comparative study between fast and slow induction of propofol given by target-controlled infusion: expected propofol concentration at the effect site. Randomized controlled trial

    Directory of Open Access Journals (Sweden)

    Ricardo Francisco Simoni

    2015-04-01

    Full Text Available BACKGROUND AND OBJECTIVE: Studies have shown that the rate of propofol infusion may influence the predicted propofol concentration at the effect site (Es. The aim of this study was to evaluate the Es predicted by the Marsh pharmacokinetic model (ke0 0.26 min-1 in loss of consciousness during fast or slow induction. METHOD: The study included 28 patients randomly divided into two equal groups. In slow induction group (S, target-controlled infusion (TCI of propofol with plasma, Marsh pharmacokinetic model (ke0 0.26 min-1 with target concentration (Tc at 2.0-µg mL-1 were administered. When the predicted propofol concentration at the effect site (Es reached half of Es value, Es was increased to previous Es + 1 µg mL-1, successively, until loss of consciousness. In rapid induction group (R, patients were induced with TCI of propofol with plasma (6.0 µg mL-1 at effect site, and waited until loss of consciousness. RESULTS: In rapid induction group, Tc for loss of consciousness was significantly lower compared to slow induction group (1.67 ± 0.76 and 2.50 ± 0.56 µg mL-1, respectively, p = 0.004. CONCLUSION: The predicted propofol concentration at the effect site for loss of consciousness is different for rapid induction and slow induction, even with the same pharmacokinetic model of propofol and the same balance constant between plasma and effect site.

  4. Should historic sites protection be targeted at the most famous? Evidence from a contingent valuation in Scotland

    OpenAIRE

    Kuhfuss, Laure; Hanley, Nick; Whyte, Russell

    2016-01-01

    This research was supported by Historic Environment Scotland. We used a contingent valuation survey of a random sample of the general public living in Scotland to estimate how willingness to pay (WTP) for the conservation of historic sites (such as castles and stone circles) varies with how well-known these sites are and whether people have visited them. Each respondent was asked to state a maximum WTP in terms of higher income taxes for the conservation of two sites, one of which was "fam...

  5. Drugability of extracellular targets: discovery of small molecule drugs targeting allosteric, functional, and subunit-selective sites on GPCRs and ion channels.

    Science.gov (United States)

    Grigoriadis, Dimitri E; Hoare, Samuel R J; Lechner, Sandra M; Slee, Deborah H; Williams, John A

    2009-01-01

    Beginning with the discovery of the structure of deoxyribose nucleic acid in 1953, by James Watson and Francis Crick, the sequencing of the entire human genome some 50 years later, has begun to quantify the classes and types of proteins that may have relevance to human disease with the promise of rapidly identifying compounds that can modulate these proteins so as to have a beneficial and therapeutic outcome. This so called 'drugable space' involves a variety of membrane-bound proteins including the superfamily of G-protein-coupled receptors (GPCRs), ion channels, and transporters among others. The recent number of novel therapeutics targeting membrane-bound extracellular proteins that have reached the market in the past 20 years however pales in magnitude when compared, during the same timeframe, to the advancements made in the technologies available to aid in the discovery of these novel therapeutics. This review will consider select examples of extracellular drugable targets and focus on the GPCRs and ion channels highlighting the corticotropin releasing factor (CRF) type 1 and gamma-aminobutyric acid receptors, and the Ca(V)2.2 voltage-gated ion channel. These examples will elaborate current technological advancements in drug discovery and provide a prospective framework for future drug development.

  6. 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.

  7. Structure–function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

    Science.gov (United States)

    Teplova, Marianna; Hafner, Markus; Teplov, Dmitri; Essig, Katharina; Tuschl, Thomas; Patel, Dinshaw J.

    2013-01-01

    Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins. PMID:23630077

  8. Structure-function studies of STAR family Quaking proteins bound to their in vivo RNA target sites

    Energy Technology Data Exchange (ETDEWEB)

    Teplova, Marianna; Hafner, Markus; Teplov, Dmitri; Essig, Katharina; Tuschl, Thomas; Patel, Dinshaw J. [MSKCC; (Rockefeller)

    2013-09-27

    Mammalian Quaking (QKI) and its Caenorhabditis elegans homolog, GLD-1 (defective in germ line development), are evolutionarily conserved RNA-binding proteins, which post-transcriptionally regulate target genes essential for developmental processes and myelination. We present X-ray structures of the STAR (signal transduction and activation of RNA) domain, composed of Qua1, K homology (KH), and Qua2 motifs of QKI and GLD-1 bound to high-affinity in vivo RNA targets containing YUAAY RNA recognition elements (RREs). The KH and Qua2 motifs of the STAR domain synergize to specifically interact with bases and sugar-phosphate backbones of the bound RRE. Qua1-mediated homodimerization generates a scaffold that enables concurrent recognition of two RREs, thereby plausibly targeting tandem RREs present in many QKI-targeted transcripts. Structure-guided mutations reduced QKI RNA-binding affinity in vitro and in vivo, and expression of QKI mutants in human embryonic kidney cells (HEK293) significantly decreased the abundance of QKI target mRNAs. Overall, our studies define principles underlying RNA target selection by STAR homodimers and provide insights into the post-transcriptional regulatory function of mammalian QKI proteins.

  9. Impact of alternative respiration and target-site mutations on responses of germinating conidia of Magnaporthe grisea to Qo-inhibiting fungicides.

    Science.gov (United States)

    Avila-Adame, Cruz; Köller, Wolfram

    2003-03-01

    Qo-inhibiting fungicides act as respiration inhibitors by binding to the Qo center of cytochrome b. Sensitivities of fungi to Qo inhibitors can be influenced by the induction of alternative respiration or by mutational changes of the cytochrome b target site. Previous studies on both mechanisms in Magnaporthe grisea (Hebert) Barr were focused on the mycelial stage of the pathogen. The present study describes the expression and impact of both resistance mechanisms during the stage of conidia germination. In the absence of a host, alternative respiration provided a >500-fold rescue from azoxystrobin during the germination of conidia derived from four wild-type isolates of M. grisea. This rescue potential during conidia gemination was substantially more pronounced than for mycelial growth. However, the pronounced effectiveness of alternative respiration during conidia germination was not apparent when barley leaves were protected with azoxystrobin prior to inoculation with conidia. In a comparison of a wild-type strain and an alternative respiration-deficient mutant, azoxystrobin efficacies in suppressing symptom development differed by a factor of two, with full disease control achieved for both genotypes at 1 microg ml(-1) azoxystrobin. In contrast, conidia derived from two QoI-resistant target site mutants were highly resistant to azoxystrobin and trifloxystrobin and fully capable of infecting leaf surfaces protected with 10 microg ml(-1) of azoxystrobin. Both target-site mutants had emerged spontaneously in the presence of high azoxystrobin doses when residual mycelial growth was supported by alternative respiration. The effective silencing of alternative respiration in protective applications of Qo-inhibiting fungicides might constitute a strategy of slowing the emergence of highly resistant target site mutants.

  10. Haemodynamic consequences of targeted single- and dual-site right ventricular pacing in adults with congenital heart disease undergoing surgical pulmonary valve replacement

    Science.gov (United States)

    Plymen, Carla M.; Finlay, Malcolm; Tsang, Victor; O'leary, Justin; Picaut, Nathalie; Cullen, Shay; Walker, Fiona; Deanfield, John E; Hsia, T.Y.; Bolger, Aidan P.; Lambiase, Pier D.

    2015-01-01

    Aims The purpose of this study was to create an epicardial electroanatomic map of the right ventricle (RV) and then apply post-operative-targeted single- and dual-site RV temporary pacing with measurement of haemodynamic parameters. Cardiac resynchronization therapy is an established treatment for symptomatic left ventricular (LV) dysfunction. In congenital heart disease, RV dysfunction is a common cause of morbidity—little is known regarding the potential benefits of CRT in this setting. Methods and results Sixteen adults (age = 32 ± 8 years; 6 M, 10 F) with right bundle branch block (RBBB) and repaired tetralogy of Fallot (n = 8) or corrected congenital pulmonary stenosis (n = 8) undergoing surgical pulmonary valve replacement (PVR) for pulmonary regurgitation underwent epicardial RV mapping and haemodynamic assessment of random pacing configurations including the site of latest RV activation. The pre-operative pulmonary regurgitant fraction was 49 ± 10%; mean LV end-diastolic volume (EDV) 85 ± 19 mL/min/m2 and RVEDV 183 ± 89 mL/min/m2 on cardiac magnetic resonance imaging. The mean pre-operative QRS duration is 136 ± 26 ms. The commonest site of latest activation was the RV free wall and DDD pacing here alone or combined with RV apical pacing resulted in significant increases in cardiac output (CO) vs. AAI pacing (P < 0.01 all measures). DDDRV alternative site pacing significantly improved CO by 16% vs. AAI (P = 0.018), and 8.5% vs. DDDRV apical pacing (P = 0.02). Conclusion Single-site RV pacing targeted to the region of latest activation in patients with RBBB undergoing PVR induces acute improvements in haemodynamics and supports the concept of ‘RV CRT’. Targeted pacing in such patients has therapeutic potential both post-operatively and in the long term. PMID:25371427

  11. The relative contribution of target-site mutations in complex acaricide resistant phenotypes as assessed by marker assisted backcrossing in Tetranychus urticae.

    Science.gov (United States)

    Riga, Maria; Bajda, Sabina; Themistokleous, Christos; Papadaki, Stavrini; Palzewicz, Maria; Dermauw, Wannes; Vontas, John; Leeuwen, Thomas Van

    2017-08-23

    The mechanisms underlying insecticide and acaricide resistance in insects and mites are often complex, including additive effects of target-site insensitivity, increased metabolism and transport. The extent to which target-site resistance mutations contribute to the resistance phenotype is, however, not well studied. Here, we used marker-assisted backcrossing to create 30 congenic lines carrying nine mutations (alone, or in combination in a few cases) associated with resistance to avermectins, pyrethroids, mite growth inhibitors and mitochondrial complex III inhibitors (QoI) in a polyphagous arthropod pest, the spider mite Tetranychus urticae. Toxicity tests revealed that mutations in the voltage-gated sodium channel, chitin synthase 1 and cytochrome b confer high levels of resistance and, when fixed in a population, these mutations alone can result in field failure of acaricide treatment. In contrast, although we confirmed the implication of mutations in glutamate-gated chloride channels in abamectin and milbemectin insensitivity, these mutations do not lead to the high resistance levels that are often reported in abamectin resistant strains of T. urticae. Overall, this study functionally validates reported target-site resistance mutations in T. urticae, by uncoupling them from additional mechanisms, allowing to finally investigate the strength of the conferred phenotype in vivo.

  12. Particle bombardment-mediated transient expression to identify localization signals in plant disease resistance proteins and target sites for the proteolytic activity of pathogen effectors.

    Science.gov (United States)

    Takemoto, Daigo; Jones, David A

    2014-01-01

    Plant pathogens, including fungi, oomycetes, bacteria, aphids, and nematodes, produce a variety of effector proteins to counter plant disease resistance mechanisms. After delivery into the cytosol of the plant cell, effectors may target proteins localized to different compartments within the plant cell. Plants, in turn, have evolved disease resistance (R) proteins to recognize the action of effectors. Elucidation of the subcellular localization of pathogen effectors, the plant proteins they target, and plant disease resistance proteins is essential to fully understand their interactions during pathogen challenge. In recent years, expression of fluorescent protein fusions has been widely used to determine the subcellular localization of plant proteins and pathogen effectors. Use of fluorescent proteins enables researchers to monitor the dynamic behavior of proteins in living cells. Among various methods available for the introduction of genes into plant cells, particle bombardment-mediated transient expression is the most rapid method suitable for both the identification of localization signals in proteins of interest and their dissection via amino acid substitutions generated using site-directed mutagenesis. This chapter describes a rapid procedure for particle bombardment-mediated transient expression in leaf epidermal cells. This method is also applicable to detection of pathogen effector protease activities directed against target proteins in the plant cell and analysis of protease recognition sites within these target proteins.

  13. 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.

  14. High-power ultralong-wavelength Tm-doped silica fiber laser cladding-pumped with a random distributed feedback fiber laser

    OpenAIRE

    Xiaoxi Jin; Xueyuan Du; Xiong Wang; Pu Zhou; Hanwei Zhang; Xiaolin Wang; Zejin Liu

    2016-01-01

    We demonstrated a high-power ultralong-wavelength Tm-doped silica fiber laser operating at 2153?nm with the output power exceeding 18?W and the slope efficiency of 25.5%. A random distributed feedback fiber laser with the center wavelength of 1173?nm was employed as pump source of Tm-doped fiber laser for the first time. No amplified spontaneous emissions or parasitic oscillations were observed when the maximum output power reached, which indicates that employing 1173?nm random distributed fe...

  15. The effect of local anatomy on the electric field induced by TMS: evaluation at 14 different target sites

    NARCIS (Netherlands)

    Janssen, A.J.E.M.; Oostendorp, T.F.; Stegeman, D.F.

    2014-01-01

    Many human cortical regions are targeted with transcranial magnetic stimulation (TMS). The stimulus intensity used for a certain region is generally based on the motor threshold stimulation intensity determined over the motor cortex (M1). However, it is well known that differences exist in

  16. 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.

  17. Genetic variants in microRNAs and microRNA target sites predict biochemical recurrence after radical prostatectomy in localized prostate cancer.

    Science.gov (United States)

    Huang, Shu-Pin; Lévesque, Eric; Guillemette, Chantal; Yu, Chia-Cheng; Huang, Chao-Yuan; Lin, Victor C; Chung, I-Che; Chen, Lih-Chyang; Laverdière, Isabelle; Lacombe, Louis; Fradet, Yves; Chang, Ta-Yuan; Lee, Hong-Zin; Juang, Shin-Hun; Bao, Bo-Ying

    2014-12-01

    Recent evidence indicates that microRNAs might participate in prostate cancer initiation, progression and treatment response. Germline variations in microRNAs might alter target gene expression and modify the efficacy of prostate cancer therapy. To determine whether genetic variants in microRNAs and microRNA target sites are associated with the risk of biochemical recurrence (BCR) after radical prostatectomy (RP). We retrospectively studied two independent cohorts composed of 320 Asian and 526 Caucasian men with pathologically organ-confined prostate cancer who had a median follow-up of 54.7 and 88.8 months after RP, respectively. Patients were systematically genotyped for 64 single-nucleotide polymorphisms (SNPs) in microRNAs and microRNA target sites, and their prognostic significance on BCR was assessed by Kaplan-Meier analysis and Cox regression model. After adjusting for known clinicopathologic risk factors, two SNPs (MIR605 rs2043556 and CDON rs3737336) remained associated with BCR. The numbers of risk alleles showed a cumulative effect on BCR [perallele hazard ratio (HR) 1.60, 95% confidence interval (CI) 1.16-2.21, p for trend = 0.005] in Asian cohort, and the risk was replicated in Caucasian cohort (HR 1.55, 95% CI 1.15-2.08, p for trend = 0.004) and in combined analysis (HR 1.57, 95% CI 1.26-1.96, p for trend <0.001). Results warrant replication in larger cohorts. This is the first study demonstrating that SNPs in microRNAs and microRNA target sites can be predictive biomarkers for BCR after RP. © 2014 UICC.

  18. fhlA repression by OxyS RNA: kissing complex formation at two sites results in a stable antisense-target RNA complex.

    Science.gov (United States)

    Argaman, L; Altuvia, S

    2000-07-28

    OxyS is a small untranslated RNA that is induced in response to oxidative stress in Escherichia coli. This small RNA acts as a global regulator affecting the expression of multiple genes. OxyS represses the translation of fhlA, a transcriptional activator for formate metabolism. Previously, we have shown that fhlA repression by OxyS is mediated through base-pairing with a short sequence overlapping the ribosome binding site. Here we show that the OxyS-fhlA interaction involves a second site residing further downstream, within the coding region of fhlA. Mutations that disrupt pairing at this site affect the ability of OxyS to prevent 30 S ribosomes from binding to fhlA mRNA. Structure probing of fhlA mRNA demonstrates that both sites reside in the loops of two stem-loop structures. OxyS-fhlA pairing analysis shows that OxyS binds wild-type fhlA with an apparent dissociation constant of 25 nM, indicating that kissing complex formation between OxyS and fhlA results in a stable antisense-target complex. Mutations at either site, which disrupt pairing of OxyS to fhlA, decrease the stability of this complex. Our results indicate that kissing complex formation is sufficient to repress fhlA translation by OxyS. Copyright 2000 Academic Press.

  19. Site-specific modification of AAV vector particles with biophysical probes and targeting ligands using biotin ligase.

    Science.gov (United States)

    Stachler, Matthew D; Chen, Irwin; Ting, Alice Y; Bartlett, Jeffrey S

    2008-08-01

    We have developed a highly specific and robust new method for labeling adeno-associated virus (AAV) vector particles with either biophysical probes or targeting ligands. Our approach uses the Escherichia coli enzyme biotin ligase (BirA), which ligates biotin to a 15-amino-acid biotin acceptor peptide (BAP) in a sequence-specific manner. In this study we demonstrate that by using a ketone isotere of biotin as a cofactor we can ligate this probe to BAP-modified AAV capsids. Because ketones are absent from AAV, BAP-modified AAV particles can be tagged with the ketone probe and then specifically conjugated to hydrazide- or hydroxylamine-functionalized molecules. We demonstrate this two-stage modification methodology in the context of a mammalian cell lysate for the labeling of AAV vector particles with various fluorophores, and for the attachment of a synthetic cyclic arginine-glycine-aspartate (RGD) peptide (c(RGDfC)) to target integrin receptors that are present on neovasculature. Fluorophore labeling allowed the straightforward determination of intracellular particle distribution. Ligand conjugation mediated a significant increase in the transduction of endothelial cells in vitro, and permitted the intravascular targeting of AAV vectors to tumor-associated vasculature in vivo. These results suggest that this approach holds significant promise for future studies aimed at understanding and modifying AAV vector-cellular interactions.

  20. Genome-wide mapping indicates that p73 and p63 co-occupy target sites and have similar dna-binding profiles in vivo.

    Directory of Open Access Journals (Sweden)

    Annie Yang

    2010-07-01

    Full Text Available The p53 homologs, p63 and p73, share approximately 85% amino acid identity in their DNA-binding domains, but they have distinct biological functions.Using chromatin immunoprecipitation and high-resolution tiling arrays covering the human genome, we identify p73 DNA binding sites on a genome-wide level in ME180 human cervical carcinoma cells. Strikingly, the p73 binding profile is indistinguishable from the previously described binding profile for p63 in the same cells. Moreover, the p73:p63 binding ratio is similar at all genomic loci tested, suggesting that there are few, if any, targets that are specific for one of these factors. As assayed by sequential chromatin immunoprecipitation, p63 and p73 co-occupy DNA target sites in vivo, suggesting that p63 and p73 bind primarily as heterotetrameric complexes in ME180 cells.The observation that p63 and p73 associate with the same genomic targets suggest that their distinct biological functions are due to cell-type specific expression and/or protein domains that involve functions other than DNA binding.

  1. 3 UTR-located ALU Elements: Donors of Potetial miRNA Target Sites and Mediators of Network miRNA-based Regulatory Interactions

    Directory of Open Access Journals (Sweden)

    Ivan Minkov

    2006-01-01

    Full Text Available Recent research data reveal complex, network-based interactions between mobile elements and regulatory systems of eukaryotic cells. In this article, we focus on regulatory interactions between Alu elements and micro RNAs (miRNAs. Our results show that the majority of the Alu sequences inserted in 3’UTRs of analyzed human genes carry strong potential target sites for at least 53 different miRNAs. Thus, 3’UTR-locared Alu elements may play the role of mobile regulatory modules that supply binding sites for miRNA regulation. Their abundance and ability to distribute a set of certain miRNA target sites may have important role in establishment, extension, network-like organization, and, as we suppose – in the regulation and environment-dependent activation/inactivation of some elements of the miRNA regulatory system, as well as for a larger scale RNA-based regulatory interactions. The Alu-miRNA connection may be crucial especially for the primate/human evolution.

  2. Characterization of the minimum domain required for targeting budding yeast myosin II to the site of cell division

    Directory of Open Access Journals (Sweden)

    Tolliday Nicola J

    2006-06-01

    Full Text Available Abstract Background All eukaryotes with the exception of plants use an actomyosin ring to generate a constriction force at the site of cell division (cleavage furrow during mitosis and meiosis. The structure and filament forming abilities located in the C-terminal or tail region of one of the main components, myosin II, are important for localising the molecule to the contractile ring (CR during cytokinesis. However, it remains poorly understood how myosin II is recruited to the site of cell division and how this recruitment relates to myosin filament assembly. Significant conservation between species of the components involved in cytokinesis, including those of the CR, allows the use of easily genetically manipulated organisms, such as budding yeast (Saccharomyces cerevisiae, in the study of cytokinesis. Budding yeast has a single myosin II protein, named Myo1. Unlike most other class II myosins, the tail of Myo1 has an irregular coiled coil. In this report we use molecular genetics, biochemistry and live cell imaging to characterize the minimum localisation domain (MLD of budding yeast Myo1. Results We show that the MLD is a small region in the centre of the tail of Myo1 and that it is both necessary and sufficient for localisation of Myo1 to the yeast bud neck, the pre-determined site of cell division. Hydrodynamic measurements of the MLD, purified from bacteria or yeast, show that it is likely to exist as a trimer. We also examine the importance of a small region of low coiled coil forming probability within the MLD, which we call the hinge region. Removal of the hinge region prevents contraction of the CR. Using fluorescence recovery after photobleaching (FRAP, we show that GFP-tagged MLD is slightly more dynamic than the GFP-tagged full length molecule but less dynamic than the GFP-tagged Myo1 construct lacking the hinge region. Conclusion Our results define the intrinsic determinant for the localization of budding yeast myosin II and show

  3. 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

  4. Targeting a Single Alternative Polyadenylation Site Coordinately Blocks Expression of Androgen Receptor mRNA Splice Variants in Prostate Cancer.

    Science.gov (United States)

    Van Etten, Jamie L; Nyquist, Michael; Li, Yingming; Yang, Rendong; Ho, Yeung; Johnson, Rachel; Ondigi, Olivia; Voytas, Daniel F; Henzler, Christine; Dehm, Scott M

    2017-10-01

    Prostate cancer is the second leading cause of male cancer deaths due to disease progression to castration-resistant prostate cancer (CRPC). Androgen receptor (AR) splice variants including AR-V7 function as constitutively active transcription factors in CRPC cells, thereby promoting resistance to AR-targeted therapies. To date, there are no AR variant-specific treatments for CRPC. Here we report that the splicing of AR variants AR-V7 as well as AR-V1 and AR-V9 is regulated coordinately by a single polyadenylation signal in AR intron 3. Blocking this signal with morpholino technology or silencing of the polyadenylation factor CPSF1 caused a splice switch that inhibited expression of AR variants and blocked androgen-independent growth of CRPC cells. Our findings support the development of new therapies targeting the polyadenylation signal in AR intron 3 as a strategy to prevent expression of a broad array of AR variants in CRPC. Cancer Res; 77(19); 5228-35. ©2017 AACR. ©2017 American Association for Cancer Research.

  5. Targeting the GPIbα Binding Site of Thrombin To Simultaneously Induce Dual Anticoagulant and Antiplatelet Effects

    Science.gov (United States)

    2015-01-01

    Exosite 2 of human thrombin contributes to two opposing pathways, the anticoagulant pathway and the platelet aggregation pathway. We reasoned that an exosite 2 directed allosteric thrombin inhibitor should simultaneously induce anticoagulant and antiplatelet effects. To assess this, we synthesized SbO4L based on the sulfated tyrosine-containing sequence of GPIbα. SbO4L was synthesized in three simple steps in high yield and found to be a highly selective, direct inhibitor of thrombin. Michelis–Menten kinetic studies indicated a noncompetitive mechanism of inhibition. Competitive inhibition studies suggested ideal competition with heparin and glycoprotein Ibα, as predicted. Studies with site-directed mutants of thrombin indicated that SbO4L binds to Arg233, Lys235, and Lys236 of exosite 2. SbO4L prevented thrombin-mediated platelet activation and aggregation as expected on the basis of competition with GPIbα. SbO4L presents a novel paradigm of simultaneous dual anticoagulant and antiplatelet effects achieved through the GPIbα binding site of thrombin. PMID:24635452

  6. [Comparative study between fast and slow induction of propofol given by target-controlled infusion: expected propofol concentration at the effect site. Randomized controlled trial].

    Science.gov (United States)

    Simoni, Ricardo Francisco; Miziara, Luiz Eduardo de Paula Gomes; Esteves, Luis Otávio; Silva, Diógenes de Oliveira; Ribeiro, Cristina Alves; Smith, Mariana Oki; Paula, Leonardo Ferreira de; Cangiani, Luis Henrique

    2015-01-01

    studies have shown that rate of propofol infusion may influence the predicted propofol concentration at the effect site (Es). The aim of this study was to evaluate the Es predicted by the Marsh pharmacokinetic model (ke0 0.26min(-1)) in loss of consciousness during fast or slow induction. the study included 28 patients randomly divided into two equal groups. In slow induction group (S), target-controlled infusion (TCI) of propofol with plasma, Marsh pharmacokinetic model (ke0 0.26min(-1)) with target concentration (Tc) at 2.0-μg.mL(-1) were administered. When the predicted propofol concentration at the effect site (Es) reached half of Es value, Es was increased to previous Es + 1μg.mL(-1), successively, until loss of consciousness. In rapid induction group (R), patients were induced with TCI of propofol with plasma (6.0μg.ml(-1)) at Es, and waited until loss of consciousness. in rapid induction group, Tc for loss of consciousness was significantly lower compared to slow induction group (1.67±0.76 and 2.50±0.56μg.mL(-1), respectively, p=0.004). the predicted propofol concentration at the effect site for loss of consciousness is different for rapid induction and slow induction, even with the same pharmacokinetic model of propofol and the same balance constant between plasma and effect site. Copyright © 2014 Sociedade Brasileira de Anestesiologia. Publicado por Elsevier Editora Ltda. All rights reserved.

  7. Non Random Distribution of DMD Deletion Breakpoints and Implication of Double Strand Breaks Repair and Replication Error Repair Mechanisms.

    Science.gov (United States)

    Marey, Isabelle; Ben Yaou, Rabah; Deburgrave, Nathalie; Vasson, Aurélie; Nectoux, Juliette; Leturcq, France; Eymard, Bruno; Laforet, Pascal; Behin, Anthony; Stojkovic, Tanya; Mayer, Michèle; Tiffreau, Vincent; Desguerre, Isabelle; Boyer, François Constant; Nadaj-Pakleza, Aleksandra; Ferrer, Xavier; Wahbi, Karim; Becane, Henri-Marc; Claustres, Mireille; Chelly, Jamel; Cossee, Mireille

    2016-05-27

    Dystrophinopathies are mostly caused by copy number variations, especially deletions, in the dystrophin gene (DMD). Despite the large size of the gene, deletions do not occur randomly but mainly in two hot spots, the main one involving exons 45 to 55. The underlying mechanisms are complex and implicate two main mechanisms: Non-homologous end joining (NHEJ) and micro-homology mediated replication-dependent recombination (MMRDR). Our goals were to assess the distribution of intronic breakpoints (BPs) in the genomic sequence of the main hot spot of deletions within DMD gene and to search for specific sequences at or near to BPs that might promote BP occurrence or be associated with DNA break repair. Using comparative genomic hybridization microarray, 57 deletions within the intron 44 to 55 region were mapped. Moreover, 21 junction fragments were sequenced to search for specific sequences. Non-randomly distributed BPs were found in introns 44, 47, 48, 49 and 53 and 50% of BPs clustered within genomic regions of less than 700bp. Repeated elements (REs), known to promote gene rearrangement via several mechanisms, were present in the vicinity of 90% of clustered BPs and less frequently (72%) close to scattered BPs, illustrating the important role of such elements in the occurrence of DMD deletions. Palindromic and TTTAAA sequences, which also promote DNA instability, were identified at fragment junctions in 20% and 5% of cases, respectively. Micro-homologies (76%) and insertions or deletions of small sequences were frequently found at BP junctions. Our results illustrate, in a large series of patients, the important role of RE and other genomic features in DNA breaks, and the involvement of different mechanisms in DMD gene deletions: Mainly replication error repair mechanisms, but also NHEJ and potentially aberrant firing of replication origins. A combination of these mechanisms may also be possible.

  8. A peptide mimetic targeting trans-homophilic NCAM binding sites promotes spatial learning and neural plasticity in the hippocampus

    DEFF Research Database (Denmark)

    Kraev, Igor; Henneberger, Christian; Rossetti, Clara

    2011-01-01

    cultures and improves spatial learning in rats, both under basal conditions and under conditions involving a deficit in a key plasticity-promoting posttranslational modification of NCAM, its polysialylation. We also found that plannexin enhances excitatory synaptic transmission in hippocampal area CA1......, where it also increases the number of mushroom spines and the synaptic expression of the AMPAR subunits GluA1 and GluA2. Altogether, these findings provide compelling evidence that plannexin is an important facilitator of synaptic functional, structural and molecular plasticity in the hippocampal CA1......The key roles played by the neural cell adhesion molecule (NCAM) in plasticity and cognition underscore this membrane protein as a relevant target to develop cognitive-enhancing drugs. However, NCAM is a structurally and functionally complex molecule with multiple domains engaged in a variety...

  9. Genetic variations creating microRNA target sites in the FXN 3'-UTR affect frataxin expression in Friedreich ataxia.

    Directory of Open Access Journals (Sweden)

    Simonetta Bandiera

    Full Text Available Friedreich's ataxia (FRDA is a severe neurodegenerative disease caused by GAA repeat expansion within the first intron of the frataxin gene. It has been suggested that the repeat is responsible for the disease severity due to impaired transcription thereby reducing expression of the protein. However, genotype-phenotype correlation is imperfect, and the influence of other gene regions of the frataxin gene is unknown. We hypothesized that FRDA patients may harbor specific regulatory variants in the 3'-UTR. We sequenced the 3'-UTR region of the frataxin gene in a cohort of 57 FRDA individuals and 58 controls. Seven single nucleotide polymorphisms (SNPs out of 19 were polymorphic in our case-control sample. These SNPs defined several haplotypes with one reaching 89% of homozygosity in patients versus 24% in controls. In another cohort of 47 FRDA Reunionese patients, 94% patients were found to be homozygous for this haplotype. We found that this FRDA 3'-UTR conferred a 1.2-fold decrease in the expression of a reporter gene versus the alternative haplotype configuration. We established that differential targeting by miRNA could account for this functional variability. We specifically demonstrated the involvement of miR-124 (i.e hsa-mir-124-3p in the down-regulation of FRDA-3'-UTR. Our results suggest for the first time that post-transcriptional regulation of frataxin occurs through the 3'-UTR and involves miRNA targeting. We propose that the involvement of miRNAs in a FRDA-specific regulation of frataxin may provide a rationale to increase residual levels of frataxin through miRNA-inhibitory molecules.

  10. Targeted identification of infection-related HLA class I-presented epitopes by stable isotope tagging of epitopes (SITE).

    Science.gov (United States)

    Meiring, H D; Soethout, E C; de Jong, A P J M; van Els, C A C M

    2007-05-01

    Identification of peptides presented in human leukocyte antigen (HLA) class I molecules after viral infection is of strategic importance for immunology and vaccine development. A powerful strategy aimed at the rapid, unambiguous identification of naturally processed HLA class I-associated peptides, which are induced by viral infection, is presented here. The methodology, stable isotope tagging of epitopes (SITE), is based on metabolic labeling of endogenously synthesized proteins during infection. This is accomplished by culturing virus-infected cells with stable isotope-labeled amino acids that are expected to be anchor residues for the human leukocyte antigen allele of interest. Subsequently, these cells are mixed with an equal number of noninfected cells, which are cultured in normal medium. Finally, peptides are acid-eluted from immunoprecipitated HLA molecules and subjected to two-dimensional nanoscale liquid chromatography-mass spectrometry analysis. Virus-induced peptides are identified through computer-assisted detection of characteristic, binomially distributed ratios of labeled and unlabeled molecules.

  11. Passive Fluidic Chip Composed of Integrated Vertical Capillary Tubes Developed for On-Site SPR Immunoassay Analysis Targeting Real Samples

    Directory of Open Access Journals (Sweden)

    Tsuneyuki Haga

    2012-05-01

    Full Text Available We have successfully developed a surface plasmon resonance (SPR measurement system for the on-site immunoassay of real samples. The system is composed of a portable SPR instrument (290 mm(W x 160 mm(D x 120 mm(H and a microfluidic immunoassay chip (16 mm(W x 16 mm(D x 4 mm(H that needs no external pump system. An integrated vertical capillary tube functions as a large volume (150 μL passive pump and a waste reservoir that has sufficient capacity for several refill operations. An immunoassay was carried out that employed the direct injection of a buffer and a test sample in sequence into a microfluidic chip that included 9 antibody bands and 10 reference reagent bands immobilized in the flow channel. By subtracting a reliable averaged reference sensorgram from the antibody, we effectively reduced the influence of the non-specific binding, and then our chip successfully detected the specific binding of spiked IgG in non-homogeneous milk. IgG is a model antigen that is certain not to be present in non-homogeneous milk, and non-homogeneous milk is a model of real sample that includes many interfering foreign substances that induce non-specific binding. The direct injection of a real sample with no pretreatment enabled us to complete the entire immunoassay in several minutes. This ease of operation and short measuring time are acceptable for on-site agricultural, environmentaland medical testing.

  12. 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.

  13. Modelling site-specific N2O emission factors from Austrian agricultural soils for targeted mitigation measures (NitroAustria)

    Science.gov (United States)

    Amon, Barbara; Zechmeister-Boltenstern, Sophie; Kasper, Martina; Foldal, Cecilie; Schiefer, Jasmin; Kitzler, Barbara; Schwarzl, Bettina; Zethner, Gerhard; Anderl, Michael; Sedy, Katrin; Gaugitsch, Helmut; Dersch, Georg; Baumgarten, Andreas; Haas, Edwin; Kiese, Ralf

    2016-04-01

    Results from a previous project "FarmClim" highlight that the IPCC default emission factor is not able to reflect region specific N2O emissions from Austrian arable soils. The methodology is limited in identifying hot spots and hot moments of N2O emissions. When estimations are based on default emission factors no recommendations can be given on optimisation measures that would lead to a reduction of soil N2O emissions. The better the knowledge is about Nitrogen and Carbon budgets in Austrian agricultural managed soils the better the situation can be reflected in the Austrian GHG emission inventory calculations. Therefore national and regionally modelled emission factors should improve the evidence for national deviation from the IPCC default emission factors and reduce the uncertainties. The overall aim of NitroAustria is to identify the drivers for N2O emissions on a regional basis taking different soil types, climate, and agricultural management into account. We use the LandscapeDNDC model to update the N2O emission factors for N fertilizer and animal manure applied to soils. Key regions in Austria were selected and region specific N2O emissions calculated. The model runs at sub-daily time steps and uses data such as maximum and minimum air temperature, precipitation, radiation, and wind speed as meteorological drivers. Further input data are used to reflect agricultural management practices, e.g., planting/harvesting, tillage, fertilizer application, irrigation and information on soil and vegetation properties for site characterization and model initialization. While at site scale, arable management data (crop cultivation, rotations, timings etc.) is obtained by experimental data from field trials or observations, at regional scale such data need to be generated using region specific proxy data such as land use and management statistics, crop cultivations and yields, crop rotations, fertilizer sales, manure resulting from livestock units etc. The farming

  14. 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

  15. Qualitative Sybr Green real-time detection of single nucleotide polymorphisms responsible for target-site resistance in insect pests: the example of Myzus persicae and Musca domestica.

    Science.gov (United States)

    Puggioni, V; Chiesa, O; Panini, M; Mazzoni, E

    2017-02-01

    Chemical insecticides have been widely used to control insect pests, leading to the selection of resistant populations. To date, several single nucleotide polymorphisms (SNPs) have already been associated with insecticide resistance, causing reduced sensitivity to many classes of products. Monitoring and detection of target-site resistance is currently one of the most important factors for insect pest management strategies. Several methods are available for this purpose: automated and high-throughput techniques (i.e. TaqMan or pyrosequencing) are very costly; cheaper alternatives (i.e. RFLP or PASA-PCRs) are time-consuming and limited by the necessity of a final visualization step. This work presents a new approach (QSGG, Qualitative Sybr Green Genotyping) which combines the specificity of PASA-PCR with the rapidity of real-time PCR analysis. The specific real-time detection of Cq values of wild-type or mutant alleles (amplified used allele-specific primers) allows the calculation of ΔCqW-M values and the consequent identification of the genotypes of unknown samples, on the basis of ranges previously defined with reference clones. The methodology is applied here to characterize mutations described in Myzus persicae and Musca domestica and we demonstrate it represents a valid, rapid and cost-effective technique that can be adopted for monitoring target-site resistance in field populations of these and other insect species.

  16. Identifying the antiasthmatic target of doxofylline using immobilized β2 -adrenoceptor based high-performance affinity chromatography and site-directed molecular docking.

    Science.gov (United States)

    Zhang, Yajun; Zeng, Kaizhu; Wang, Jing; Gao, Haiyang; Nan, Yefei; Zheng, Xiaohui

    2016-10-01

    As a xanthine derivative, doxofylline is believed to be dominant for fighting against asthma in practice. Unlike other xanthines, the antiasthmatic effects of doxofylline lack any definite proof of target and mediating mechanism according to previous reports. In this work, the interaction between doxofylline and β2 -AR was investigated by high performance affinity chromatography using frontal analysis and nonlinear model. The methodology involved the immobilization of β2 -AR on the silica gel by a random linking method, the determination of the binding parameters by frontal analysis and nonlinear chromatography and the exploration of the binding mechanism by site-directed molecular docking. The association constant for doxofylline binding to immobilized β2 -AR was determined to be 7.70 × 10(4)  M(-1) by nonlinear chromatography and 5.91 × 10(4)  M(-1) by frontal analysis. Ser(169) and Ser(173) were the binding sites for the receptor-drug interaction on which hydrogen bond was believed to be the main driven force during the interaction. These results indicated that the antiasthmatic effects of doxofylline may be behind the mediating mechanism of β2 -AR. High performance affinity chromatography based on immobilized receptor has potential to become an alternative for drug target confirmation and drug-receptor interaction analysis. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  17. Left Ventricular Lead Placement Targeted at the Latest Activated Site Guided by Electrophysiological Mapping in Coronary Sinus Branches Improves Response to Cardiac Resynchronization Therapy.

    Science.gov (United States)

    Liang, Yanchun; Yu, Haibo; Zhou, Weiwei; Xu, Guoqing; Sun, Y I; Liu, Rong; Wang, Zulu; Han, Yaling

    2015-12-01

    Electrophysiological mapping (EPM) in coronary sinus (CS) branches is feasible for guiding LV lead placement to the optimal, latest activated site at cardiac resynchronization therapy (CRT) procedures. However, whether this procedure optimizes the response to CRT has not been demonstrated. This study was to evaluate effects of targeting LV lead at the latest activated site guided by EPM during CRT. Seventy-six consecutive patients with advanced heart failure who were referred for CRT were divided into mapping (MG) and control groups (CG). In MG, the LV lead, also used as a mapping bipolar electrode, was placed at the latest activated site determined by EPM in CS branches. In CG, conventional CRT procedure was performed. Patients were followed for 6 months after CRT. Baseline characteristics were comparable between the 2 groups. In MG (n = 29), EPM was successfully performed in 85 of 91 CS branches during CRT. A LV lead was successfully placed at the latest activated site guided by EPM in 27 (93.1%) patients. Compared with CG (n = 47), MG had a significantly higher rate (86.2% vs. 63.8%, P = 0.039) of response (>15% reduction in LV end-systolic volume) to CRT, a higher percentage of patients with clinical improvement of ≥2 NYHA functional classes (72.4% vs. 44.7%, P = 0.032), and a shorter QRS duration (P = 0.004). LV lead placed at the latest activated site guided by EPM resulted in a significantly greater CRT response, and a shorter QRS duration. © 2015 Wiley Periodicals, Inc.

  18. Redesign of a Rural Building in a Heritage Site in Italy: Towards the Net Zero Energy Target

    Directory of Open Access Journals (Sweden)

    Maurizio Cellura

    2017-07-01

    Full Text Available In order to achieve the ambitious objective of decarbonising the economy, it is mandatory, especially in Europe and in Italy, to include the retrofitting of existing buildings. In a country where a large share of existing buildings have heritage value, it is important to design effective retrofit solutions also in historical buildings. In this context, the paper describes the experience of re-design of an existing rural building located in Sicily, inside the ancient Greeks' “Valley of the Temples”. An energy audit was performed on the building, and its energy uses were thoroughly investigated. A building model was developed in the TRNSYS environment and its performances validated. The validated model was used for redesign studies aimed towards the achievement of the Net Zero Energy Building target. The best performing solutions to be applied to a case study like the Sanfilippo House were those regarding the management of the building, as in the case of the natural ventilation and the energy systems setpoints, that would allow a large impact (up to 10% reductions in energy uses on the energy performances of the building with no invasiveness, and those with very limited invasiveness and high impact on the energy efficiency of the building, as in the lighting scenario (up to 30% energy uses reduction. The most invasive actions can only be justified in the case of high energy savings, as in the case of the insulation of the roof, otherwise they should be disregarded.

  19. Pharmacological Targeting Of Neuronal Kv7.2/3 Channels: A Focus On Chemotypes And Receptor Sites.

    Science.gov (United States)

    Miceli, Francesco; Soldovieri, Maria Virginia; Ambrosino, Paolo; Manocchio, Laura; Medoro, Alessandro; Mosca, Ilaria; Taglialatela, Maurizio

    2017-10-12

    The Kv7 (KCNQ) subfamily of voltage-gated potassium channels consists of 5 members (Kv7.1-5) each showing a characteristic tissue distribution and physiological roles. Given their functional heterogeneity, Kv7 channels represent important pharmacological targets for development of new drugs for neuronal, cardiac and metabolic diseases. In the present manuscript, we focus on describing the pharmacological relevance and the potential therapeutic applications of drugs acting on neuronally-expressed Kv7.2/3 channels, placing particular emphasis on the different modulator chemotypes, and highlighting their pharmacodynamic and, whenever possible, pharmacokinetic peculiarities. The present work is based on an in-depth search of the currently available scientific literature, and on our own experience and knowledge in the field of neuronal Kv7 channel pharmacology. Space limitations impeded to describe the full pharmacological potential of Kv7 channels; thus, we have chosen to focus on neuronal channels composed of Kv7.2 and Kv7.3 subunits, and to mainly concentrate on their involvement in epilepsy. An astonishing heterogeneity in the molecular scaffolds exploitable to develop Kv7.2/3 modulators is evident, with important structural/functional peculiarities of distinct compound classes. In the present work we have attempted to show the current status and growing potential of the Kv7 pharmacology field. We anticipate a bright future for the field, and we express our hopes that the efforts herein reviewed will result in an improved treatment of hyperexcitability (or any other) diseases. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  20. The Effects of a MAP2K5 MicroRNA Target Site SNP on Risk for Anxiety and Depressive Disorders

    Science.gov (United States)

    Jensen, Kevin P.; Kranzler, Henry R.; Stein, Murray B.; Gelernter, Joel

    2014-01-01

    Functional variants that contribute to genomewide association study (GWAS) signals are difficult to identify. MicroRNAs could contribute to some of these gene-trait relationships. We compiled a set of GWAS trait gene SNPs that were predicted to affect microRNA regulation of mRNA. Trait associations were tested in a sample of 6725 European-American (EA) and African-American (AA) subjects that were interviewed using the polydiagnostic SSADDA to diagnose major psychiatric disorders. A predicted miR-330-3p target site SNP (rs41305272) in mitogen-activated protein kinase kinase 5 (MAP2K5) mRNA was in LD (d’=1.0, r2=0.02) with a reported GWAS-identified variant for restless legs syndrome (RLS), a disorder frequently comorbid with anxiety and depression, possibly because of a shared pathophysiology. We examined the SNP’s association with mood and anxiety-related disorders. Rs41305272 was associated with agoraphobia (Ag) in EAs (odds ratio[OR]=1.95, p=0.007; 195 cases) and AAs (OR=3.2, p=0.03; 148 cases) and major depressive disorder (MDD) in AAs (OR=2.64, p=0.01; 427 cases), but not EAs (465 cases). Rs41305272*T carrier frequency was correlated with the number of anxiety and depressive disorders diagnosed per subject. RLS was not evaluated in our subjects. Predicted miR-330-3p target genes were enriched in pathways relevant to psychiatric disorders. These findings suggest that microRNA target site information may be useful in the analysis of GWAS signals for complex traits. MiR-330-3p and MAP2K5 are potentially important contributors to mood and anxiety-related traits. With support from additional studies, these findings could add to the large number of risk genes identified through association to medical disorders that have primary psychiatric effects. PMID:24436253

  1. Comparison of Target-Capture and Restriction-Site Associated DNA Sequencing for Phylogenomics: A Test in Cardinalid Tanagers (Aves, Genus: Piranga).

    Science.gov (United States)

    Manthey, Joseph D; Campillo, Luke C; Burns, Kevin J; Moyle, Robert G

    2016-07-01

    Restriction-site associated DNA sequencing (RAD-seq) and target capture of specific genomic regions, such as ultraconserved elements (UCEs), are emerging as two of the most popular methods for phylogenomics using reduced-representation genomic data sets. These two methods were designed to target different evolutionary timescales: RAD-seq was designed for population-genomic level questions and UCEs for deeper phylogenetics. The utility of both data sets to infer phylogenies across a variety of taxonomic levels has not been adequately compared within the same taxonomic system. Additionally, the effects of uninformative gene trees on species tree analyses (for target capture data) have not been explored. Here, we utilize RAD-seq and UCE data to infer a phylogeny of the bird genus Piranga The group has a range of divergence dates (0.5-6 myr), contains 11 recognized species, and lacks a resolved phylogeny. We compared two species tree methods for the RAD-seq data and six species tree methods for the UCE data. Additionally, in the UCE data, we analyzed a complete matrix as well as data sets with only highly informative loci. A complete matrix of 189 UCE loci with 10 or more parsimony informative (PI) sites, and an approximately 80% complete matrix of 1128 PI single-nucleotide polymorphisms (SNPs) (from RAD-seq) yield the same fully resolved phylogeny of Piranga We inferred non-monophyletic relationships of Piranga lutea individuals, with all other a priori species identified as monophyletic. Finally, we found that species tree analyses that included predominantly uninformative gene trees provided strong support for different topologies, with consistent phylogenetic results when limiting species tree analyses to highly informative loci or only using less informative loci with concatenation or methods meant for SNPs alone. © The Author(s) 2016. Published by Oxford University Press, on behalf of the Society of Systematic Biologists. All rights reserved. For Permissions

  2. Predicted binding site information improves model ranking in protein docking using experimental and computer-generated target structures.

    Science.gov (United States)

    Maheshwari, Surabhi; Brylinski, Michal

    2015-11-23

    Protein-protein interactions (PPIs) mediate the vast majority of biological processes, therefore, significant efforts have been directed to investigate PPIs to fully comprehend cellular functions. Predicting complex structures is critical to reveal molecular mechanisms by which proteins operate. Despite recent advances in the development of new methods to model macromolecular assemblies, most current methodologies are designed to work with experimentally determined protein structures. However, because only computer-generated models are available for a large number of proteins in a given genome, computational tools should tolerate structural inaccuracies in order to perform the genome-wide modeling of PPIs. To address this problem, we developed eRank(PPI), an algorithm for the identification of near-native conformations generated by protein docking using experimental structures as well as protein models. The scoring function implemented in eRank(PPI) employs multiple features including interface probability estimates calculated by eFindSite(PPI) and a novel contact-based symmetry score. In comparative benchmarks using representative datasets of homo- and hetero-complexes, we show that eRank(PPI) consistently outperforms state-of-the-art algorithms improving the success rate by ~10 %. eRank(PPI) was designed to bridge the gap between the volume of sequence data, the evidence of binary interactions, and the atomic details of pharmacologically relevant protein complexes. Tolerating structure imperfections in computer-generated models opens up a possibility to conduct the exhaustive structure-based reconstruction of PPI networks across proteomes. The methods and datasets used in this study are available at www.brylinski.org/erankppi.

  3. 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

  4. Perturbation of discrete sites on a single protein domain with RNA aptamers: targeting of different sides of the TATA-binding protein (TBP).

    Science.gov (United States)

    Hohmura, Ken I; Shi, Hua; Hirayoshi, Kazunori

    2013-01-01

    Control of interactions among proteins is critical in the treatment of diseases, but the specificity required is not easily incorporated into small molecules. Macromolecules could be more suitable as antagonists in this situation, and RNA aptamers have become particularly promising. Here we describe a novel selection procedure for RNA aptamers against a protein that constitutes a single structural domain, the Drosophila TATA-binding protein (TBP). In addition to the conventional filter partitioning method with free TBP as target, we performed another experiment, in which the TATA-bound form of TBP was targeted. Aptamers generated by both selections were able to bind specifically to TBP, but the two groups showed characteristics which were clearly different in terms of their capability to compete with TATA-DNA, their effects on the TATA-bound form of TBP, and their effects on in vitro transcription. The method used to generate these two groups of aptamers can be used with other targets to direct aptamer specificity to discrete sites on the surface of a protein.

  5. Prediction of effect-site concentration of sufentanil by dose-response target controlled infusion of sufentanil and propofol for analgesic and sedation maintenance in burn dressing changes.

    Science.gov (United States)

    Chen, Lingyang; Wang, Mingcang; Xiang, Haifei; Lin, Xianju; Cao, Donghang; Ye, Liyue

    2014-05-01

    This study was to investigate the feasibility and efficiency of by target-controlled infusion (TCI) for analgesia and sedation during burn dressing change, and to predict the effect-site concentration of sufentanil. Eighty burn patients were randomly and evenly divided into four groups according to target sufentanil effect-site concentration (0.2, 0.3, 0.4 and 0.5 ng/ml). The sufentanil-propofol TCI was carried out during dressing changes. The effect-site concentration of propofol was maintained at 1.2 μg/ml. The dose-response relationships of sufentanil for providing adequate analgesia were evaluated by visual analog scales and Ramsay sedation scores. The effect-site concentration of sufentanil was calculated by Probit regression analysis. Incidence of respiratory depression, doctors and patients' satisfaction and adverse events were assessed. The EC50 and EC95 of sufentanil to maintain anesthesia for uncovering the inner layer dressings during TCI were 0.278 ng/ml (95% CI 0.231-0.318 ng/ml) and 0.394 ng/ml (95% CI 0.366-0.530 ng/ml), respectively, while the EC50 and EC95 of sufentanil to maintain anesthesia for wound management were 0.349 ng/ml (95% CI 0.299-0.366 ng/ml) and 0.465 ng/ml (95% CI 0.430-0.563 ng/ml), respectively. Doctors and patients' satisfaction were significantly higher in the 0.4 and 0.5 ng/ml groups than the 0.2 ng/ml group. One and three patients had respiratory depression in the 0.4 and 0.5 ng/ml groups, respectively. No adverse events occurred after operations. In conclusion, low dose sufentanil-propofol TCI for anesthesia and sedation maintenance in burn dressing changes is feasible and effective, and wound management requires higher effect-site concentrations of sufentanil than disclosing inner layer dressings. Copyright © 2013 Elsevier Ltd and ISBI. All rights reserved.

  6. Membrane docking geometry of GRP1 PH domain bound to a target lipid bilayer: an EPR site-directed spin-labeling and relaxation study.

    Directory of Open Access Journals (Sweden)

    Huai-Chun Chen

    Full Text Available The second messenger lipid PIP(3 (phosphatidylinositol-3,4,5-trisphosphate is generated by the lipid kinase PI3K (phosphoinositide-3-kinase in the inner leaflet of the plasma membrane, where it regulates a broad array of cell processes by recruiting multiple signaling proteins containing PIP(3-specific pleckstrin homology (PH domains to the membrane surface. Despite the broad importance of PIP(3-specific PH domains, the membrane docking geometry of a PH domain bound to its target PIP(3 lipid on a bilayer surface has not yet been experimentally determined. The present study employs EPR site-directed spin labeling and relaxation methods to elucidate the membrane docking geometry of GRP1 PH domain bound to bilayer-embedded PIP(3. The model target bilayer contains the neutral background lipid PC and both essential targeting lipids: (i PIP(3 target lipid that provides specificity and affinity, and (ii PS facilitator lipid that enhances the PIP(3 on-rate via an electrostatic search mechanism. The EPR approach measures membrane depth parameters for 18 function-retaining spin labels coupled to the PH domain, and for calibration spin labels coupled to phospholipids. The resulting depth parameters, together with the known high resolution structure of the co-complex between GRP1 PH domain and the PIP(3 headgroup, provide sufficient constraints to define an optimized, self-consistent membrane docking geometry. In this optimized geometry the PH domain engulfs the PIP(3 headgroup with minimal bilayer penetration, yielding the shallowest membrane position yet described for a lipid binding domain. This binding interaction displaces the PIP(3 headgroup from its lowest energy position and orientation in the bilayer, but the headgroup remains within its energetically accessible depth and angular ranges. Finally, the optimized docking geometry explains previous biophysical findings including mutations observed to disrupt membrane binding, and the rapid lateral

  7. Targeted, Site-specific quantitation of N- and O-glycopeptides using 18O-labeling and product ion based mass spectrometry.

    Science.gov (United States)

    Srikanth, Jandhyam; Agalyadevi, Rathinasamy; Babu, Ponnusamy

    2017-02-01

    The site-specific quantitation of N- and O-glycosylation is vital to understanding the function(s) of different glycans expressed at a given site of a protein under physiological and disease conditions. Most commonly used precursor ion intensity based quantification method is less accurate and other labeled methods are expensive and require enrichment of glycopeptides. Here, we used glycopeptide product (y and Y0) ions and 18O-labeling of C-terminal carboxyl group as a strategy to obtain quantitative information about fold-change and relative abundance of most of the glycoforms attached to the glycopeptides. As a proof of concept, the accuracy and robustness of this targeted, relative quantification LC-MS method was demonstrated using Rituximab. Furthermore, the N-glycopeptide quantification results were compared with a biosimilar of Rituximab and validated with quantitative data obtained from 2-AB-UHPLC-FL method. We further demonstrated the intensity fold-change and relative abundance of 46 unique N- and O-glycopeptides and aglycopeptides from innovator and biosimilar samples of Etanercept using both the normal-MS and product ion based quantitation. The results showed a very similar site-specific expression of N- and O-glycopeptides between the samples but with subtle differences. Interestingly, we have also been able to quantify macro-heterogeneity of all N- and O-glycopetides of Etanercept. In addition to applications in biotherapeutics, the developed method can also be used for site-specific quantitation of N- and O-glycopeptides and aglycopeptides of glycoproteins with known glycosylation pattern.

  8. Activation-induced cytidine deaminase targets SUV4-20-mediated histone H4K20 trimethylation to class-switch recombination sites.

    Science.gov (United States)

    Rodríguez-Cortez, Virginia C; Martínez-Redondo, Paloma; Català-Moll, Francesc; Rodríguez-Ubreva, Javier; Garcia-Gomez, Antonio; Poorani-Subramani, Ganesh; Ciudad, Laura; Hernando, Henar; Pérez-García, Arantxa; Company, Carlos; Urquiza, José M; Ramiro, Almudena R; Di Noia, Javier M; Vaquero, Alejandro; Ballestar, Esteban

    2017-08-08

    Activation-induced cytidine deaminase (AID) triggers antibody diversification in B cells by catalysing deamination and subsequently mutating immunoglobulin (Ig) genes. Association of AID with RNA Pol II and occurrence of epigenetic changes during Ig gene diversification suggest participation of AID in epigenetic regulation. AID is mutated in hyper-IgM type 2 (HIGM2) syndrome. Here, we investigated the potential role of AID in the acquisition of epigenetic changes. We discovered that AID binding to the IgH locus promotes an increase in H4K20me3. In 293F cells, we demonstrate interaction between co-transfected AID and the three SUV4-20 histone H4K20 methyltransferases, and that SUV4-20H1.2, bound to the IgH switch (S) mu site, is replaced by SUV4-20H2 upon AID binding. Analysis of HIGM2 mutants shows that the AID truncated form W68X is impaired to interact with SUV4-20H1.2 and SUV4-20H2 and is unable to bind and target H4K20me3 to the Smu site. We finally show in mouse primary B cells undergoing class-switch recombination (CSR) that AID deficiency associates with decreased H4K20me3 levels at the Smu site. Our results provide a novel link between SUV4-20 enzymes and CSR and offer a new aspect of the interplay between AID and histone modifications in setting the epigenetic status of CSR sites.

  9. Isolation of novel single-chain Cro proteins targeted for binding to the bcl-2 transcription initiation site by repertoire selection and subunit combinatorics.

    Science.gov (United States)

    Jonas, Kristina; Van Der Vries, Erhard; Nilsson, Mikael T I; Widersten, Mikael

    2005-11-01

    New designed DNA-binding proteins may be recruited to act as transcriptional regulators and could provide new therapeutic agents in the treatment of genetic disorders such as cancer. We have isolated tailored DNA-binding proteins selected for affinity to a region spanning the transcription initiation site of the human bcl-2 gene. The proteins were derived from a single-chain derivative of the lambda Cro protein (scCro), randomly mutated in its recognition helices to construct libraries of protein variants of distinct DNA-binding properties. By phage display-afforded affinity selections combined with recombination of shuffled subunits, protein variants were isolated, which displayed high affinity for the target bcl-2 sequence, as determined by electrophoretic mobility shift and biosensor assays. The proteins analyzed were moderately sequence-specific but provide a starting point for further maturation of desired function.

  10. Chemiluminescence resonance energy transfer biosensing platform for site-specific determination of DNA methylation and assay of DNA methyltransferase activity using exonuclease III-assisted target recycling amplification.

    Science.gov (United States)

    Chen, Chun; Li, Baoxin

    2014-04-15

    Site-specific determination of DNA methylation and assay of MTase activity can be used for determining specific cancer types, providing insights into the mechanism of gene repression, and developing novel drugs to treat methylation-related diseases. Herein, we develop a simple and highly sensitive chemiluminescence (CL) biosensing platform for site-specific determination of DNA methylation using Exonuclease III (Exo III)-assisted target recycling signal amplification. After bisulfite treatment of mixture of methylated DNA and unmethylated DNA, methylated DNA can hybridize with fluorescein (FAM)-labeled probe DNA to form double-stranded DNA (dsDNA), removing the FAM-labeled probe DNA from the surface of grapheme oxide, and the chemiluminescence resonance energy transfer (CRET) sensing signal can be observed and then amplified using Exo III-based recycling strategy. The biosensing platform exhibits excellent high sensitivity, and it can ever distinguish as low as 0.002% methylation level from the mixture, which is superior to most currently reported methods used for DNA methylation assay. In addition, the proposed method can also be used to sensitively assay MTase activity with determination limit of 0.007 U/mL. This CL biosensing offers the advantages of being facile, sensitive, rapid and cost-effective. These features make the system promising for future use for early cancer diagnosis and discover of new anticancer drugs. © 2013 Published by Elsevier B.V.

  11. Alpha-D-glucan nanoparticulate adjuvant induces a transient inflammatory response at the injection site and targets antigen to migratory dendritic cells.

    Science.gov (United States)

    Lu, Fangjia; Mosley, Yung-Yi C; Rodriguez Rosales, Randol J; Carmichael, Brooke E; Elesela, Srikanth; Yao, Yuan; HogenEsch, Harm

    2017-01-01

    Biodegradable nanoparticles with functionalized surfaces are attractive candidates as vaccine adjuvants. Nano-11 are cationic dendrimer-like α-D-glucan nanoparticles with a diameter of 70-80 nm. Mice injected with antigen formulated with Nano-11 developed antibody titers that were similar or greater than antigen with aluminum adjuvant. Utilizing an in vivo imaging system, Nano-11 was shown to remain at the injection site after administration and cleared gradually over the course of 3 weeks. Injection of Nano-11 induced a transient inflammatory response characterized by recruitment of a mixed population of inflammatory cells, predominantly monocytes and macrophages with relatively few neutrophils. Recruited Mac-2+macrophages efficiently phagocytized the majority of Nano-11 at the injection site. Fluorescently labeled Nano-11 was present in cells in the draining lymph nodes 1 day after injection, with the majority contained in migratory dendritic cells. Injection of ovalbumin adsorbed to Nano-11 resulted in an increase of ovalbumin-containing cells in draining lymph nodes. Nano-11 delivered more antigen to antigen-presenting cells on a per cell basis and demonstrated more specific targeting to highly immunopotentiating migratory dendritic cells compared with soluble or aluminum hydroxide adsorbed ovalbumin. These results support the efficacy of Nano-11 and its potential use as a next generation vaccine adjuvant.

  12. Establishment and Application of a High Throughput Screening System Targeting the Interaction between HCV Internal Ribosome Entry Site and Human Eukaryotic Translation Initiation Factor 3

    Directory of Open Access Journals (Sweden)

    Yuying Zhu

    2017-05-01

    Full Text Available Viruses are intracellular obligate parasites and the host cellular machinery is usually recruited for their replication. Human eukaryotic translation initiation factor 3 (eIF3 could be directly recruited by the hepatitis C virus (HCV internal ribosome entry site (IRES to promote the translation of viral proteins. In this study, we establish a fluorescence polarization (FP based high throughput screening (HTS system targeting the interaction between HCV IRES and eIF3. By screening a total of 894 compounds with this HTS system, two compounds (Mucl39526 and NP39 are found to disturb the interaction between HCV IRES and eIF3. And these two compounds are further demonstrated to inhibit the HCV IRES-dependent translation in vitro. Thus, this HTS system is functional to screen the potential HCV replication inhibitors targeting human eIF3, which is helpful to overcome the problem of viral resistance. Surprisingly, one compound HP-3, a kind of oxytocin antagonist, is discovered to significantly enhance the interaction between HCV IRES and eIF3 by this HTS system. HP-3 is demonstrated to directly interact with HCV IRES and promote the HCV IRES-dependent translation both in vitro and in vivo, which strongly suggests that HP-3 has potentials to promote HCV replication. Therefore, this HTS system is also useful to screen the potential HCV replication enhancers, which is meaningful for understanding the viral replication and screening novel antiviral drugs. To our knowledge, this is the first HTS system targeting the interaction between eIF3 and HCV IRES, which could be applied to screen both potential HCV replication inhibitors and enhancers.

  13. Targeted N-glycan deletion at the receptor-binding site retains HIV Env NFL trimer integrity and accelerates the elicited antibody response.

    Science.gov (United States)

    Dubrovskaya, Viktoriya; Guenaga, Javier; de Val, Natalia; Wilson, Richard; Feng, Yu; Movsesyan, Arlette; Karlsson Hedestam, Gunilla B; Ward, Andrew B; Wyatt, Richard T

    2017-09-01

    Extensive shielding by N-glycans on the surface of the HIV envelope glycoproteins (Env) restricts B cell recognition of conserved neutralizing determinants. Elicitation of broadly neutralizing antibodies (bNAbs) in selected HIV-infected individuals reveals that Abs capable of penetrating the glycan shield can be generated by the B cell repertoire. Accordingly, we sought to determine if targeted N-glycan deletion might alter antibody responses to Env. We focused on the conserved CD4 binding site (CD4bs) since this is a known neutralizing determinant that is devoid of glycosylation to allow CD4 receptor engagement, but is ringed by surrounding N-glycans. We selectively deleted potential N-glycan sites (PNGS) proximal to the CD4bs on well-ordered clade C 16055 native flexibly linked (NFL) trimers to potentially increase recognition by naïve B cells in vivo. We generated glycan-deleted trimer variants that maintained native-like conformation and stability. Using a panel of CD4bs-directed bNAbs, we demonstrated improved accessibility of the CD4bs on the N-glycan-deleted trimer variants. We showed that pseudoviruses lacking these Env PNGSs were more sensitive to neutralization by CD4bs-specific bNAbs but remained resistant to non-neutralizing mAbs. We performed rabbit immunogenicity experiments using two approaches comparing glycan-deleted to fully glycosylated NFL trimers. The first was to delete 4 PNGS sites and then boost with fully glycosylated Env; the second was to delete 4 sites and gradually re-introduce these N-glycans in subsequent boosts. We demonstrated that the 16055 PNGS-deleted trimers more rapidly elicited serum antibodies that more potently neutralized the CD4bs-proximal-PNGS-deleted viruses in a statistically significant manner and strongly trended towards increased neutralization of fully glycosylated autologous virus. This approach elicited serum IgG capable of cross-neutralizing selected tier 2 viruses lacking N-glycans at residue N276 (natural or

  14. The route of HIV escape from immune response targeting multiple sites is determined by the cost-benefit tradeoff of escape mutations.

    Science.gov (United States)

    Batorsky, Rebecca; Sergeev, Rinat A; Rouzine, Igor M

    2014-10-01

    Cytotoxic T lymphocytes (CTL) are a major factor in the control of HIV replication. CTL arise in acute infection, causing escape mutations to spread rapidly through the population of infected cells. As a result, the virus develops partial resistance to the immune response. The factors controlling the order of mutating epitope sites are currently unknown and would provide a valuable tool for predicting conserved epitopes. In this work, we adapt a well-established mathematical model of HIV evolution under dynamical selection pressure from multiple CTL clones to include partial impairment of CTL recognition, [Formula: see text], as well as cost to viral replication, [Formula: see text]. The process of escape is described in terms of the cost-benefit tradeoff of escape mutations and predicts a trajectory in the cost-benefit plane connecting sequentially escaped sites, which moves from high recognition loss/low fitness cost to low recognition loss/high fitness cost and has a larger slope for early escapes than for late escapes. The slope of the trajectory offers an interpretation of positive correlation between fitness costs and HLA binding impairment to HLA-A molecules and a protective subset of HLA-B molecules that was observed for clinically relevant escape mutations in the Pol gene. We estimate the value of [Formula: see text] from published experimental studies to be in the range (0.01-0.86) and show that the assumption of complete recognition loss ([Formula: see text]) leads to an overestimate of mutation cost. Our analysis offers a consistent interpretation of the commonly observed pattern of escape, in which several escape mutations are observed transiently in an epitope. This non-nested pattern is a combined effect of temporal changes in selection pressure and partial recognition loss. We conclude that partial recognition loss is as important as fitness loss for predicting the order of escapes and, ultimately, for predicting conserved epitopes that can be

  15. HPLC-Based Activity Profiling: Discovery of Piperine as a Positive GABAA Receptor Modulator Targeting a Benzodiazepine-Independent Binding Site

    Science.gov (United States)

    Zaugg, Janine; Baburin, Igor; Strommer, Barbara; Kim, Hyun-Jung; Hering, Steffen; Hamburger, Matthias

    2011-01-01

    A plant extract library was screened for GABAA receptor activity making use of a two-microelectrode voltage clamp assay on Xenopus laevis oocytes. An ethyl acetate extract of black pepper fruits [Piper nigrum L. (Piperaceae) 100 μg/mL] potentiated GABA-induced chloride currents through GABAA receptors (composed of α1, β2, and γ2S subunits) by 169.1 ± 2.4%. With the aid of an HPLC-based activity profiling approach, piperine (5) was identified as the main active compound, together with 12 structurally related less active or inactive piperamides (1–4, 6–13). Identification was achieved by on-line high-resolution mass spectrometry and off-line microprobe 1D and 2D NMR spectroscopy, using only milligram amounts of extract. Compound 5 induced a maximum potentiation of the chloride currents by 301.9 ± 26.5% with an EC50 of 52.4 ± 9.4 μM. A comparison of the modulatory activity of 5 and other naturally occurring piperamides enabled insights into structural features critical for GABAA receptor modulation. The stimulation of chloride currents through GABAA receptors by compound 5 was not antagonized by flumazenil (10 μM). These data show that piperine (5) represents a new scaffold of positive allosteric GABAA receptor modulators targeting a benzodiazepine-independent binding site. PMID:20085307

  16. Long-lasting insecticide-treated house screens and targeted treatment of productive breeding-sites for dengue vector control in Acapulco, Mexico.

    Science.gov (United States)

    Che-Mendoza, Azael; Guillermo-May, Guillermo; Herrera-Bojórquez, Josué; Barrera-Pérez, Mario; Dzul-Manzanilla, Felipe; Gutierrez-Castro, Cipriano; Arredondo-Jiménez, Juan I; Sánchez-Tejeda, Gustavo; Vazquez-Prokopec, Gonzalo; Ranson, Hilary; Lenhart, Audrey; Sommerfeld, Johannes; McCall, Philip J; Kroeger, Axel; Manrique-Saide, Pablo

    2015-02-01

    Long-lasting insecticidal net screens (LLIS) fitted to domestic windows and doors in combination with targeted treatment (TT) of the most productive Aedes aegypti breeding sites were evaluated for their impact on dengue vector indices in a cluster-randomised trial in Mexico between 2011 and 2013. Sequentially over 2 years, LLIS and TT were deployed in 10 treatment clusters (100 houses/cluster) and followed up over 24 months. Cross-sectional surveys quantified infestations of adult mosquitoes, immature stages at baseline (pre-intervention) and in four post-intervention samples at 6-monthly intervals. Identical surveys were carried out in 10 control clusters that received no treatment. LLIS clusters had significantly lower infestations compared to control clusters at 5 and 12 months after installation, as measured by adult (male and female) and pupal-based vector indices. After addition of TT to the intervention houses in intervention clusters, indices remained significantly lower in the treated clusters until 18 (immature and adult stage indices) and 24 months (adult indices only) post-intervention. These safe, simple affordable vector control tools were well-accepted by study participants and are potentially suitable in many regions at risk from dengue worldwide. © The author 2015. The World Health Organization has granted Oxford University Press permission for the reproduction of this article.

  17. Target-Site Investigation for the Plasma Prolactin Response: Mechanism-Based Pharmacokinetic-Pharmacodynamic Analysis of Risperidone and Paliperidone in the Rat.

    Science.gov (United States)

    Shimizu, Shinji; den Hoedt, Sandra M; Mangas-Sanjuan, Victor; Cristea, Sinziana; Geuer, Jana K; van den Berg, Dirk-Jan; Hartman, Robin; Bellanti, Francisco; de Lange, Elizabeth C M

    2017-02-01

    To understand the drivers in the biological system response to dopamine D2 receptor antagonists, a mechanistic semiphysiologically based (PB) pharmacokinetic-pharmacodymanic (PKPD) model was developed to describe prolactin responses to risperidone (RIS) and its active metabolite paliperidone (PAL). We performed a microdialysis study in rats to obtain detailed plasma, brain extracellular fluid (ECF), and cerebrospinal fluid (CSF) concentrations of PAL and RIS. To assess the impact of P-glycoprotein (P-gp) functioning on brain distribution, we performed experiments in the absence or presence of the P-gp inhibitor tariquidar (TQD). PK and PKPD modeling was performed by nonlinear mixed-effect modeling. Plasma, brain ECF, and CSF PK values of RIS and PAL were well described by a 12-compartmental semi-PBPK model, including metabolic conversion of RIS to PAL. P-gp efflux functionality was identified on brain ECF for RIS and PAL and on CSF only for PAL. In the PKPD analysis, the plasma drug concentrations were more relevant than brain ECF or CSF concentrations to explain the prolactin response; the estimated EC50 was in accordance with reports in the literature for both RIS and PAL. We conclude that for RIS and PAL, the plasma concentrations better explain the prolactin response than do brain ECF or CSF concentrations. This research shows that PKPD modeling is of high value to delineate the target site of drugs. Copyright © 2017 by The American Society for Pharmacology and Experimental Therapeutics.

  18. RNA-Seq analysis of rye-grass transcriptomic response to an herbicide inhibiting acetolactate-synthase identifies transcripts linked to non-target-site-based resistance.

    Science.gov (United States)

    Duhoux, Arnaud; Carrère, Sébastien; Gouzy, Jérôme; Bonin, Ludovic; Délye, Christophe

    2015-03-01

    Non-target-site resistance (NTSR) to herbicides that disrupts agricultural weed control is a worldwide concern for food security. NTSR is considered a polygenic adaptive trait driven by differential gene regulation in resistant plants. Little is known about its genetic determinism, which precludes NTSR diagnosis and evolutionary studies. We used Illumina RNA-sequencing to investigate transcriptomic differences between plants from the global major weed rye-grass sensitive or resistant to the acetolactate-synthase (ALS) inhibiting herbicide pyroxsulam. Plants were collected before and along a time-course after herbicide application. De novo transcriptome assembly yielded a resource (LOLbase) including 92,381 contigs representing potentially active transcripts that were assigned putative annotations. Early effects of ALS inhibition consistent with the literature were observed in resistant and sensitive plants, proving LOLbase data were relevant to study herbicide response. Comparison of resistant and sensitive plants identified 30 candidate NTSR contigs. Further validation using 212 plants resistant or sensitive to pyroxsulam and/or to the ALS inhibitors iodosulfuron + mesosulfuron confirmed four contigs (two cytochromes P450, one glycosyl-transferase and one glutathione-S-transferase) were NTSR markers which combined expression levels could reliably identify resistant plants. This work confirmed that NTSR is driven by differential gene expression and involves different mechanisms. It provided tools and foundation for subsequent NTSR investigations.

  19. Are ta-siRNAs only originated from the cleavage site of miRNA on its target RNAs and phased in 21-nt increments?

    Science.gov (United States)

    Yu, Lan; Meng, Yijun; Shao, Chaogang; Kahrizi, Danial

    2015-09-10

    Trans-acting siRNAs (ta-siRNAs) are a class of small RNAs playing crucial roles in the regulation of plant gene expression. According to the canonical model, specific miRNA-guided cleavage of a TAS transcript triggers and sets the registry for the subsequent production of ta-siRNAs at 21-nt increments from the cleavage site. However, a previously validated 22-nt ta-siR2140 indicated that ta-siRNAs might be initiated from other phase increments and registers, which resulted in massive ta-siRNAs missing in the canonical model. To test this hypothesis, we employed high-throughput sequencing data to thoroughly identify the miR173-triggered ta-siRNAs from TAS1/TAS2 transcripts. As a result, thousands of phased siRNAs not generated through the canonical pathway were identified and 110 novel siRNA-target interactions were further validated based on degradome sequencing data. Based on these results, we propose that the canonical biogenesis model of ta-siRNAs should be modified in order to recruit the previously unidentified ta-siRNA candidates. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. High resolution genetic mapping uncovers chitin synthase-1 as the target-site of the structurally diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole in Tetranychus urticae

    Science.gov (United States)

    Demaeght, Peter; Osborne, Edward J.; Odman-Naresh, Jothini; Grbić, Miodrag; Nauen, Ralf; Merzendorfer, Hans

    2014-01-01

    The acaricides clofentezine, hexythiazox and etoxazole are commonly referred to as ‘mite growth inhibitors’, and clofentezine and hexythiazox have been used successfully for the integrated control of plant mite pests for decades. Although they are still important today, their mode of action has remained elusive. Recently, a mutation in chitin synthase 1 (CHS1) was linked to etoxazole resistance. In this study, we identified and investigated a T. urticae strain (HexR) harboring recessive, monogenic resistance to each of hexythiazox, clofentezine, and etoxazole. To elucidate if there is a common genetic basis for the observed cross-resistance, we adapted a previously developed bulk segregant analysis method to map with high resolution a single, shared resistance locus for all three compounds. This finding indicates that the underlying molecular basis for resistance to all three compounds is identical. This locus is centered on the CHS1 gene, and as supported by additional genetic and biochemical studies, a non-synonymous variant (I1017F) in CHS1 associates with resistance to each of the tested acaricides in HexR. Our findings thus demonstrate a shared molecular mode of action for the chemically diverse mite growth inhibitors clofentezine, hexythiazox and etoxazole as inhibitors of an essential, non-catalytic activity of CHS1. Given the previously documented cross-resistance between clofentezine, hexythiazox and the benzyolphenylurea compounds flufenoxuron and cycloxuron, CHS1 should be also considered as a potential target-site of insecticidal BPUs. PMID:24859419

  1. High-power ultralong-wavelength Tm-doped silica fiber laser cladding-pumped with a random distributed feedback fiber laser.

    Science.gov (United States)

    Jin, Xiaoxi; Du, Xueyuan; Wang, Xiong; Zhou, Pu; Zhang, Hanwei; Wang, Xiaolin; Liu, Zejin

    2016-07-15

    We demonstrated a high-power ultralong-wavelength Tm-doped silica fiber laser operating at 2153 nm with the output power exceeding 18 W and the slope efficiency of 25.5%. A random distributed feedback fiber laser with the center wavelength of 1173 nm was employed as pump source of Tm-doped fiber laser for the first time. No amplified spontaneous emissions or parasitic oscillations were observed when the maximum output power reached, which indicates that employing 1173 nm random distributed feedback fiber laser as pump laser is a feasible and promising scheme to achieve high-power emission of long-wavelength Tm-doped fiber laser. The output power of this Tm-doped fiber laser could be further improved by optimizing the length of active fiber, reflectivity of FBGs, increasing optical efficiency of pump laser and using better temperature management. We also compared the operation of 2153 nm Tm-doped fiber lasers pumped with 793 nm laser diodes, and the maximum output powers were limited to ~2 W by strong amplified spontaneous emission and parasitic oscillation in the range of 1900-2000 nm.

  2. Site-specific incorporation of three toll-like receptor 2 targeting adjuvants into semisynthetic, molecularly defined nanoparticles: application to group a streptococcal vaccines.

    Science.gov (United States)

    Moyle, Peter M; Dai, Wei; Zhang, Yingkai; Batzloff, Michael R; Good, Michael F; Toth, Istvan

    2014-05-21

    Subunit vaccines offer a means to produce safer, more defined vaccines compared to traditional whole microorganism approaches. Subunit antigens, however, exhibit weak immunity, which is normally overcome through coadministration with adjuvants. Enhanced vaccine properties (e.g., improved potency) can be obtained by linking antigen and adjuvant, as observed for synthetic peptide antigens and Toll-like receptor 2 (TLR2) ligands. As few protective peptide antigens have been reported, compared to protein antigens, we sought to extend the utility of this approach to recombinant proteins, while ensuring that conjugation reactions yielded a single, molecularly defined product. Herein we describe the development and optimization of techniques that enable the efficient, site-specific attachment of three synthetic TLR2 ligands (lipid core peptide (LCP), Pam2Cys, and Pam3Cys) onto engineered protein antigens, permitting the selection of optimal TLR2 agonists during the vaccine development process. Using this approach, broadly protective (J14) and population targeted (seven M protein N-terminal antigens) multiantigenic vaccines against group A streptococcus (GAS; Streptococcus pyogenes) were produced and observed to self-assemble in PBS to yield nanoparticules (69, 101, and 123 nm, respectively). All nanoparticle formulations exhibited self-adjuvanting properties, with rapid, persistent, antigen-specific IgG antibody responses elicited toward each antigen in subcutaneously immunized C57BL/6J mice. These antibodies were demonstrated to strongly bind to the cell surface of five GAS serotypes that are not represented by vaccine M protein N-terminal antigens, are among the top 20 circulating strains in developed countries, and are associated with clinical disease, suggesting that these vaccines may elicit broadly protective immune responses.

  3. Targeted delivery of lovastatin and tocotrienol to fracture site promotes fracture healing in osteoporosis model: micro-computed tomography and biomechanical evaluation.

    Science.gov (United States)

    Ibrahim, Nurul 'Izzah; Khamis, Mohd Fadhli; Mod Yunoh, Mohd Faridz; Abdullah, Shahrum; Mohamed, Norazlina; Shuid, Ahmad Nazrun

    2014-01-01

    Osteoporosis is becoming a major health problem that is associated with increased fracture risk. Previous studies have shown that osteoporosis could delay fracture healing. Although there are potential agents available to promote fracture healing of osteoporotic bone such as statins and tocotrienol, studies on direct delivery of these agents to the fracture site are limited. This study was designed to investigate the effects of two potential agents, lovastatin and tocotrienol using targeted drug delivery system on fracture healing of postmenopausal osteoporosis rats. The fracture healing was evaluated using micro CT and biomechanical parameters. Forty-eight Sprague-Dawley female rats were divided into 6 groups. The first group was sham-operated (SO), while the others were ovariectomized (OVx). After two months, the right tibiae of all rats were fractured at metaphysis region using pulsed ultrasound and were fixed with plates and screws. The SO and OVxC groups were given two single injections of lovastatin and tocotrienol carriers. The estrogen group (OVx+EST) was given daily oral gavages of Premarin (64.5 µg/kg). The Lovastatin treatment group (OVx+Lov) was given a single injection of 750 µg/kg lovastatin particles. The tocotrienol group (OVx+TT) was given a single injection of 60 mg/kg tocotrienol particles. The combination treatment group (OVx+Lov+TT) was given two single injections of 750 µg/kg lovastatin particles and 60 mg/kg tocotrienol particles. After 4 weeks of treatment, the fractured tibiae were dissected out for micro-CT and biomechanical assessments. The combined treatment group (OVx+Lov+TT) showed significantly higher callus volume and callus strength than the OVxC group (p<0.05). Both the OVx+Lov and OVx+TT groups showed significantly higher callus strength than the OVxC group (p<0.05), but not for callus volume. In conclusion, combined lovastatin and tocotrienol may promote better fracture healing of osteoporotic bone.

  4. Potential Natural Products for Alzheimer’s Disease: Targeted Search Using the Internal Ribosome Entry Site of Tau and Amyloid-β Precursor Protein

    Directory of Open Access Journals (Sweden)

    Yun-Chieh Tasi

    2015-04-01

    Full Text Available Overexpression of the amyloid precursor protein (APP and the hyperphosphorylation of the tau protein are vital in the understanding of the cause of Alzheimer’s disease (AD. As a consequence, regulation of the expression of both APP and tau proteins is one important approach in combating AD. The APP and tau proteins can be targeted at the levels of transcription, translation and protein structural integrity. This paper reports the utilization of a bi-cistronic vector containing either APP or tau internal ribosome entry site (IRES elements flanked by β-galactosidase gene (cap-dependent and secreted alkaline phosphatase (SEAP (cap-independent to discern the mechanism of action of memantine, an N-methyl-d-aspartate (NMDA receptor antagonist. Results indicate that memantine could reduce the activity of both the APP and tau IRES at a concentration of ~10 μM (monitored by SEAP activity without interfering with the cap-dependent translation as monitored by the β-galactosidase assay. Western blot analysis of the tau protein in neuroblastoma (N2A and rat hippocampal cells confirmed the halting of the expression of the tau proteins. We also employed this approach to identify a preparation named NB34, extracts of Boussingaultia baselloides (madeira-vine fermented with Lactobacillus spp., which can function similarly to memantine in both IRES of APP and Tau. The water maze test demonstrated that NB34 could improve the spatial memory of a high fat diet induced neurodegeneration in apolipoprotein E-knockout (ApoE−/− mice. These results revealed that the bi-cistronic vector provided a simple, and effective platform in screening and establishing the mechanistic action of potential compounds for the treatment and management of AD.

  5. Site-specific conjugation of the quencher on peptide's N-terminal for the synthesis of a targeted non-spreading activatable optical probe.

    Science.gov (United States)

    Simard, Bryan; Mironov, Gleb G; Tomanek, Boguslaw; van Veggel, Frank C J M; Abulrob, Abedelnasser

    2016-06-01

    Optical imaging offers high sensitivity and portability at low cost. The design of 'smart' or 'activatable' probes can decrease the background noise and increase the specificity of the signal. By conjugating a fluorescent dye and a compatible quencher on each side of an enzyme's substrate, the signal remains in its 'off ' state until it reaches the area where a specific enzyme is expressed. However, the signal can leak from that area unless the dye is attached to a molecule able to bind to a specific target also presented in that area. The aim of this study was to (i) specifically conjugate the quencher on the α-amino group of the peptide's N-terminus, (ii) conjugate the dye on the ε-amino group of a lysine in C-terminus, and (iii) conjugate the carboxyl group of the peptide's C-terminus to an amino group present on an antibody, using carbodiimide chemistry. The use of protecting groups, such as Boc or Fmoc, to allow site-specific conjugation, presents several drawbacks including 'on beads labeling', additional steps required for deprotection and removal from the resin, decreased yield, and dye degradation. A method of preferential labeling of α-amino N-terminal group in slightly acidic solution, proposed by Selo et al. (1996) has partially solved the problem. The present study reports improvements of the method allowing to (i) avoid the homo-bilabeling, (ii) increase the yield of the N-terminal labeling by two folds, and (iii) decrease the cost by 44-fold. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

  6. Low effect-site concentration of propofol target-controlled infusion reduces the risk of hypotension during endoscopy in a Taiwanese population.

    Science.gov (United States)

    Hsu, Wen-Hung; Wang, Sophie S W; Shih, Hsiang-Yao; Wu, Meng-Chieh; Chen, Yi-Yu; Kuo, Fu-Chen; Yang, Hui-Ying; Chiu, Shun-Li; Chu, Koung-Shing; Cheng, Kuang-I; Wu, Deng-Chyang; Lu, I-Cheng

    2013-03-01

    Target-controlled infusion (TCI) of propofol is an effective way of delivering propofol during endoscopy. However, the ideal effect-site concentration (Ce) of propofol has not yet been defined in an Asian population. This study aimed to determine the ideal Ce of propofol in painless gastrointestinal endoscopy in a Taiwanese population. A total of 121 consecutive patients undergoing diagnostic endoscopy were recruited for this study. The endoscopic procedure was carried out within 1 h. TCI of propofol was utilized during the procedure. All patients received the same regimen to induce conscious sedation, including a bolus of midazolam (0.04 mg/kg) and fentanyl (0.5 μg/kg). The Ce of propofol was calculated using the Schneider model. Patients were randomly assigned to either the low Ce group (1.5-2.5 μg/mL) or high Ce group (3.0-4.0 μg/mL). Their cardiovascular and respiratory events were monitored during the procedure and the patients' post-procedure satisfaction was evaluated. The mean requirement for propofol was 232.02 mg in the low Ce group and 329.56 mg in the high Ce group, respectively (P hypotension were observed in the high Ce group (P = 0.026). The post-procedure satisfaction rate between the two groups was comparable. A low Ce of propofol TCI (1.5-2.5 μg/mL) achieved adequate anesthesia, reduced the risk of hypotension, and attained a high satisfaction rate in a Taiwanese population undergoing diagnostic painless endoscopy. © 2012 The Authors. Journal of Digestive Diseases © 2012 Chinese Medical Association Shanghai Branch, Chinese Society of Gastroenterology, Renji Hospital Affiliated to Shanghai Jiaotong University School of Medicine and Wiley Publishing Asia Pty Ltd.

  7. Targeted delivery of lovastatin and tocotrienol to fracture site promotes fracture healing in osteoporosis model: micro-computed tomography and biomechanical evaluation.

    Directory of Open Access Journals (Sweden)

    Nurul 'Izzah Ibrahim

    Full Text Available Osteoporosis is becoming a major health problem that is associated with increased fracture risk. Previous studies have shown that osteoporosis could delay fracture healing. Although there are potential agents available to promote fracture healing of osteoporotic bone such as statins and tocotrienol, studies on direct delivery of these agents to the fracture site are limited. This study was designed to investigate the effects of two potential agents, lovastatin and tocotrienol using targeted drug delivery system on fracture healing of postmenopausal osteoporosis rats. The fracture healing was evaluated using micro CT and biomechanical parameters. Forty-eight Sprague-Dawley female rats were divided into 6 groups. The first group was sham-operated (SO, while the others were ovariectomized (OVx. After two months, the right tibiae of all rats were fractured at metaphysis region using pulsed ultrasound and were fixed with plates and screws. The SO and OVxC groups were given two single injections of lovastatin and tocotrienol carriers. The estrogen group (OVx+EST was given daily oral gavages of Premarin (64.5 µg/kg. The Lovastatin treatment group (OVx+Lov was given a single injection of 750 µg/kg lovastatin particles. The tocotrienol group (OVx+TT was given a single injection of 60 mg/kg tocotrienol particles. The combination treatment group (OVx+Lov+TT was given two single injections of 750 µg/kg lovastatin particles and 60 mg/kg tocotrienol particles. After 4 weeks of treatment, the fractured tibiae were dissected out for micro-CT and biomechanical assessments. The combined treatment group (OVx+Lov+TT showed significantly higher callus volume and callus strength than the OVxC group (p<0.05. Both the OVx+Lov and OVx+TT groups showed significantly higher callus strength than the OVxC group (p<0.05, but not for callus volume. In conclusion, combined lovastatin and tocotrienol may promote better fracture healing of osteoporotic bone.

  8. [Investigation of hepatitis B virus integration sites in hilar cholangiocarcinoma tissues].

    Science.gov (United States)

    Qu, Zhen-liang; Cui, Nai-qiang; Xi, Zhao-hua; Du, Zhi

    2011-08-01

    To study the phenomena of hepatitis B virus (HBV) integration into the tissues of hilar cholangiocarcinoma (HCCA) and to identify the integration sites in the host genome. Ten fresh HCCA samples were collected from the tissues by surgical ablation, 1 normal hilar bile duct sample selected as control. Cellular DNA were extracted by Wizard SV Genomic DNA Purification System. PCR-derived assay (HBV-Alu-PCR) was employed to amplify the viral-host junctions which contain the HBV sequence and the adjacent cellular flanking sequences. The PCR products were purified and subjected to sequencing by ABI-3730XL Auto DNA Analyzer. The sequence analysis of viral-host junctions was performed by DNASIS MAX 3.0 bioinformatics software. The insertion sites between viral and cellular sequences were identified through homology comparison using NCBI BLAST and MapViewer search. In 10 HCCA samples, 5 were demonstrated to have HBV integration fragments with total 6 inserted sites identified. Sequence analysis from viral-host junction showed that HBV X gene inserted into host genome at random distribution with truncated fragments. HBV integration recurrently targeted the unknown region in upstream of CXXC finger protein-1 (CpG-binding protein) gene (4 cases). p53 tumor suppressor gene was also found at the integration site. There is high integration rate of HBV DNA into cellular genome of HCCA. HBV integration is found frequently into or close to cancer-related genes. The findings demonstrate that HBV infection might have association with the pathogenesis of HCCA.

  9. Fragment-Based Design of Ligands Targeting a Novel Site on the Integrase Enzyme of Human Immunodeficiency Virus;#8197;1

    Energy Technology Data Exchange (ETDEWEB)

    Wielens, Jerome; Headey, Stephen J.; Deadman, John J.; Rhodes, David I.; Parker, Michael W.; Chalmers, David K.; Scanlon, Martin J. (SVIMR-A); (Avea); (Monash)

    2011-08-17

    Fragment-based screening has been used to identify a novel ligand binding site on HIV-1 integrase. Crystal structures of fragments bound at this site (shown) have been used to design elaborated second-generation compounds that bind with higher affinity and good ligand efficiency.

  10. In vitro levamisole selection pressure on larval stages of Haemonchus contortus over nine generations gives rise to drug resistance and target site gene expression changes specific to the early larval stages only.

    Science.gov (United States)

    Sarai, Ranbir S; Kopp, Steven R; Knox, Malcolm R; Coleman, Glen T; Kotze, Andrew C

    2015-06-30

    There is some evidence that resistance to levamisole and pyrantel in trichostrongylid nematodes is due to changes in the composition of nicotinic acetylcholine receptors (nAChRs) which represent the drug target site. Altered expression patterns of genes coding for nAChR subunits, as well as the presence of truncated versions of several subunits, have been implicated in observed resistances. The studies have mostly compared target sites in worm isolates of very different genetic background, and hence the ability to associate the molecular changes with drug sensitivity alone have been clouded to some extent. The present study aimed to circumvent this issue by following target site gene expression pattern changes as resistance developed in Haemonchus contortus worms under laboratory selection pressure with levamisole. We applied drug selection pressure to early stage larvae in vitro over nine generations, and monitored changes in larval and adult drug sensitivities and target site gene expression patterns. High level resistance developed in larvae, with resistance factors of 94-fold and 1350-fold at the IC50 and IC95, respectively, in larval development assays after nine generations of selection. There was some cross-resistance to bephenium (70-fold increase in IC95). The expression of all the putative subunit components of levamisole-sensitive nAChRs, as well as a number of ancillary protein genes, particularly Hco-unc-29.1 and -ric-3, were significantly decreased (up to 5.5-fold) in the resistant larvae at generation nine compared to the starting population. However, adult worms did not show any resistance to levamisole, and showed an inverse pattern of gene expression changes, with many target site genes showing increased expression compared to the starting population. A comparison of the larval/adult drug sensitivity data with the known relationships for field-derived isolates indicated that the adults of our selected population should have been highly resistant

  11. Gene regulatory factors of the sea urchin embryo. II. Two dissimilar proteins, P3A1 and P3A2, bind to the same target sites that are required for early territorial gene expression

    OpenAIRE

    Höög, Christer; Calzone, Frank J.; Cutting, Ann E.; Britten, Roy J.; Davidson, Eric H

    1991-01-01

    Previous work demonstrated that a negative regulatory interaction mediated by factor(s) termed 'P3A' is required for correct territory-specific gene expression in the sea urchin embryo. A probe derived from a P3A target site in the skeletogenic SM50 gene of Strongylocentrotus purpuratus was used to isolate a cDNA clone coding for a factor that binds specifically to this site. This factor, called P3A1, contains two sequence elements that belong to the Zn finger class of DNA-binding motifs, and...

  12. A Single-Target Mitochondrial RNA Editing Factor of Funaria hygrometrica Can Fully Reconstitute RNA Editing at Two Sites in Physcomitrella patens.

    Science.gov (United States)

    Schallenberg-Rüdinger, Mareike; Oldenkott, Bastian; Hiss, Manuel; Trinh, Phuong Le; Knoop, Volker; Rensing, Stefan A

    2017-03-01

    Nuclear-encoded pentatricopeptide repeat (PPR) proteins are key factors for site-specific RNA editing, converting cytidines into uridines in plant mitochondria and chloroplasts. All editing factors in the model moss Physcomitrella patens have a C-terminal DYW domain with similarity to cytidine deaminase. However, numerous editing factors in flowering plants lack such a terminal DYW domain, questioning its immediate role in the pyrimidine base conversion process. Here we further investigate the Physcomitrella DYW-type PPR protein PPR_78, responsible for mitochondrial editing sites cox1eU755SL and rps14eU137SL. Complementation assays with truncated proteins demonstrate that the DYW domain is essential for full PPR_78 editing functionality. The DYW domain can be replaced, however, with its counterpart from another editing factor, PPR_79. The PPR_78 ortholog of the related moss Funaria hygrometrica fully complements the Physcomitrella mutant for editing at both sites, although the editing site in rps14 is lacking in Funaria. Editing factor orthologs in different taxa may thus retain editing capacity for multiple sites despite the absence of editing requirement. © The Author 2017. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  13. Application of virtual screening and molecular dynamics for the analysis of selectivity of inhibitors of HU proteins targeted to the DNA-recognition site

    Science.gov (United States)

    Talyzina, A. A.; Agapova, Yu. K.; Podshivalov, D. D.; Timofeev, V. I.; Sidorov-Biryukov, D. D.; Rakitina, T. V.

    2017-11-01

    DNA-Binding HU proteins are essential for the maintenance of genomic DNA supercoiling and compaction in prokaryotic cells and are promising pharmacological targets for the design of new antibacterial agents. The virtual screening for low-molecular-weight compounds capable of specifically interacting with the DNA-recognition loop of the HU protein from the mycoplasma Spiroplasma melliferum was performed. The ability of the initially selected ligands to form stable complexes with the protein target was assessed by molecular dynamics simulation. One compound, which forms an unstable complex, was eliminated by means of a combination of computational methods, resulting in a decrease in the number of compounds that will pass to the experimental test phase. This approach can be used to solve a wide range of problems related to the search for and validation of low-molecular-weight inhibitors specific for a particular protein target.

  14. Photo-thermal study of a layer of randomly distributed gold nanoparticles: from nano-localization to macro-scale effects

    Science.gov (United States)

    Pezzi, Luigia; Palermo, Giovanna; Veltri, Alessandro; Cataldi, Ugo; Bürgi, Thomas; Ritacco, Tiziana; Giocondo, Michele; Umeton, Cesare; De Luca, Antonio

    2017-11-01

    We present an experimental characterization and a comprehensive theoretical modeling of macroscopic plasmonic heat production that takes place in a single layer of small gold nanoparticles (GNPs), randomly distributed on a glass substrate, covered with different host media and acted on by a resonant radiation. We have performed a detailed experimental study of the temperature variations of three different systems, obtained by varying the density of nanoparticles. Due to the macroscopic dimension of the spot size, the used laser irradiates a huge number of nanoparticles, inducing a broad thermo-plasmonic effect that modifies the thermal conductivity of the entire system; starting from the state of art, we have implemented a simple model that enables to evaluate the resulting new thermal conductivity. We have also extended our theoretical approach to the macroscale, including an analysis of the effects predicted for different NP densities and laser spot size values, as well as for different values of the laser intensity, which can be as low as 0.05 W cm-2 . Theoretically predicted temperature variations are in excellent agreement with experimental results.

  15. Engineering metal-binding sites of bacterial CusF to enhance Zn/Cd accumulation and resistance by subcellular targeting

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Pengli; Yuan, Jinhong [Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093 (China); Zhang, Hui [Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093 (China); Deng, Xin [Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637 (United States); Ma, Mi [Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093 (China); Zhang, Haiyan, E-mail: hyz@ibcas.ac.cn [Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093 (China)

    2016-01-25

    Highlights: • mCusF is specifically targeted to different subcellular compartments in Arabidopsis. • Plants expressing vacuole-targeted mCusF exhibit strongest Zn resistance. • All transgenic lines accumulate more Zn under Zn exposure. • All transgenic lines enhance root-to-shoot translocation of Cd. • Metal homeostasis is improved in mCusF plants under Cd exposure. - Abstract: The periplasmic protein CusF acts as a metallochaperone to mediate Cu resistance in Escherichia coli. CusF does not contain cysteine residues and barely binds to divalent cations. Here, we addressed effects of cysteine-substitution mutant (named as mCusF) of CusF on zinc/cadmium (Zn/Cd) accumulation and resistance. We targeted mCusF to different subcellular compartments in Arabidopsis. We found that plants expressing vacuole-targeted mCusF were more resistant to excess Zn than WT and plants with cell wall-targeted or cytoplasmic mCusF. Under long-term exposure to excess Zn, all transgenic lines accumulated more Zn (up to 2.3-fold) in shoots than the untransformed plants. Importantly, plants with cytoplasmic mCusF showed higher efficiency of Zn translocation from root to shoot than plants with secretory pathway-targeted-mCusF. Furthermore, the transgenic lines exhibited enhanced resistance to Cd and significant increase in root-to-shoot Cd translocation. We also found all transgenic plants greatly improved manganese (Mn) and iron (Fe) homeostasis under Cd exposure. Our results demonstrate heterologous expression of mCusF could be used to engineer a new phytoremediation strategy for Zn/Cd and our finding also deepen our insights into mechanistic basis for relieving Cd toxicity in plants through proper root/shoot partitioning mechanism and homeostatic accumulation of Mn and Fe.

  16. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline

    Science.gov (United States)

    Park, Ki Soo; Oh, Seung Soo; Soh, H. Tom; Park, Hyun Gyu

    2014-08-01

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to

  17. Liposome-mediated targeting of enzymes to cancer cells for site-specific activation of prodrugs : Comparison with the corresponding antibody-enzyme conjugate

    NARCIS (Netherlands)

    Fonseca, Maria José; Jagtenberg, Joycelyn C.; Haisma, Hidde J.; Storm, Gert

    Purpose. Immunoenzymosomes are tumor-targeted immunoliposomes bearing enzymes on their surface. These enzymes are capable of converting relatively nontoxic prodrugs into active cytostatic agents. The aims of this study were to compare the enzyme delivery capability of immunoenzymosomes with that of

  18. Identification of multiple target sites for a glutathione conjugate on glutathione-S-transferase by matrix-assisted laser desorption/ionization mass spectrometry

    NARCIS (Netherlands)

    Jespersen, S.; Ploemen, J.H.T.M.; Bladeren, P.J.; Niessen, W.M.A.; Tjaden, U.R.; Greef, J. van der

    1996-01-01

    A mass spectrometric method providing qualitative site-specific information regarding covalent modification of proteins is described. The method involves comparison of unmodified and modified proteins by matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) peptide mapping in

  19. Target-controlled formation of silver nanoclusters in abasic site-incorporated duplex DNA for label-free fluorescence detection of theophylline.

    Science.gov (United States)

    Park, Ki Soo; Oh, Seung Soo; Soh, H Tom; Park, Hyun Gyu

    2014-09-07

    A novel, label-free, fluorescence based sensor for theophylline has been developed. In the new sensor system, an abasic site-incorporated duplex DNA probe serves as both a pocket for recognition of theophylline and a template for the preparation of fluorescent silver nanoclusters. The strategy relies on theophylline-controlled formation of fluorescent silver nanoclusters from abasic site-incorporated duplex DNA. When theophylline is not present, silver ions interact with the cytosine groups opposite to the abasic site in duplex DNA. This interaction leads to efficient formation of intensely red fluorescent silver nanoclusters. In contrast, when theophylline is bound at the abasic site through pseudo base-pairing with appropriately positioned cytosines, silver ion binding to the cytosine nucleobase is prevented. Consequently, fluorescent silver nanoclusters are not formed causing a significant reduction of the fluorescence signal. By employing this new sensor, theophylline can be highly selectively detected at a concentration as low as 1.8 μM. Finally, the diagnostic capability and practical application of this sensor were demonstrated by its use in detecting theophylline in human blood serum.

  20. Engineering metal-binding sites of bacterial CusF to enhance Zn/Cd accumulation and resistance by subcellular targeting.

    Science.gov (United States)

    Yu, Pengli; Yuan, Jinhong; Zhang, Hui; Deng, Xin; Ma, Mi; Zhang, Haiyan

    2016-01-25

    The periplasmic protein CusF acts as a metallochaperone to mediate Cu resistance in Escherichia coli. CusF does not contain cysteine residues and barely binds to divalent cations. Here, we addressed effects of cysteine-substitution mutant (named as mCusF) of CusF on zinc/cadmium (Zn/Cd) accumulation and resistance. We targeted mCusF to different subcellular compartments in Arabidopsis. We found that plants expressing vacuole-targeted mCusF were more resistant to excess Zn than WT and plants with cell wall-targeted or cytoplasmic mCusF. Under long-term exposure to excess Zn, all transgenic lines accumulated more Zn (up to 2.3-fold) in shoots than the untransformed plants. Importantly, plants with cytoplasmic mCusF showed higher efficiency of Zn translocation from root to shoot than plants with secretory pathway-targeted-mCusF. Furthermore, the transgenic lines exhibited enhanced resistance to Cd and significant increase in root-to-shoot Cd translocation. We also found all transgenic plants greatly improved manganese (Mn) and iron (Fe) homeostasis under Cd exposure. Our results demonstrate heterologous expression of mCusF could be used to engineer a new phytoremediation strategy for Zn/Cd and our finding also deepen our insights into mechanistic basis for relieving Cd toxicity in plants through proper root/shoot partitioning mechanism and homeostatic accumulation of Mn and Fe. Copyright © 2015 Elsevier B.V. All rights reserved.

  1. HOMOLOGY MODELLING AND BINDING SITE IDENTIFICATION OF 1DEOXY D-XYLULOSE 5 PHOSPHATE REDUCTOISOMERASE OF PLASMODIUM FALCIPARUM: NEW DRUG TARGET FOR PLSMODIUM FALCIPARUM

    OpenAIRE

    JYOTSNA CHOUBEY; ASHISH PATEL; Verma, M. K.; SHAILENDRA GUPTA

    2010-01-01

    Malaria is major global health problem. Malaria parasite had developed resistance to the drug being used till date. It implies the development of new effective drug with different mode of action. Apicoplast in malaria and related parasite offer various new target for drug therapy[1]. Apicoplast contains various metabolic pathways that differ from those of host thereby presenting ideal strategies for drug therapy. Plasmodium falciparum 1deoxy- Dxylulose 5- phosphate reductoisomerase (pfDXR) is...

  2. Identification of Plagl1/Zac1 binding sites and target genes establishes its role in the regulation of extracellular matrix genes and the imprinted gene network.

    Science.gov (United States)

    Varrault, Annie; Dantec, Christelle; Le Digarcher, Anne; Chotard, Laëtitia; Bilanges, Benoit; Parrinello, Hugues; Dubois, Emeric; Rialle, Stéphanie; Severac, Dany; Bouschet, Tristan; Journot, Laurent

    2017-10-13

    PLAGL1/ZAC1 undergoes parental genomic imprinting, is paternally expressed, and is a member of the imprinted gene network (IGN). It encodes a zinc finger transcription factor with anti-proliferative activity and is a candidate tumor suppressor gene on 6q24 whose expression is frequently lost in various neoplasms. Conversely, gain of PLAGL1 function is responsible for transient neonatal diabetes mellitus, a rare genetic disease that results from defective pancreas development. In the present work, we showed that Plagl1 up-regulation was not associated with DNA damage-induced cell cycle arrest. It was rather associated with physiological cell cycle exit that occurred with contact inhibition, growth factor withdrawal, or cell differentiation. To gain insights into Plagl1 mechanism of action, we identified Plagl1 target genes by combining chromatin immunoprecipitation and genome-wide transcriptomics in transfected cell lines. Plagl1-elicited gene regulation correlated with multiple binding to the proximal promoter region through a GC-rich motif. Plagl1 target genes included numerous genes involved in signaling, cell adhesion, and extracellular matrix composition, including collagens. Plagl1 targets also included 22% of the 409 genes that make up the IGN. Altogether, this work identified Plagl1 as a transcription factor that coordinated the regulation of a subset of IGN genes and controlled extracellular matrix composition. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  3. A novel W1999S mutation and non-target site resistance impact on acetyl-CoA carboxylase inhibiting herbicides to varying degrees in a UK Lolium multiflorum population.

    Science.gov (United States)

    Kaundun, Shiv Shankhar; Bailly, Geraldine C; Dale, Richard P; Hutchings, Sarah-Jane; McIndoe, Eddie

    2013-01-01

    Acetyl-CoA carboxylase (ACCase) inhibiting herbicides are important products for the post-emergence control of grass weed species in small grain cereal crops. However, the appearance of resistance to ACCase herbicides over time has resulted in limited options for effective weed control of key species such as Lolium spp. In this study, we have used an integrated biological and molecular biology approach to investigate the mechanism of resistance to ACCase herbicides in a Lolium multiflorum Lam. from the UK (UK21). The study revealed a novel tryptophan to serine mutation at ACCase codon position 1999 impacting on ACCase inhibiting herbicides to varying degrees. The W1999S mutation confers dominant resistance to pinoxaden and partially recessive resistance to cycloxydim and sethoxydim. On the other hand, plants containing the W1999S mutation were sensitive to clethodim and tepraloxydim. Additionally population UK21 is characterised by other resistance mechanisms, very likely non non-target site based, affecting several aryloxyphenoxyproprionate (FOP) herbicides but not the practical field rate of pinoxaden. The positive identification of wild type tryptophan and mutant serine alleles at ACCase position 1999 could be readily achieved with an original DNA based derived cleaved amplified polymorphic sequence (dCAPS) assay that uses the same PCR product but two different enzymes for positively identifying the wild type tryptophan and mutant serine alleles identified here. This paper highlights intrinsic differences between ACCase inhibiting herbicides that could be exploited for controlling ryegrass populations such as UK21 characterised by compound-specific target site and non-target site resistance.

  4. A novel W1999S mutation and non-target site resistance impact on acetyl-CoA carboxylase inhibiting herbicides to varying degrees in a UK Lolium multiflorum population.

    Directory of Open Access Journals (Sweden)

    Shiv Shankhar Kaundun

    Full Text Available Acetyl-CoA carboxylase (ACCase inhibiting herbicides are important products for the post-emergence control of grass weed species in small grain cereal crops. However, the appearance of resistance to ACCase herbicides over time has resulted in limited options for effective weed control of key species such as Lolium spp. In this study, we have used an integrated biological and molecular biology approach to investigate the mechanism of resistance to ACCase herbicides in a Lolium multiflorum Lam. from the UK (UK21.The study revealed a novel tryptophan to serine mutation at ACCase codon position 1999 impacting on ACCase inhibiting herbicides to varying degrees. The W1999S mutation confers dominant resistance to pinoxaden and partially recessive resistance to cycloxydim and sethoxydim. On the other hand, plants containing the W1999S mutation were sensitive to clethodim and tepraloxydim. Additionally population UK21 is characterised by other resistance mechanisms, very likely non non-target site based, affecting several aryloxyphenoxyproprionate (FOP herbicides but not the practical field rate of pinoxaden. The positive identification of wild type tryptophan and mutant serine alleles at ACCase position 1999 could be readily achieved with an original DNA based derived cleaved amplified polymorphic sequence (dCAPS assay that uses the same PCR product but two different enzymes for positively identifying the wild type tryptophan and mutant serine alleles identified here.This paper highlights intrinsic differences between ACCase inhibiting herbicides that could be exploited for controlling ryegrass populations such as UK21 characterised by compound-specific target site and non-target site resistance.

  5. Global mapping of binding sites for Nrf2 identifies novel targets in cell survival response through ChIP-Seq profiling and network analysis.

    Science.gov (United States)

    Malhotra, Deepti; Portales-Casamar, Elodie; Singh, Anju; Srivastava, Siddhartha; Arenillas, David; Happel, Christine; Shyr, Casper; Wakabayashi, Nobunao; Kensler, Thomas W; Wasserman, Wyeth W; Biswal, Shyam

    2010-09-01

    The Nrf2 (nuclear factor E2 p45-related factor 2) transcription factor responds to diverse oxidative and electrophilic environmental stresses by circumventing repression by Keap1, translocating to the nucleus, and activating cytoprotective genes. Nrf2 responses provide protection against chemical carcinogenesis, chronic inflammation, neurodegeneration, emphysema, asthma and sepsis in murine models. Nrf2 regulates the expression of a plethora of genes that detoxify oxidants and electrophiles and repair or remove damaged macromolecules, such as through proteasomal processing. However, many direct targets of Nrf2 remain undefined. Here, mouse embryonic fibroblasts (MEF) with either constitutive nuclear accumulation (Keap1(-/-)) or depletion (Nrf2(-/-)) of Nrf2 were utilized to perform chromatin-immunoprecipitation with parallel sequencing (ChIP-Seq) and global transcription profiling. This unique Nrf2 ChIP-Seq dataset is highly enriched for Nrf2-binding motifs. Integrating ChIP-Seq and microarray analyses, we identified 645 basal and 654 inducible direct targets of Nrf2, with 244 genes at the intersection. Modulated pathways in stress response and cell proliferation distinguish the inducible and basal programs. Results were confirmed in an in vivo stress model of cigarette smoke-exposed mice. This study reveals global circuitry of the Nrf2 stress response emphasizing Nrf2 as a central node in cell survival response.

  6. Traces of DU in samples of environmental bio-monitors (non-flowering plants, fungi) and soil from target sites of the Western Balkan region

    Energy Technology Data Exchange (ETDEWEB)

    Zunic, Zora S. [Institute of Nuclear Sciences ' Vinca' , Mike Petrovica Alasa 12-14, P.O. Box 522, 11001 Belgrade (Serbia); Mietelski, Jerzy W. [Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Radzikowskiego 152 (Poland)], E-mail: jerzy.mietelski@ifj.edu.pl; Blazej, Sylwia; Gaca, Pawel; Tomankiewicz, Ewa [The Henryk Niewodniczanski Institute of Nuclear Physics, Polish Academy of Sciences, 31-342 Krakow, Radzikowskiego 152 (Poland); Ujic, Predrag; Celikovic, Igor; Cuknic, Olivera; Demajo, Miroslav [Institute of Nuclear Sciences ' Vinca' , Mike Petrovica Alasa 12-14, P.O. Box 522, 11001 Belgrade (Serbia)

    2008-08-15

    This paper reports results of gamma and alpha spectrometric measurements for mosses, lichens, fungi and soil samples from areas in the Balkans targeted by depleted uranium (DU). Samples were collected in 2002 and 2003 in the vicinity of several villages, principally Han Pijesak (Bosnia and Herzegovina, hit by DU in 1995) and Bratoselce (South Serbia, hit by DU in 1999) and in lesser numbers from Gornja Stubla, Kosovo (which is identified as a high natural radon/thoron area) and Presevo close to the Kosovo border. In the course of gamma spectrometric measurements some results suggested samples with unusual high uranium contents which might be considered to be a signature for the presence of DU, although many samples had very high detection limits. Alpha spectrometric measurements directly proved the presence of DU for five samples, all from directly targeted places. These were samples of mosses, lichens and soil. For some samples homogeneity tests were applied which showed a rather even distribution of DU in these samples. No trace of DU was found in any sample from a dwelling.

  7. Assessment of the performance of the Marsh model in effect site mode for target controlled infusion of propofol during the maintenance phase of general anaesthesia in an unselected population of neurosurgical patients.

    Science.gov (United States)

    Cowley, Nicholas J; Hutton, Peter; Clutton-Brock, Thomas H

    2013-10-01

    Propofol target-controlled infusion (TCI) in effect site mode has become popular since it became commercially available. We have performed a study to assess the pharmacokinetic performance of the Marsh model in effect site mode in an unselected group of patients during neurosurgery during the maintenance phase of anaesthesia. Fifty American Society of Anesthesiologists (ASA) physical status classes 1 to 3 adults underwent elective neurosurgery receiving propofol TCI using the Marsh model in effect site mode. Propofol dose titration and level of patient monitoring was determined by the attending anaesthesiologist. Arterial blood was sampled at regular intervals during the maintenance phase of anaesthesia and measured plasma propofol concentrations were compared with those estimated using TCI. Large tertiary referral centre in Birmingham, UK, with a specialist neuroanaesthesia service. Fifty ASA status I to III adult patients undergoing elective neurosurgery. Performance of Marsh model as assessed by median performance error (bias) and median absolute performance error (imprecision). Performance of the Marsh model showed a positive bias (median performance error) of 27.6%, and imprecision (median absolute performance error) of 29.4%. Analysis of pooled data demonstrated greatest bias in the early phase (15 to 30 min) of anaesthesia (mean prediction error of 51.6%). Analysis of covariates demonstrated that obesity (BMI >30 kg m(-2)) contributed around half of the bias detected (mean prediction error 47 vs. 23%, P 2) actually demonstrated significantly lower prediction errors. Pharmacokinetic analysis suggests that the performance of the Marsh model in effect site mode is poor in this broad patient population. The greatest bias demonstrated occurred in the early maintenance phase of anaesthesia. Of the covariates analysed, obesity contributed most significantly to an increased bias. Despite overall poor performance of the Marsh model, attending anaesthesiologists

  8. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses

    Directory of Open Access Journals (Sweden)

    Adam C. Wilkinson

    2013-10-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2−/− Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  9. Single site-specific integration targeting coupled with embryonic stem cell differentiation provides a high-throughput alternative to in vivo enhancer analyses.

    Science.gov (United States)

    Wilkinson, Adam C; Goode, Debbie K; Cheng, Yi-Han; Dickel, Diane E; Foster, Sam; Sendall, Tim; Tijssen, Marloes R; Sanchez, Maria-Jose; Pennacchio, Len A; Kirkpatrick, Aileen M; Göttgens, Berthold

    2013-01-01

    Comprehensive analysis of cis-regulatory elements is key to understanding the dynamic gene regulatory networks that control embryonic development. While transgenic animals represent the gold standard assay, their generation is costly, entails significant animal usage, and in utero development complicates time-course studies. As an alternative, embryonic stem (ES) cells can readily be differentiated in a process that correlates well with developing embryos. Here, we describe a highly effective platform for enhancer assays using an Hsp68/Venus reporter cassette that targets to the Hprt locus in mouse ES cells. This platform combines the flexibility of Gateway® cloning, live cell trackability of a fluorescent reporter, low background and the advantages of single copy insertion into a defined genomic locus. We demonstrate the successful recapitulation of tissue-specific enhancer activity for two cardiac and two haematopoietic enhancers. In addition, we used this assay to dissect the functionality of the highly conserved Ets/Ets/Gata motif in the Scl+19 enhancer, which revealed that the Gata motif is not required for initiation of enhancer activity. We further confirmed that Gata2 is not required for endothelial activity of the Scl+19 enhancer using Gata2(-/-) Scl+19 transgenic embryos. We have therefore established a valuable toolbox to study gene regulatory networks with broad applicability.

  10. Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.

    Directory of Open Access Journals (Sweden)

    Andreas Kuehne

    2017-06-01

    Full Text Available In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data. The algorithm sections the metabolic network into modules of metabolites with consistent changes. Metabolic reactions that connect different modules are the most likely sites of metabolic regulation. In contrast to most state-of-the-art methods, the MNS algorithm is independent of arbitrary pathway definitions, and its probabilistic nature facilitates assessments of noisy and incomplete measurements. With serial (i.e., time-resolved data, the MNS algorithm also indicates the sequential order of metabolic regulation. We demonstrated the power and flexibility of the MNS algorithm with three, realistic case studies with bacterial and human cells. Thus, this approach enables the identification of mechanistic regulatory events from large-scale metabolomics data, and contributes to the understanding of metabolic processes and their interplay with cellular signaling and regulation processes.

  11. Metabolic network segmentation: A probabilistic graphical modeling approach to identify the sites and sequential order of metabolic regulation from non-targeted metabolomics data.

    Science.gov (United States)

    Kuehne, Andreas; Mayr, Urs; Sévin, Daniel C; Claassen, Manfred; Zamboni, Nicola

    2017-06-01

    In recent years, the number of large-scale metabolomics studies on various cellular processes in different organisms has increased drastically. However, it remains a major challenge to perform a systematic identification of mechanistic regulatory events that mediate the observed changes in metabolite levels, due to complex interdependencies within metabolic networks. We present the metabolic network segmentation (MNS) algorithm, a probabilistic graphical modeling approach that enables genome-scale, automated prediction of regulated metabolic reactions from differential or serial metabolomics data. The algorithm sections the metabolic network into modules of metabolites with consistent changes. Metabolic reactions that connect different modules are the most likely sites of metabolic regulation. In contrast to most state-of-the-art methods, the MNS algorithm is independent of arbitrary pathway definitions, and its probabilistic nature facilitates assessments of noisy and incomplete measurements. With serial (i.e., time-resolved) data, the MNS algorithm also indicates the sequential order of metabolic regulation. We demonstrated the power and flexibility of the MNS algorithm with three, realistic case studies with bacterial and human cells. Thus, this approach enables the identification of mechanistic regulatory events from large-scale metabolomics data, and contributes to the understanding of metabolic processes and their interplay with cellular signaling and regulation processes.

  12. Structure-function analysis of the glioma targeting NFL-TBS.40-63 peptide corresponding to the tubulin-binding site on the light neurofilament subunit.

    Directory of Open Access Journals (Sweden)

    Raphael Berges

    Full Text Available We previously reported that a 24 amino acid peptide (NFL-TBS.40-63 corresponding to the tubulin-binding site located on the light neurofilament subunit, selectively enters in glioblastoma cells where it disrupts their microtubule network and inhibits their proliferation. Here, we analyzed the structure-function relationships using an alanine-scanning strategy, in order to identify residues essential for these biological activities. We showed that the majority of modified peptides present a decreased or total loss to penetrate in these cells, or to alter microtubules. Correspondingly, circular dichroism measurements showed that this peptide forms either β-sheet or α-helix structures according to the solvent and that alanine substitution modified or destabilized the structure, in relation with changes in the biological activities. Moreover, substitution of serine residues by phosphoserine or aspartic acid concomitantly decreased the cell penetrating activity and the structure stability. These results indicate the importance of structure for the activities, including selectivity to glioblastoma cells of this peptide, and its regulation by phosphorylation.

  13. Development and validation of an efficient HPLC method for quantification of voriconazole in plasma and microdialysate reflecting an important target site.

    Science.gov (United States)

    Simmel, Franziska; Soukup, Jens; Zoerner, Alexander; Radke, Joachim; Kloft, Charlotte

    2008-10-01

    Voriconazole is a very potent antifungal agent used to treat serious fungal infections (candidiasis); it is also the therapy of choice for aspergillosis. After standard dosing, several factors affect exposure of voriconazole, resulting in large variability and demanding further elucidation of drug distribution. For measurements at the site of action, microdialysis is considered to be an outstanding minimally invasive method. For determination of voriconazole in microdialysate and human plasma a new, efficient, reliable, and robust HPLC assay using UV detection at 254 nm has been developed and validated. After simple sample preparation using acetonitrile for plasma and for microdialysate, 20 microL were injected and separated on an RP-18 column. The chromatographic run time was less than 4 min. Overall, the assay showed high precision (CV 93.9 to 99.5%) and accuracy (RE -96.7 to +107%) for both matrices. Of the 36 drug products typically co-administered with voriconazole, none except ambroxol interfered with its peak signal, and this interference was successfully managed. In summary, the method is highly suitable for application in (pre)clinical microdialysis studies, e.g., of critically ill patients with invasive mycoses.

  14. Single-nucleotide polymorphism in microRNA-binding site of SULF1 target gene as a protective factor against the susceptibility to breast cancer: a case-control study.

    Science.gov (United States)

    Zhou, Qiong; Jiang, Yiwei; Yin, Wenjin; Wang, Yaohui; Lu, Jinsong

    2016-01-01

    Numerous clinical studies have suggested that chemopreventive drugs for breast cancer such as tamoxifen and exemestane can effectively reduce the incidence of estrogen receptor (ER)-positive breast cancer. However, it remains unclear how to identify those who are susceptible to ER-positive breast cancer. Accordingly, there is a great demand for a probe into the predisposing factors so as to provide precise chemoprevention. Recent evidence has indicated that ERα expression can be regulated by microRNAs (miRNAs), such as miR-206, in breast cancer. We assumed that single-nucleotide polymorphisms (SNPs) in the miR-206-binding sites of the target genes may be associated with breast cancer susceptibility with different ER statuses. We genotyped the SNPs that reside in and around the miR-206-binding sites of two target genes - heparan sulfatase 1 (SULF1) and RPTOR-independent companion of mammalian target of rapamycin Complex 2 (RICTOR) - which were related to the progression or metastasis of breast cancer cells in 710 breast cancer patients and 294 controls by the matrix-assisted laser desorption ionization-time of flight mass spectrometry method. Modified odds ratios (ORs) with their 95% confidence intervals (CIs) were calculated by a multivariate logistic regression analysis to evaluate the potential association between the SNPs and breast cancer susceptibility. For rs3802278, which is located in the 3'-untranslated region (3'-UTR) of SULF1, the frequency of the AA genotype was less in breast cancer patients than that in the controls as compared to that of the GG + GA genotype not only for ER-positive breast cancer patients (adjusted OR =0.663, P=0.032) but also for hormone receptor-positive breast cancer patients (adjusted OR =0.610, P=0.018). Besides, the frequency of the AA genotype was less than that of the GG genotype between the ER-positive breast cancer patients and the controls (adjusted OR =0.791, P=0.038). For rs66916453, which is located in the 3'-UTR of

  15. Target Laboratory

    Data.gov (United States)

    Federal Laboratory Consortium — [Part of the ATLAS user facility.] The Physics Division operates a target development laboratory that produces targets and foils of various thickness and substrates,...

  16. Impact of the β-Lactam Resistance Modifier (−-Epicatechin Gallate on the Non-Random Distribution of Phospholipids across the Cytoplasmic Membrane of Staphylococcus aureus

    Directory of Open Access Journals (Sweden)

    Helena Rosado

    2015-07-01

    Full Text Available The polyphenol (−-epicatechin gallate (ECg inserts into the cytoplasmic membrane (CM of methicillin-resistant Staphylococcus aureus (MRSA and reversibly abrogates resistance to β-lactam antibiotics. ECg elicits an increase in MRSA cell size and induces thickened cell walls. As ECg partially delocalizes penicillin-binding protein PBP2 from the septal division site, reduces PBP2 and PBP2a complexation and induces CM remodelling, we examined the impact of ECg membrane intercalation on phospholipid distribution across the CM and determined if ECg affects the equatorial, orthogonal mode of division. The major phospholipids of the staphylococcal CM, lysylphosphatidylglycerol (LPG, phosphatidylglycerol (PG, and cardiolipin (CL, were distributed in highly asymmetric fashion; 95%–97% of LPG was associated with the inner leaflet whereas PG (~90% and CL (~80% were found predominantly in the outer leaflet. ECg elicited small, significant changes in LPG distribution. Atomic force microscopy established that ECg-exposed cells divided in similar fashion to control bacteria, with a thickened band of encircling peptidoglycan representing the most recent plane of cell division, less distinct ribs indicative of previous sites of orthogonal division and concentric rings and “knobbles” representing stages of peptidoglycan remodelling during the cell cycle. Preservation of staphylococcal membrane lipid asymmetry and mode of division in sequential orthogonal planes appear key features of ECg-induced stress.

  17. The κB transcriptional enhancer motif and signal sequences of V(DJ recombination are targets for the zinc finger protein HIVEP3/KRC: a site selection amplification binding study

    Directory of Open Access Journals (Sweden)

    Wu Lai-Chu

    2002-08-01

    Full Text Available Abstract Background The ZAS family is composed of proteins that regulate transcription via specific gene regulatory elements. The amino-DNA binding domain (ZAS-N and the carboxyl-DNA binding domain (ZAS-C of a representative family member, named κB DNA binding and recognition component (KRC, were expressed as fusion proteins and their target DNA sequences were elucidated by site selection amplification binding assays, followed by cloning and DNA sequencing. The fusion proteins-selected DNA sequences were analyzed by the MEME and MAST computer programs to obtain consensus motifs and DNA elements bound by the ZAS domains. Results Both fusion proteins selected sequences that were similar to the κB motif or the canonical elements of the V(DJ recombination signal sequences (RSS from a pool of degenerate oligonucleotides. Specifically, the ZAS-N domain selected sequences similar to the canonical RSS nonamer, while ZAS-C domain selected sequences similar to the canonical RSS heptamer. In addition, both KRC fusion proteins selected oligonucleoties with sequences identical to heptamer and nonamer sequences within endogenous RSS. Conclusions The RSS are cis-acting DNA motifs which are essential for V(DJ recombination of antigen receptor genes. Due to its specific binding affinity for RSS and κB-like transcription enhancer motifs, we hypothesize that KRC may be involved in the regulation of V(DJ recombination.

  18. Degree of resistance of hetero- and homozygous resistant genotypes of a target-site resistant blackgrass biotype (haplotype Leu1781 in dose-response experiments with clethodim and cycloxydim

    Directory of Open Access Journals (Sweden)

    Wagner, Jean

    2014-02-01

    Full Text Available In dose-response experiments and by molecular analyses the reaction of a black grass biotype (Alopecurus myosuroides with target site resistance to ACCase inhibitors (Ile1781-Leu was examined for the response to clethodim and cycloxydim and compared to the responses of the homozygous and heterozygous subpopulations. To decipher the population into the homo- and heterozygous sub-populations, individual plants of the resistant biotype were analyzed for the haplotype Leu1781 by means of SNP analytics (pyrosequencing. For the entire population, significant different resistance factors (RF of 8 and 153 resulted for clethodim and cycloxydim, respectively. For the heterozygous sub-population a RF of 6 was estimated for clethodim and 118 for cycloxydim. For the homozygous sub-population a RF of 10 for clethodim and 136 for cycloxydim was estimated. The RF between the homo- and heterozygous sub-populations for each herbicide were, however, not significantly different. Despite this, a tendency of the heterozygous sub-population being less resistant was indicated. Therefore, it is hypothesized that the selection of resistance depends not only on the herbicide used, but on the frequency of the genotypes in a field population. Furthermore, the significant different reaction of black grass with the haplotype 1781 to both tested herbicides reflects the meaning of the individual constellation of active ingredient, resistance mechanisms and genotype for selection and spread of resistance.

  19. 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

  20. Human Subtilisin Kexin Isozyme-1 (SKI-1)/Site-1 Protease (S1P) regulates cytoplasmic lipid droplet abundance: A potential target for indirect-acting anti-dengue virus agents.

    Science.gov (United States)

    Hyrina, Anastasia; Meng, Fanrui; McArthur, Steven J; Eivemark, Sharlene; Nabi, Ivan R; Jean, François

    2017-01-01

    Viral hijacking and manipulation of host-cell biosynthetic pathways by human enveloped viruses are shared molecular events essential for the viral lifecycle. For Flaviviridae members such as hepatitis C virus and dengue virus (DENV), one of the key subsets of cellular pathways that undergo manipulation is the lipid metabolic pathways, underlining the importance of cellular lipids and, in particular, lipid droplets (LDs) in viral infection. Here, we hypothesize that targeting cellular enzymes that act as key regulators of lipid homeostasis and LD formation could represent a powerful approach to developing a novel class of broad-spectrum antivirals against infection associated with all DENV serotypes (1-4) circulating around the world. Using PF-429242, an active-site-directed inhibitor of SKI-1/S1P, we demonstrate that inhibition of SKI-1/S1P enzymatic activity in human hepatoma Huh-7.5.1 cells results in a robust reduction of the LD numbers and LD-positive areas and provides a means of effectively inhibiting infection by DENV (1-4). Pre-treatment of Huh-7.5.1 cells with PF-429242 results in a dose-dependent inhibition of DENV infection [median inhibitory dose (EC50) = 1.2 microM; median cytotoxic dose (CC50) = 81 microM; selectivity index (SI) = 68)] and a ~3-log decrease in DENV-2 titer with 20 microM of PF-429242. Post-treatment of DENV-2 infected Huh-7.5.1 cells with PF-429242 does not affect viral RNA abundance, but it does compromise the assembly and/or release of infectious virus particles. PF-429242 antiviral activity is reversed by exogenous oleic acid, which acts as an inducer of LD formation in PF-429242-treated and non-treated control cells. Collectively, our results demonstrate that human SKI-1/S1P is a potential target for indirect-acting pan-serotypic anti-DENV agents and reveal new therapeutic opportunities associated with the use of lipid-modulating drugs for controlling DENV infection.

  1. Site Features

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of various site features from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times...

  2. 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

  3. Site Calibration

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    This Site Calibration report is describing the results of a measured site calibration for a site in Denmark. The calibration is carried out by DTU Wind Energy in accordance with Ref.[3] and Ref.[4]. The measurement period is given. The site calibration is carried out before a power performance...... measurement on a given turbine to clarify the influence from the terrain on the ratio between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment...

  4. Flanking region sequence information to refine microRNA target ...

    Indian Academy of Sciences (India)

    Prakash

    block of four bases or more could be required by the target sites to find suitable interactions with the targeting ... end, and (ii) randomized target UTRs retaining the same nucleotide composition, in order to avoid any ... analysis were the complete target region of 70-base flanking sequences around the microRNA target site.

  5. Antiproton Target

    CERN Multimedia

    1980-01-01

    Antiproton target used for the AA (antiproton accumulator). The first type of antiproton production target used from 1980 to 1982 comprised a rod of copper 3mm diameter and 120mm long embedded in a graphite cylinder that was itself pressed into a finned aluminium container. This assembly was air-cooled and it was used in conjunction with the Van der Meer magnetic horn. In 1983 Fermilab provided us with lithium lenses to replace the horn with a view to increasing the antiproton yield by about 30%. These lenses needed a much shorter target made of heavy metal - iridium was chosen for this purpose. The 50 mm iridium rod was housed in an extension to the original finned target container so that it could be brought very close to the entrance to the lithium lens. Picture 1 shows this target assembly and Picture 2 shows it mounted together with the lithium lens. These target containers had a short lifetime due to a combination of beam heating and radiation damage. This led to the design of the water-cooled target in...

  6. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Gómez Arranz, Paula

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed....

  7. Site assessment

    DEFF Research Database (Denmark)

    Villanueva, Héctor; Vesth, Allan

    This report describes the site assessment of given position in a given site, for a wind turbine with a well-defined hub height and rotor diameter. The analysis is carried out in accordance to IEC 61400-12-1 [1], and both an obstacle assessment and a terrain assessment are performed...

  8. Site calibration

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Georgieva Yankova, Ginka

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. The site calibration is carried out before a power performance measurement on a given turbine to clarify the influence from the terrain on the ratio...... between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment is detailed described in [2]. The possible measurement sector for power performance...... according to [1] is also described in [2] and no results from the site calibration have shown any necessary exclusion from this sector. All parts of the sensors and the measurement system have been installed by DTU....

  9. Randomized distributed access to mutually exclusive resources

    Directory of Open Access Journals (Sweden)

    Moshe Dror

    2005-01-01

    they generally suffer from the need for extensive interagent communication. In this paper, we develop a randomized approach to make multiagent resource-allocation decisions with the objective of maximizing expected concurrency measured by the number of the active agents. This approach does not assume a centralized mechanism and has no need for interagent communication. Compared to existing autonomous-decentralized-decision-making (ADDM-based approaches for resource-allocation, our work emphasizes achieving the highest degree of agent autonomy and is able to handle more general resource requirements.

  10. Targeted nanotechnology for cancer imaging.

    Science.gov (United States)

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

    2014-09-30

    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. Copyright © 2014 Elsevier B.V. All rights reserved.

  11. Superfund Sites

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — This layer represents active Superfund Sites published by the Environmental Protection Agency (EPA). These data were extracted from the Superfund Enterprise...

  12. Site characterization techniques

    Science.gov (United States)

    ,

    1995-01-01

    Geoelectrical methods have been used since the 1920's to search for metallic ore deposits. During the last decade, traditional mining geophysical techniques have been adapted for environmental site characterization. Geoelectrical geophysics is now a well developed engineering specialty, with different methods to focus both on a range of targets and on depths below the surface. Most methods have also been adapted to borehole measurements.

  13. Targeted Learning

    CERN Document Server

    van der Laan, Mark J

    2011-01-01

    The statistics profession is at a unique point in history. The need for valid statistical tools is greater than ever; data sets are massive, often measuring hundreds of thousands of measurements for a single subject. The field is ready to move towards clear objective benchmarks under which tools can be evaluated. Targeted learning allows (1) the full generalization and utilization of cross-validation as an estimator selection tool so that the subjective choices made by humans are now made by the machine, and (2) targeting the fitting of the probability distribution of the data toward the targe

  14. Integration sites of Epstein-Barr virus genome on chromosomes of human lymphoblastoid cell lines

    Energy Technology Data Exchange (ETDEWEB)

    Wuu, K.D.; Chen, Y.J.; Wang-Wuu, S. [Institute of Genetics, Taipei (Taiwan, Province of China)

    1994-09-01

    Epstein-Barr virus (EBV) is the pathogen of infectious mononucleosis. The viral genome is present in more than 95% of the African cases of Burkitt lymphoma and it is usually maintained in episomal form in the tumor cells. Viral integration has been described only for Nanalwa which is a Burkitt lymphoma cell line lacking episomes. In order to examine the role of EBV in the immortalization of human Blymphocytes, we investigated whether the EBV integration into the human genome is essential. If the integration does occur, we would like to know whether the integration is randomly distributed or whether the viral DNA integrates preferentially at certain sites. Fourteen in vitro immortalized human lymphoblastoid cell lines (LCLs) were examined by fluorescence in situ hybridization (FISH) with a biotinylated EBV BamHI w DNA fragment as probe. The episomal form of EBV DNA was found in all cells of these cell lines, while only about 65% of the cells have the integrated viral DNA. This might suggest that integration is not a pre-requisite for cell immortalization. Although all chromosomes, except Y, have been found with integrated viral genome, chromsomes 1 and 5 are the most frequent EBV DNA carrier (p<0.05). Nine chromosome bands, namely, 1p31, 1q31, 2q32, 3q13, 3q26, 5q14, 6q24, 7q31 and 12q21, are preferential targets for EBV integration (p<0.001). Eighty percent of the total 938 EBV hybridization signals were found to be at G-band-positive area. This suggests that the mechanism of EBV integration might be different from that of the retroviruses, which specifically integrate to G-band-negative areas. Thus, we conclude that the integration of EBV to host genome is non-random and it may have something to do with the structure of chromosome and DNA sequences.

  15. Sites internet

    Science.gov (United States)

    Couderc

    2000-07-01

    http://biotribune.com/ Biotribune.com ou la biologie medicale sur internet. Ce site est concu comme un portail sur la biologie clinique. Accueil d'internautes sur une page comportant, entre autres, les rubriques : actualite, evenements, revue des connaissances, rubrique juridique et petites annonces. Biotribune propose regulierement des dossiers rediges par des specialistes comportant une mise a jour des connaissances orientee sur l'interet diagnostique des tests de biologie clinique. Le site propose egalement une revue de presse scientifique avec des resumes courts d'articles parus dans les grands journaux internationaux tels que The Lancet, New England Journal of Medicine, Science, etc. Vous pouvez aussi y tester vos connaissances grace a des cas cliniques et des QCM. Ce site propose egalement des petites annonces pratiques pour les laboratoires de ville (remplacement, materiel d'occasion, etc.). Les problemes touchant l'assurance qualite, les RMO et la nomenclature font egalement l'objet d'information et de commentaires. Enfin, vous pourrez vous inscrire a l'un des forums proposes : discussion biomedicale ou opinion et reaction sur les sujets touchant au professionnel de la biologie medicale. En conclusion, un site complet et agreable que l'on souhaite voir s'enrichir et se renouveler regulierement. http://www.arcol.asso.fr Site du Comite francais de coordination de recherche sur l'atherosclerose et le cholesterol (Arcol). Ce site s'adresse a la fois aux cliniciens, aux biologistes et aux non-specialistes interesses par la pathologie cardio-vasculaire et ses traitements. On y trouve des rubriques tres didactiques sur la physiopathologie et les facteurs de risque de l'atherosclerose, la prise en charge nutritionnelle et medicamenteuse des patients. On peut tester ses connaissances a l'aide des nombreux cas cliniques richement commentes. Ce site regulierement mis a jour contient egalement les recommandations nationales et internationales sur la prise en charge du

  16. Site Practice

    DEFF Research Database (Denmark)

    Wahedi, Haseebullah

    2016-01-01

    different practices in the construction phase. The research is based on an ethnographic study of a case in Denmark. The empirical data were collected through direct observations and semi-structured interviews with site managers, contract managers, foremen and craftsmen. Findings revealed...... that the construction phase comprises several communities and practices, leading to various uses of the drawings. The results indicated that the craftsmen used drawings to position themselves in the correct location, and that the site managers and contract managers used them as management tools and legal documents...

  17. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2001-04-01

    The objectives, the programme, and the achievements of the Site Restoration Department of SCK-CEN in 2000 are summarised. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and activities related to the management of decommissioning projects. The department provides consultancy and services to external organisations.

  18. Targeted oxidation of Torpedo californica acetylcholinesterase by singlet oxygen: identification of N-formylkynurenine tryptophan derivatives within the active-site gorge of its complex with the photosensitizer methylene blue.

    Science.gov (United States)

    Triquigneaux, Mathilde M; Ehrenshaft, Marilyn; Roth, Esther; Silman, Israel; Ashani, Yakov; Mason, Ronald P; Weiner, Lev; Deterding, Leesa J

    2012-11-15

    The principal role of AChE (acetylcholinesterase) is termination of impulse transmission at cholinergic synapses by rapid hydrolysis of the neurotransmitter acetylcholine. The active site of AChE is near the bottom of a long and narrow gorge lined with aromatic residues. It contains a CAS (catalytic 'anionic' subsite) and a second PAS (peripheral 'anionic' site), the gorge mouth, both of which bind acetylcholine via π-cation interactions, primarily with two conserved tryptophan residues. It was shown previously that generation of (1)O(2) by illumination of MB (Methylene Blue) causes irreversible inactivation of TcAChE (Torpedo californica AChE), and suggested that photo-oxidation of tryptophan residues might be responsible. In the present study, structural modification of the TcAChE tryptophan residues induced by MB-sensitized oxidation was investigated using anti-N-formylkynurenine antibodies and MS. From these analyses, we determined that N-formylkynurenine derivatives were specifically produced from Trp(84) and Trp(279), present at the CAS and PAS respectively. Peptides containing these two oxidized tryptophan residues were not detected when the competitive inhibitors, edrophonium and propidium (which should displace MB from the gorge) were present during illumination, in agreement with their efficient protection against the MB-induced photo-inactivation. Thus the bound MB elicited selective action of (1)O(2) on the tryptophan residues facing on to the water-filled active-site gorge. The findings of the present study thus demonstrate the localized action and high specificity of MB-sensitized photo-oxidation of TcAChE, as well as the value of this enzyme as a model system for studying the mechanism of action and specificity of photosensitizing agents.

  19. Lys-63-linked Ubiquitination of γ-Aminobutyric Acid (GABA), Type B1, at Multiple Sites by the E3 Ligase Mind Bomb-2 Targets GABAB Receptors to Lysosomal Degradation*

    Science.gov (United States)

    Zemoura, Khaled; Trümpler, Claudia; Benke, Dietmar

    2016-01-01

    GABAB receptors are heterodimeric G protein-coupled receptors, which control neuronal excitability by mediating prolonged inhibition. The magnitude of GABAB receptor-mediated inhibition essentially depends on the amount of receptors in the plasma membrane. However, the factors regulating cell surface expression of GABAB receptors are poorly characterized. Cell surface GABAB receptors are constitutively internalized and either recycled to the plasma membrane or degraded in lysosomes. The signal that sorts GABAB receptors to lysosomes is currently unknown. Here we show that Mind bomb-2 (MIB2)-mediated Lys-63-linked ubiquitination of the GABAB1 subunit at multiple sites is the lysosomal sorting signal for GABAB receptors. We found that inhibition of lysosomal activity in cultured rat cortical neurons increased the fraction of Lys-63-linked ubiquitinated GABAB receptors and enhanced the expression of total as well as cell surface GABAB receptors. Mutational inactivation of four putative ubiquitination sites in the GABAB1 subunit significantly diminished Lys-63-linked ubiquitination of GABAB receptors and prevented their lysosomal degradation. We identified MIB2 as the E3 ligase triggering Lys-63-linked ubiquitination and lysosomal degradation of GABAB receptors. Finally, we show that sustained activation of glutamate receptors, a condition occurring in brain ischemia that down-regulates GABAB receptors, considerably increased the expression of MIB2 and Lys-63-linked ubiquitination of GABAB receptors. Interfering with Lys-63-linked ubiquitination by overexpressing ubiquitin mutants or GABAB1 mutants deficient in Lys-63-linked ubiquitination prevented glutamate-induced down-regulation of the receptors. These findings indicate that Lys-63-linked ubiquitination of GABAB1 at multiple sites by MIB2 controls sorting of GABAB receptors to lysosomes for degradation under physiological and pathological conditions. PMID:27573246

  20. Direct targeted glycation of the free sulfhydryl group of cysteine residue (Cys-34) of BSA. Mapping of the glycation sites of the anti-tumor Thomsen-Friedenreich neoglycoconjugate vaccine prepared by Michael addition reaction.

    Science.gov (United States)

    Demian, Wael L L; Kottari, Naresh; Shiao, Tze Chieh; Randell, Edward; Roy, René; Banoub, Joseph H

    2014-12-01

    We present in this manuscript the characterization of the exact glycation sites of the Thomsen-Friedenreich antigen-BSA vaccine (TF antigen:BSA) prepared using a Michael addition reaction between the saccharide antigen as an electrophilic acceptor and the nucleophilic thiol and L-Lysine ε-amino groups of BSA using different ligation conditions. Matrix laser desorption ionization time-of-flight mass spectrometry of the neoglycoconjugates prepared with TF antigen:protein ratios of 2:1 and 8:1, allowed to observe, respectively, the protonated molecules for each neoglycoconjugates: [M + H](+) at m/z 67,599 and 70,905. The measurements of these molecular weights allowed us to confirm exactly the carbohydrate:protein ratios of these two synthetic vaccines. These were found to be closely formed by a TF antigen:BSA ratios of 2:1 and 8:1, respectively. Trypsin digestion and liquid chromatography coupled with electrospray ionization mass spectrometry allowed us to identify the series of released glycopeptide and peptide fragments. De novo sequencing affected by low-energy collision dissociation tandem mass spectrometry was then employed to unravel the precise glycation sites of these neoglycoconjugate vaccines. Finally, we identified, respectively, three diagnostic and characteristic glycated peptides for the synthetic glycoconjugate possessing a TF antigen:BSA ratio 2:1, whereas we have identified for the synthetic glycoconjugate having a TF:BSA ratio 8:1 a series of 14 glycated peptides. The net increase in the occupancy sites of these neoglycoconjugates was caused by the large number of glycoforms produced during the chemical ligation of the synthetic carbohydrate antigen onto the protein carrier. Copyright © 2014 John Wiley & Sons, Ltd.

  1. Meeting the Aichi targets

    DEFF Research Database (Denmark)

    Funk, Stephan M; Conde, Dalia Amor; Lamoreux, John

    2017-01-01

    &s), is an excellent opportunity to achieve the Aichi 2020 Targets T11 (protected areas) and T12 (preventing species extinctions). AZE taxa have small, single-site populations that are especially vulnerable to human-induced extinctions, particularly for the many amphibians. We show that AZEs&s can be protected...... feasibly and cost-effectively, but action is urgent. We argue that the Alliance, whose initial main aim was to identify AZEs&s, must be followed up by a second-generation initiative that directs and co-ordinates AZE conservation activities on the ground. The prominent role of zoos, conservation NGOs...

  2. A role for the gene regulatory module microRNA172/TARGET OF EARLY ACTIVATION TAGGED 1/FLOWERING LOCUS T (miRNA172/TOE1/FT) in the feeding sites induced by Meloidogyne javanica in Arabidopsis thaliana.

    Science.gov (United States)

    Díaz-Manzano, Fernando E; Cabrera, Javier; Ripoll, Juan-José; Del Olmo, Iván; Andrés, Mari Fe; Silva, Ana Cláudia; Barcala, Marta; Sánchez, María; Ruíz-Ferrer, Virginia; de Almeida-Engler, Janice; Yanofsky, Martin F; Piñeiro, Manuel; Jarillo, Jose Antonio; Fenoll, Carmen; Escobar, Carolina

    2018-01-01

    Root knot nematodes (RKNs) penetrate into the root vascular cylinder, triggering morphogenetic changes to induce galls, de novo formed 'pseudo-organs' containing several giant cells (GCs). Distinctive gene repression events observed in early gall/GCs development are thought to be mediated by post-transcriptional silencing via microRNAs (miRNAs), a process that is far from being fully characterized. Arabidopsis thaliana backgrounds with altered activities based on target 35S::MIMICRY172 (MIM172), 35S::TARGET OF EARLY ACTIVATION TAGGED 1 (TOE1)-miR172-resistant (35S::TOE1R ) and mutant (flowering locus T-10 (ft-10)) lines were used for functional analysis of nematode infective and reproductive parameters. The GUS-reporter lines, MIR172A-E::GUS, treated with auxin (IAA) and an auxin-inhibitor (a-(phenyl ethyl-2-one)-indole-3-acetic acid (PEO-IAA)), together with the MIR172C AuxRE::GUS line with two mutated auxin responsive elements (AuxREs), were assayed for nematode-dependent gene expression. Arabidopsis thaliana backgrounds with altered expression of miRNA172, TOE1 or FT showed lower susceptibility to the RKNs and smaller galls and GCs. MIR172C-D::GUS showed restricted promoter activity in galls/GCs that was regulated by auxins through auxin-responsive factors. IAA induced their activity in galls while PEO-IAA treatment and mutations in AuxRe motifs abolished it. The results showed that the regulatory module miRNA172/TOE1/FT plays an important role in correct GCs and gall development, where miRNA172 is modulated by auxins. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

  3. Site Restoration

    Energy Technology Data Exchange (ETDEWEB)

    Noynaert, L.; Bruggeman, A.; Cornelissen, R.; Massaut, V.; Rahier, A

    2002-04-01

    The objectives, the programme, and the achievements of SCK-CEN's Site Restoration Department for 2001 are described. Main activities include the decommissioning of the BR3 PWR-reactor as well as other clean-up activities, projects on waste minimisation and the management of spent fuel and the flow of dismantled materials and the recycling of materials from decommissioning activities based on the smelting of metallic materials in specialised foundries. The department provides consultancy and services to external organisations and performs R and D on new techniques including processes for the treatment of various waste components including the reprocessing of spent fuel, the treatment of tritium, the treatment of liquid alkali metals into cabonates through oxidation, the treatment of radioactive organic waste and the reconditioning of bituminised waste products.

  4. ACTIVE TARGETING WITH PARTICULATE CARRIER SYSTEMS IN THE BLOOD COMPARTMENT

    NARCIS (Netherlands)

    CROMMELIN, DJA; SCHERPHOF, G; STORM, G

    1995-01-01

    This review deals with active targeting of particulate drug carriers through (1) physico-chemical (e.g., complex formation between a homing device and a surface exposed molecule at the target site) and (2) physical means, Target sites discussed are restricted to those in the blood circulation.

  5. Achieving Plant CRISPR Targeting that Limits Off-Target Effects

    Directory of Open Access Journals (Sweden)

    Jeffrey D. Wolt

    2016-11-01

    Full Text Available The CRISPR-Cas9 system (clustered regularly interspaced short palindromic repeats with associated Cas9 protein has been used to generate targeted changes for direct modification of endogenous genes in an increasing number of plant species; but development of plant genome editing has not yet fully considered potential off-target mismatches that may lead to unintended changes within the genome. Assessing the specificity of CRISPR-Cas9 for increasing editing efficiency as well as the potential for unanticipated downstream effects from off-target mutations is an important regulatory consideration for agricultural applications. Increasing genome-editing specificity entails developing improved design methods that better predict the prevalence of off-target mutations as a function of genome composition and design of the engineered ribonucleoprotein (RNP. Early results from CRISPR-Cas9 genome editing in plant systems indicate that the incidence of off-target mutation frequencies is quite low; however, by analyzing CRISPR-edited plant lines and improving both computational tools and reagent design, it may be possible to further decrease unanticipated effects at potential mismatch sites within the genome. This will provide assurance that CRISPR-Cas9 reagents can be designed and targeted with a high degree of specificity. Improved and experimentally validated design tools for discriminating target and potential off-target positions that incorporate consideration of the designed nuclease fidelity and selectivity will help to increase confidence for regulatory decision making for genome-edited plants.

  6. Site-directed mutagenesis, in vivo electroporation and mass spectrometry in search for determinants of the subcellular targeting of Rab7b paralogue in the model eukaryote Paramecium octaurelia.

    Science.gov (United States)

    Wyroba, E; Kwaśniak, P; Miller, K; Kobyłecki, K; Osińska, M

    2016-04-11

    Protein products of the paralogous genes resulting from the whole genome duplication may acquire new function. The role of post-translational modifications (PTM) in proper targeting of Paramecium Rab7b paralogue - distinct from that of Rab7a directly involved in phagocytosis - was studied using point mutagenesis, proteomic analysis and double immunofluorescence after in vivo electroporation of the mutagenized protein. Here we show that substitution of Thr200 by Ala200 resulted in diminished incorporation of [P32] by 37.4% and of 32 [C14-]UDP-glucose by 24%, respectively, into recombinant Rab7b_200 in comparison to the non-mutagenized control. Double confocal imaging revealed that Rab7b_200 was mistargeted upon electroporation into living cells contrary to non- mutagenized recombinant Rab7b correctly incorporated in the cytostome area. We identified the peptide ion at m/z=677.63+ characteristic for the glycan group attached to Thr200 in Rab7b using nano LC-MS/MS and comparing the peptide map of this protein with that after deglycosylation with the mixture of five enzymes of different specificity. Based on the mass of this peptide ion and quantitative radioactive assays with [P32]and  [C14-]UDP- glucose, the suggested composition of the adduct attached to Thr200 might be (Hex)1(HexNAc)1(Phos)3 or (HexNAc)1 (Deoxyhexose)1 (Phos)1 (HexA)1. These data indicate that PTM of Thr200 located in the hypervariable C-region of Rab7b in Paramecium is crucial for the proper localization/function of this protein. Moreover, these proteins differ also in other PTM: the number of phosphorylated amino acids in Rab7b is much higher than in Rab7a.

  7. Novel molecular multilevel targeted antitumor agents

    Directory of Open Access Journals (Sweden)

    Poonam Sonawane

    2017-01-01

    Conclusion: We believe that our receptor-directed intracellular organelle-targeted proteins can be employed for numerous specific and safer treatment applications when drugs have specific intracellular sites of their action.

  8. MEET ISOLDE - Target Production

    CERN Multimedia

    2017-01-01

    MEET ISOLDE - Target Production. Everything at ISOLDE starts with a target and the target production team realise on more then 50 years of experience to build and develop new targets for ISOLDE’s wide physics program.

  9. 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...

  10. Bitopic Ligands and Metastable Binding Sites

    DEFF Research Database (Denmark)

    Fronik, Philipp; Gaiser, Birgit I; Sejer Pedersen, Daniel

    2017-01-01

    G protein-coupled receptors (GPCRs) belong to a large superfamily of membrane receptors mediating a variety of physiological functions. As such they are attractive targets for drug therapy. However, it remains a challenge to develop subtype selective GPCR ligands due to the high conservation...... sites. Computational studies on ligand binding to GPCRs have revealed transient, low-affinity binding sites, termed metastable binding sites. Metastable binding sites may provide a new source of allosteric binding sites that could be exploited in the design of bitopic ligands. Unlike the bitopic ligands...

  11. 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)

  12. Protospacer adjacent motif (PAM)-distal sequences engage CRISPR Cas9 DNA target cleavage

    National Research Council Canada - National Science Library

    Cencic, Regina; Miura, Hisashi; Malina, Abba; Robert, Francis; Ethier, Sylvain; Schmeing, T Martin; Dostie, Josée; Pelletier, Jerry

    2014-01-01

    ...') protospacer adjacent motifs (PAM). Yet among 43 ChIP-seq sites harboring seed regions analyzed for mutational status, we find editing only at the intended on-target locus and one off-target site...

  13. Contaminated Sites in Iowa

    Data.gov (United States)

    Iowa State University GIS Support and Research Facility — Sites contaminated by hazardous materials or wastes. These sites are those administered by the Contaminated Sites Section of Iowa DNR. Many are sites which are...

  14. Triclosan–bacteria interactions: single or multiple target sites?

    National Research Council Canada - National Science Library

    Gomez Escalada, M; Russell, A.D; Maillard, J.‐Y; Ochs, D

    2005-01-01

    ...‐organisms at different stages of their phase of population growth. Methods and Results:  Triclosan minimum inhibitory concentrations against several test organisms were determined in broth and agar using standard protocols...

  15. Pharmacogenomics of GPCR Drug Targets

    DEFF Research Database (Denmark)

    Hauser, Alexander Sebastian; Chavali, Sreenivas; Masuho, Ikuo

    2017-01-01

    Natural genetic variation in the human genome is a cause of individual differences in responses to medications and is an underappreciated burden on public health. Although 108 G-protein-coupled receptors (GPCRs) are the targets of 475 (∼34%) Food and Drug Administration (FDA)-approved drugs...... and account for a global sales volume of over 180 billion US dollars annually, the prevalence of genetic variation among GPCRs targeted by drugs is unknown. By analyzing data from 68,496 individuals, we find that GPCRs targeted by drugs show genetic variation within functional regions such as drug......- and effector-binding sites in the human population. We experimentally show that certain variants of μ-opioid and Cholecystokinin-A receptors could lead to altered or adverse drug response. By analyzing UK National Health Service drug prescription and sales data, we suggest that characterizing GPCR variants...

  16. Processes and effects of targeted online advertising among children

    OpenAIRE

    Reijmersdal, E.A. van; 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 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)...

  17. Desert Test Site Uniformity Analysis

    Science.gov (United States)

    Kerola, Dana X.; Bruegge, Carol J.

    2009-01-01

    Desert test sites such as Railroad Valley (RRV) Nevada, Egypt-1, and Libya-4 are commonly targeted to assess the on-orbit radiometric performance of sensors. Railroad Valley is used for vicarious calibration experiments, where a field-team makes ground measurements to produce accurate estimates of top-of-atmosphere (TOA) radiances. The Sahara desert test sites are not instrumented, but provide a stable target that can be used for sensor cross-comparisons, or for stability monitoring of a single sensor. These sites are of interest to NASA's Atmospheric Carbon Observation from Space (ACOS) and JAXA's Greenhouse Gas Observation SATellite (GOSAT) programs. This study assesses the utility of these three test sites to the ACOS and GOSAT calibration teams. To simulate errors in sensor-measured radiance with pointing errors, simulated data have been created using MODIS Aqua data. MODIS data are further utilized to validate the campaign data acquired from June 22 through July 5, 2009. The first GOSAT vicarious calibration experiment was conducted during this timeframe.

  18. A novel putative miRNA target enhancer signal.

    Directory of Open Access Journals (Sweden)

    Thorsten Schmidt

    Full Text Available It is known that miRNA target sites are very short and the effect of miRNA-target site interaction alone appears as being unspecific. Recent experiments suggest further context signals involved in miRNA target site recognition and regulation. Here, we present a novel GC-rich RNA motif downstream of experimentally supported miRNA target sites in human mRNAs with no similarity to previously reported functional motifs. We demonstrate that the novel motif can be found in at least one third of all transcripts regulated by miRNAs. Furthermore, we show that motif occurrence and the frequency of miRNA target sites as well as the stability of their duplex structures correlate. The finding, that the novel motif is significantly associated with miRNA target sites, suggests a functional role of the motif in miRNA target site biology. Beyond, the novel motif has the impact to improve prediction of miRNA target sites significantly.

  19. Ocean Disposal Site Monitoring

    Science.gov (United States)

    EPA is responsible for managing all designated ocean disposal sites. Surveys are conducted to identify appropriate locations for ocean disposal sites and to monitor the impacts of regulated dumping at the disposal sites.

  20. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Rinne, C.A.; Curry, R.H.; Hagan, J.W.; Seiler, S.W.; Sommer, D.J. (Westinghouse Hanford Co., Richland, WA (USA)); Yancey, E.F. (Pacific Northwest Lab., Richland, WA (USA))

    1990-01-01

    The Hanford Site Development Plan (Site Development Plan) is intended to guide the short- and long-range development and use of the Hanford Site. All acquisition, development, and permanent facility use at the Hanford Site will conform to the approved plan. The Site Development Plan also serves as the base document for all subsequent studies that involve use of facilities at the Site. This revision is an update of a previous plan. The executive summary presents the highlights of the five major topics covered in the Site Development Plan: general site information, existing conditions, planning analysis, Master Plan, and Five-Year Plan. 56 refs., 67 figs., 31 tabs.

  1. Superfund Site Information - Site Sampling Data

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes Superfund site-specific sampling information including location of samples, types of samples, and analytical chemistry characteristics of...

  2. SITE COMPREHENSIVE LISTING (CERCLIS) (Superfund) - NPL Sites

    Data.gov (United States)

    U.S. Environmental Protection Agency — National Priorities List (NPL) Sites - The Comprehensive Environmental Response, Compensation and Liability Information System (CERCLIS) (Superfund) Public Access...

  3. 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

  4. Novel targeted therapies for inflammatory bowel disease

    DEFF Research Database (Denmark)

    Coskun, Mehmet; Vermeire, Severine; Nielsen, Ole Haagen

    2017-01-01

    Our growing understanding of the immunopathogenesis of inflammatory bowel disease (IBD) has opened new avenues for developing targeted therapies. These advances in treatment options targeting different mechanisms of action offer new hope for personalized management. In this review we highlight...... to intestinal sites of inflammation (e.g., sphingosine 1-phosphate receptor modulators). We also provide an update on the current status in clinical development of these new classes of therapeutics....

  5. Hanford Site Development Plan

    Energy Technology Data Exchange (ETDEWEB)

    Hathaway, H.B.; Daly, K.S.; Rinne, C.A.; Seiler, S.W.

    1993-05-01

    The Hanford Site Development Plan (HSDP) provides an overview of land use, infrastructure, and facility requirements to support US Department of Energy (DOE) programs at the Hanford Site. The HSDP`s primary purpose is to inform senior managers and interested parties of development activities and issues that require a commitment of resources to support the Hanford Site. The HSDP provides an existing and future land use plan for the Hanford Site. The HSDP is updated annually in accordance with DOE Order 4320.1B, Site Development Planning, to reflect the mission and overall site development process. Further details about Hanford Site development are defined in individual area development plans.

  6. Region 9 NPL Sites (Superfund Sites) Polygons

    Science.gov (United States)

    NPL site POLYGON locations for the US EPA Region 9. NPL (National Priorities List) sites are hazardous waste sites that are eligible for extensive long-term cleanup under the Superfund program. Eligibility is determined by a scoring method called Hazard Ranking System. Sites with high scores are listed on the NPL. Area covered by this data set include Arizona, California, Nevada, Hawaii, Guam, American Samoa, Northern Marianas and Trust Territories. Attributes include NPL status codes, NPL industry type codes and environmental indicators. Related table, NPL_Contaminants contains information about contaminated media types and chemicals. This is a one-to-many relate and can be related to the feature class using the relationship classes under the Feature Data Set ENVIRO_CONTAMINANT. Generally, each NPL polygon has a separate source. Information about sources for each polygon can be found in the related table, NPL_POLY_METADATA. This table contains a record for each site that has information about the source. Polygons for non-Federal Facility sites were updated in January, 2007 for the Superfund Work Load Models project. Each polygon was approved by the site RPM. Where available, the majority of these polygons represent the surface expression of the extent of the contamination. All Federal Facilities are represented by the facility boundary. The following sites currently have no polygon data available at this time: Alameda Naval Air Station, Jet Pr

  7. Targeting vaccines to dendritic cells

    DEFF Research Database (Denmark)

    Foged, Camilla; Sundblad, Anne; Hovgaard, Lars

    2002-01-01

    to be far superior to that of B-cells and macrophages. DC are localized at strategic places in the body at sites used by pathogens to enter the organism, and are thereby in an optimal position to capture antigens. In general, vaccination strategies try to mimic the invasiveness of the pathogens. DC...... are considered to play a central role for the provocation of primary immune responses by vaccination. A rational way of improving the potency and safety of new and already existing vaccines could therefore be to direct vaccines specifically to DC. There is a need for developing multifunctional vaccine drug...... delivery systems (DDS) with adjuvant effect that target DC directly and induce optimal immune responses. This paper will review the current knowledge of DC physiology as well as the progress in the field of novel vaccination strategies that directly or indirectly aim at targeting DC....

  8. Computational identification of uncharacterized cruzain binding sites.

    Directory of Open Access Journals (Sweden)

    Jacob D Durrant

    2010-05-01

    Full Text Available Chagas disease, caused by the unicellular parasite Trypanosoma cruzi, claims 50,000 lives annually and is the leading cause of infectious myocarditis in the world. As current antichagastic therapies like nifurtimox and benznidazole are highly toxic, ineffective at parasite eradication, and subject to increasing resistance, novel therapeutics are urgently needed. Cruzain, the major cysteine protease of Trypanosoma cruzi, is one attractive drug target. In the current work, molecular dynamics simulations and a sequence alignment of a non-redundant, unbiased set of peptidase C1 family members are used to identify uncharacterized cruzain binding sites. The two sites identified may serve as targets for future pharmacological intervention.

  9. Emerging targets in treating pain.

    Science.gov (United States)

    Chang, David S; Raghavan, Rahul; Christiansen, Sandy; Cohen, Steven P

    2015-08-01

    To provide an overview on drug targets and emerging pharmacological treatment options for chronic pain. Chronic pain poses an enormous socioeconomic burden for the more than 30% of people who suffer from it, costing over $600 billion per year in the USA. In recent years, there has been a surge in preclinical and clinical research endeavors to try to stem this epidemic. Preclinical studies have identified a wide array of potential targets, with some of the most promising translational research being performed on novel opioid receptors, cannabinoid receptors, selective ion channel blockers, cytokine inhibitors, nerve growth factor inhibitors, N-methyl-D-aspartate receptor antagonists, glial cell inhibitors, and bisphosphonates. There are many obstacles for the development of effective medications to treat chronic pain, including the inherent challenges in identifying pathophysiological mechanisms, the overlap and multiplicity of pain pathways, and off-target adverse effects stemming from the ubiquity of drug target receptor sites and the lack of highly selective receptor ligands. Despite these barriers, the number and diversity of potential therapies have continued to grow, to include disease-modifying and individualized drug treatments.

  10. Site amplifications for generic rock sites

    Science.gov (United States)

    Boore, D.M.; Joyner, W.B.

    1997-01-01

    Seismic shear-wave velocity as a function of depth for generic rock sites has been estimated from borehole data and studies of crustal velocities, and these velocities have been used to compute frequency-dependent amplifications for zero attenuation for use in simulations of strong ground motion. We define a generic rock site as one whose velocity at shallow depths equals the average of those from the rock sites sampled by the borehole data. Most of the boreholes are in populated areas; for that reason, the rock sites sampled are of particular engineering significance. We consider two generic rock sites: rock, corresponding to the bulk of the borehole data, and very hard rock, such as is found in glaciated regions in large areas of eastern North America or in portions of western North America. The amplifications on rock sites can be in excess of 3.5 at high frequencies, in contrast to the amplifications of less than 1.2 on very hard rock sites. The consideration of unattenuated amplification alone is computationally convenient, but what matters for ground-motion estimation is the combined effect of amplification and attenuation. For reasonable values of the attenuation parameter K0, the combined effect of attenuation and amplification for rock sites peaks between about 2 and 5 Hz with a maximum level of less than 1.8. The combined effect is about a factor of 1.5 at 1 Hz and is less than unity for frequencies in the range of 10 to 20 Hz (depending on K0). Using these amplifications, we find provisional values of about ???? = 70 bars and K0 = 0.035 sec for rock sites in western North America by fitting our empirically determined response spectra for an M 6.5 event to simulated values. The borehole data yield shear velocities (V??30) of 618 and 306 m/sec for "rock" and "soil" sites, respectively, when averaged over the upper 30 m. From this, we recommend that V??30 equals 620 and 310 m/sec for applications requiring the average velocity for rock and soil sites in

  11. 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

  12. 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

  13. Targeted therapies for cancer

    Science.gov (United States)

    ... so they cannot spread. How Does Targeted Therapy Work? Targeted therapy drugs work in a few different ... M. is also a founding member of Hi-Ethics and subscribes to the principles of the Health ...

  14. Reflectance Reference Targets (OTTER)

    Data.gov (United States)

    National Aeronautics and Space Administration — ABSTRACT: Spectral reflectance measurements of flat field targets as reference points representative of pseudo-invariant targets as measured by Spectron SE590...

  15. Reflectance Reference Targets (OTTER)

    Data.gov (United States)

    National Aeronautics and Space Administration — Spectral reflectance measurements of flat field targets as reference points representative of pseudo-invariant targets as measured by Spectron SE590 spectrophotometer

  16. Efficient on-site construction

    DEFF Research Database (Denmark)

    Thuesen, Christian Langhoff; Hvam, Lars

    2011-01-01

    selected market – optimising cost and value. Based on the platform, the company has managed to create a high-quality product at low cost. In fact, they have managed to reduce costs by more than 30 per cent, enabling the company to sell houses to people that normally would not be able to afford a house...... from the German platform such as: platform does not imply that “off-site manufacturing” is the most optimal production method, rather it is a matter of handling complexity; strong commitment and loyalty from the whole organization is needed; importance of having a specific customer focus (target...... costing); and incremental rather than radical innovation. Originality/value – The findings challenge the predominant understanding of industrialisation of the construction processes, illustrating how substantial improvements can be achieved through platform thinking, on-site production and traditional...

  17. Balancing target flexibility and target denaturation in computational fragment-based inhibitor discovery.

    Science.gov (United States)

    Foster, Theresa J; MacKerell, Alexander D; Guvench, Olgun

    2012-09-05

    Accounting for target flexibility and selecting "hot spots" most likely to be able to bind an inhibitor continue to be challenges in the field of structure-based drug design, especially in the case of protein-protein interactions. Computational fragment-based approaches using molecular dynamics (MD) simulations are a promising emerging technology having the potential to address both of these challenges. However, the optimal MD conditions permitting sufficient target flexibility while also avoiding fragment-induced target denaturation remain ambiguous. Using one such technology (Site Identification by Ligand Competitive Saturation, SILCS), conditions were identified to either prevent denaturation or identify and exclude trajectories in which subtle but important denaturation was occurring. The target system used was the well-characterized protein cytokine IL-2, which is involved in a protein-protein interface and, in its unliganded crystallographic form, lacks surface pockets that can serve as small-molecule binding sites. Nonetheless, small-molecule inhibitors have previously been discovered that bind to two "cryptic" binding sites that emerge only in the presence of ligand binding, highlighting the important role of IL-2 flexibility. Using the above conditions, SILCS with hydrophobic fragments was able to identify both sites based on favorable fragment binding while avoiding IL-2 denaturation. An important additional finding was that acetonitrile, a water-miscible fragment, fails to identify either site yet can induce target denaturation, highlighting the importance of fragment choice. Copyright © 2012 Wiley Periodicals, Inc.

  18. Targets for Precision Measurements

    Science.gov (United States)

    Loveland, W.; Yao, L.; Asner, D. M.; Baker, R. G.; Bundgaard, J.; Burgett, E.; Cunningham, M.; Deaven, J.; Duke, D. L.; Greife, U.; Grimes, S.; Heffner, M.; Hill, T.; Isenhower, D.; Klay, J. L.; Kleinrath, V.; Kornilov, N.; Laptev, A. B.; Massey, T. N.; Meharchand, R.; Qu, H.; Ruz, J.; Sangiorgio, S.; Selhan, B.; Snyder, L.; Stave, S.; Tatishvili, G.; Thornton, R. T.; Tovesson, F.; Towell, D.; Towell, R. S.; Watson, S.; Wendt, B.; Wood, L.

    2014-05-01

    The general properties needed in targets (sources) for high precision, high accuracy measurements are reviewed. The application of these principles to the problem of developing targets for the Fission TPC is described. Longer term issues, such as the availability of actinide materials, improved knowledge of energy losses and straggling and the stability of targets during irradiation are also discussed.

  19. Setting Asset Performance Targets

    NARCIS (Netherlands)

    Green, D.; Hodkiewicz, M.; Masschelein, S.; Schoenmaker, R.; Muruvan, S.

    2015-01-01

    Setting targets is a common way for organisations to establish performance expectations. However the validity of targets is challenged when performance is influenced by factors beyond the control of the manager. This project examines the issue of target setting for a single asset performance measure

  20. Rock Springs Site 12 hydraulic/explosive true in situ oil shale fracturing experiment

    Energy Technology Data Exchange (ETDEWEB)

    Parrish, R.L.; Boade, R.R.; Stevens, A.L.; Long, A. Jr.; Turner, T.F.

    1980-06-01

    The experiment plan involved the creation and characterization of three horizontal hydraulic fractures, followed by the insertion and simultaneous detonation of slurry explosive in the two lower fractures. Core analyses, wellbore logging, and airflow and /sup 85/Kr tracer tests were used for site characterization and assessment of the hydraulic and explosive fracturing. Tiltmeters, wellhead pressure and flow gages, and in-formation pressure, flow and crack-opening sensors were used to monitor hydrofracture creation and explosive insertion. Explosive detonation diagnostic data were taken with stress and time-of-arrival gages and surface and in-formation accelerometers. The post-fracturing assessments indicated that: (1) hydrofracture creation and explosive insertion and detonation were accomplished essentially as planned; (2) induced fractures were randomly distributed through the shale with no extensively fractured regions or dislocation of shale; and (3) enhancement of permeability was limited to enlargement of the explosive-filled fractures.

  1. Radar Observations of Recent Mars Landing Sites

    Science.gov (United States)

    Larsen, K. W.; Haldemann, A. F. C.; Jurgens, R. F.; Slade, M. A.

    2004-01-01

    The Mars Exploration Rovers Spirit and Opportunity will arrive at their respective landing sites of Gusev Crater and Terra Meridiani in January 2004. During the 2001 and 2003 Mars Oppositions both landing sites were targeted for a series of radar observations using the telescopes of the Goldstone Deep Space Communications Complex (GDSCC). This paper will present results of terrestrial delay- Doppler radar observations of the landing sites, predictions for the surface properties that will be encountered, and, after successful landings, correlation between the predicted and observed surface properties. The in-situ observations made by both missions serve as ground truth for the validation of the high resolution radar mapping results.

  2. Validation of molecular targets in prostate cancer.

    NARCIS (Netherlands)

    Schalken, J.A.

    2005-01-01

    As prostate cancer is not a single disease, it is important to identify the pivotal pathway in the patient being treated. The molecular environment is the site of current oncological research to define new therapeutic targets for hormone-refractory disease, offering the potential to eventually

  3. NPL Site Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  4. NPL Site Locations

    Data.gov (United States)

    U.S. Environmental Protection Agency — The National Priorities List (NPL) is a list published by EPA of Superfund sites. A site must be added to this list before remediation can begin under Superfund. The...

  5. Site Area Boundaries

    Data.gov (United States)

    U.S. Environmental Protection Agency — This dataset consists of site boundaries from multiple Superfund sites in U.S. EPA Region 8. These data were acquired from multiple sources at different times and...

  6. Development of distributed target

    CERN Document Server

    Yu Hai Jun; Li Qin; Zhou Fu Xin; Shi Jin Shui; Ma Bing; Chen Nan; Jing Xiao Bing

    2002-01-01

    Linear introduction accelerator is expected to generate small diameter X-ray spots with high intensity. The interaction of the electron beam with plasmas generated at the X-ray converter will make the spot on target increase with time and debase the X-ray dose and the imaging resolving power. A distributed target is developed which has about 24 pieces of thin 0.05 mm tantalum films distributed over 1 cm. due to the structure adoption, the distributed target material over a large volume decreases the energy deposition per unit volume and hence reduces the temperature of target surface, then reduces the initial plasma formalizing and its expansion velocity. The comparison and analysis with two kinds of target structures are presented using numerical calculation and experiments, the results show the X-ray dose and normalized angle distribution of the two is basically the same, while the surface of the distributed target is not destroyed like the previous block target

  7. Site-specific attachment to recombinant antibodies via introduced surface cysteine residues.

    Science.gov (United States)

    Lyons, A; King, D J; Owens, R J; Yarranton, G T; Millican, A; Whittle, N R; Adair, J R

    1990-08-01

    Many diagnostic and therapeutic applications of monoclonal antibodies require the covalent linking of effector or reporter molecules to the immunoglobulin polypeptides. Existing methods generally involve the non-selective modification of amino acid side chains, producing one or more randomly distributed attachment sites. This results in heterogeneous labelling of the antibody molecules and often to a decrease in antigen-binding due to the modification of residues close to the antigen-binding site. We report a novel strategy for site-specifically labelling antibodies through surface cysteine residues. Examination of molecular structures was used to identify amino acids of the CH1 domain of the IgG heavy chain that were accessible to solvent but not to larger molecules. Site-directed mutagenesis was used to substitute cysteine residues at these positions in the heavy chain of a mouse/human chimaeric version of the tumour-binding monoclonal antibody, B72.3. Expression of the modified antibody genes in mammalian cells yielded correctly assembled proteins that had thiol groups in pre-determined positions and showed no loss of antigen-binding activity. One of the mutants was used to demonstrate the site-specific attachment of a radio-iodinated ligand to the chimaeric B72.3 antibody.

  8. Drupal 7 Multilingual Sites

    CERN Document Server

    Pol, Kristen

    2012-01-01

    A practical book with plenty of screenshots to guide you through the many features of multilingual Drupal. A demo ecommerce site is provided if you want to practice on a sample site, although you can apply the techniques learnt in the book directly to your site too. Any Drupal users who know the basics of building a Drupal site and are familiar with the Drupal UI, will benefit from this book. No previous knowledge of localization or internationalization is required.

  9. Site Calibration report

    DEFF Research Database (Denmark)

    Gómez Arranz, Paula; Vesth, Allan

    This report describes the site calibration carried out at Østerild, during a given period. The site calibration was performed with two Windcube WLS7 (v1) lidars at ten measurements heights. The lidar is not a sensor approved by the current version of the IEC 61400-12-1 [1] and therefore the site...

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

    Energy Technology Data Exchange (ETDEWEB)

    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.

  11. A ligand's view of target similarity

    DEFF Research Database (Denmark)

    Garland, Stephen L; Gloriam, David E

    2011-01-01

    shows with several examples how focusing on the binding site(s) has a clear advantage when it comes to establishing sequence-correlated pharmacological profiles. By organizing and comparing sequence and structural data it is possible to "borrow" SAR from similar targets to increase the speed of lead......-finding and, potentially, to produce ligands for previously intractable receptors. Sequence motifs correlated with ligands can be applied in the design of target-specific focused libraries that are both efficient and cost-effective and should provide increased hit-rates over diversity screening. Furthermore......, in the optimization phase, the binding motif approach offers the possibility to identify quickly the most likely off-target candidates to be chosen for selectivity screening, as well as potentially characterizing those pockets which may best be exploited for improved selectivity....

  12. Olkiluoto site description 2011

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2012-12-15

    This fourth version of the Olkiluoto Site Report, produced by the OMTF (Olkiluoto Modelling Task Force), updates the Olkiluoto Site Report 2008 with the data and knowledge obtained up to December 2010. A descriptive model of the site (the Site Descriptive Model, SDM), i.e. a model describing the geological and hydrogeological structure of the site, properties of the bedrock and the groundwater and its flow, and the associated interacting processes and mechanisms. The SDM is divided into six parts: surface system, geology, rock mechanics, hydrogeology, hydrogeochemistry and transport properties.

  13. Site Calibration, FGW

    DEFF Research Database (Denmark)

    Kock, Carsten Weber; Vesth, Allan

    This Site Calibration report is describing the results of a measured site calibration for a site in Denmark. The calibration is carried out by DTU Wind Energy in accordance with Ref.[3] and Ref.[4]. The measurement period is given. The site calibration is carried out before a power performance...... measurement on a given turbine to clarify the influence from the terrain on the ratio between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment...

  14. Site Environmental Report, 1993

    Energy Technology Data Exchange (ETDEWEB)

    1994-06-01

    The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, ``General Environmental Protection Program.`` This 1993 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, US Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in the Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here.

  15. Selecting a repository site

    Energy Technology Data Exchange (ETDEWEB)

    Ghovanlou, A.H. (MITRE Corp., McLean, VA); Ettlinger, L.; Cotton, T.; Barnard, W.; Siever, R.

    1982-01-01

    Present knowledge about the regional and local geologic predictions as it relates to waste repository sites and some related knowledge gained from oil and mining explorations are summarized. The types of geologic testing involved in selecting a repository site are described, and a simple analytic scheme for estimating the costs of such a program is discussed. This scheme is based on the sequential accumulation of knowledge throughout the process of siting. It is concluded that several sites should be investigated simultaneously since there is a trade-off to be made between the economic costs of carrying forward all the sites that pass the screening process and the political costs of selecting from a limited number of qualified sites. This would help to insure that a qualified site would be publicly acceptable at some point in the future. (BLM)

  16. Inertial Confinement fusion targets

    Science.gov (United States)

    Hendricks, C. D.

    1982-01-01

    Inertial confinement fusion (ICF) targets are made as simple flat discs, as hollow shells or as complicated multilayer structures. Many techniques were devised for producing the targets. Glass and metal shells are made by using drop and bubble techniques. Solid hydrogen shells are also produced by adapting old methods to the solution of modern problems. Some of these techniques, problems, and solutions are discussed. In addition, the applications of many of the techniques to fabrication of ICF targets is presented.

  17. Target Window Reliability

    Energy Technology Data Exchange (ETDEWEB)

    Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-02-11

    The target window design implemented and tested in experiments at ANL have performed without failure for the available beam of 6 mm FWHM on a 12 mm diameter target. However, scaling that design to a 25 mm diameter target size for a 12 mm FWHM beam has proven problematic. Combined thermal and mechanical (pressure induced) stresses and strains are too high to maintain the small coolant gaps and provide adequate fatigue lifetime.

  18. The ISOLDE target robots

    CERN Multimedia

    Maximilein Brice

    2002-01-01

    ISOLDE targets need to be changed frequently, around 80 times per year. The high radiation levels do not permit this to be done by human hands and the target changes are effected by 2 industrial robots (picture _01). On the left, in the distance, the front-end of the GPS (General Purpose Separator) is seen, while the HRS (High Resolution Separator) is at the right. Also seen are the doors to the irradiated-target storage.

  19. Hanford Site Comprehensive site Compliance Evaluation Report

    Energy Technology Data Exchange (ETDEWEB)

    Tollefson, K.S.

    1997-08-05

    This document is the second annual submittal by WHC, ICF/KH, PNL and BHI and contains the results of inspections of the stormwater outfalls listed in the Hanford Site Storm Water Pollution Prevention Plan (SWPPP) (WHC 1993a) as required by General Permit No. WA-R-00-000F (WA-R-00-A17F): This report also describes the methods used to conduct the Storm Water Comprehensive Site Compliance Evaluation, as required in Part IV, Section D, {ampersand} C of the General Permit, summarizes the results of the compliance evaluation, and documents significant leaks and spills.

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

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    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.

  1. Earthquake Hazards Program: Risk-Targeted Ground Motion Calculator

    Data.gov (United States)

    U.S. Geological Survey, Department of the Interior — This tool is used to calculate risk-targeted ground motion values from probabilistic seismic hazard curves in accordance with the site-specific ground motion...

  2. Tumor-Targeting Peptides for Therapeutic Gene Delivery

    National Research Council Canada - National Science Library

    Pasqualini, Renata

    2000-01-01

    The identification of markers expressed on specific tumors would give valuable insights into the specialization of tumor vasculature, and would also provide a means of targeting distinct tumor sites...

  3. Targeting the tumor microenvironment

    Energy Technology Data Exchange (ETDEWEB)

    Kenny, P.A.; Lee, G.Y.; Bissell, M.J.

    2006-11-07

    Despite some notable successes cancer remains, for the most part, a seemingly intractable problem. There is, however, a growing appreciation that targeting the tumor epithelium in isolation is not sufficient as there is an intricate mutually sustaining synergy between the tumor epithelial cells and their surrounding stroma. As the details of this dialogue emerge, new therapeutic targets have been proposed. The FDA has already approved drugs targeting microenvironmental components such as VEGF and aromatase and many more agents are in the pipeline. In this article, we describe some of the 'druggable' targets and processes within the tumor microenvironment and review the approaches being taken to disrupt these interactions.

  4. Target Assembly Facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Target Assembly Facility integrates new armor concepts into actual armored vehicles. Featuring the capability ofmachining and cutting radioactive materials, it...

  5. Determination of the accuracy for targeted irradiations of cellular substructures at SNAKE

    Energy Technology Data Exchange (ETDEWEB)

    Siebenwirth, C. [Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München, Munich (Germany); Institut für Angewandte Physik und Messtechnik (LRT2), Universität der Bundeswehr München, Neubiberg (Germany); Greubel, C. [Institut für Angewandte Physik und Messtechnik (LRT2), Universität der Bundeswehr München, Neubiberg (Germany); Drexler, S.E. [Department of Radiation Oncology, Ludwig-Maximilians-Universität München, Munich (Germany); Girst, S.; Reindl, J. [Institut für Angewandte Physik und Messtechnik (LRT2), Universität der Bundeswehr München, Neubiberg (Germany); Walsh, D.W.M. [Institut für Angewandte Physik und Messtechnik (LRT2), Universität der Bundeswehr München, Neubiberg (Germany); Department of Radiation Oncology, Klinikum rechts der Isar, Technische Universität München, Munich (Germany); Dollinger, G. [Institut für Angewandte Physik und Messtechnik (LRT2), Universität der Bundeswehr München, Neubiberg (Germany); Friedl, A.A. [Department of Radiation Oncology, Ludwig-Maximilians-Universität München, Munich (Germany); and others

    2015-04-01

    In the last 10 years the ion microbeam SNAKE, installed at the Munich 14 MV tandem accelerator, has been successfully used for radiobiological experiments by utilizing pattern irradiation without targeting single cells. Now for targeted irradiation of cellular substructures a precise irradiation device was added to the live cell irradiation setup at SNAKE. It combines a sub-micrometer single ion irradiation facility with a high resolution optical fluorescence microscope. Most systematic errors can be reduced or avoided by using the same light path in the microscope for beam spot verification as well as for and target recognition. In addition online observation of the induced cellular responses is possible. The optical microscope and the beam delivering system are controlled by an in-house developed software which integrates the open-source image analysis software, CellProfiler, for semi-automatic target recognition. In this work the targeting accuracy was determined by irradiation of a cross pattern with 55 MeV carbon ions on nucleoli in U2OS and HeLa cells stably expressing a GFP-tagged repair protein MDC1. For target recognition, nuclei were stained with Draq5 and nucleoli were stained with Syto80 or Syto83. The damage response was determined by live-cell imaging of MDC1-GFP accumulation directly after irradiation. No systematic displacement and a random distribution of about 0.7 μm (SD) in x-direction and 0.8 μm (SD) in y-direction were observed. An independent analysis after immunofluorescence staining of the DNA damage marker yH2AX yielded similar results. With this performance a target with a size similar to that of nucleoli (i.e. a diameter of about 3 μm) is hit with a probability of more than 80%, which enables the investigation of the radiation response of cellular subcompartments after targeted ion irradiation in the future.

  6. Target visibility for multiple maneuvering target tracking

    Science.gov (United States)

    Sabordo, Madeleine G.; Aboutanios, Elias

    2015-05-01

    We present a recursion of the probability of target visibility and its applications to analysis of track life and termination in the context of Global Nearest Neighbour (GNN) approach and Probability Hypothesis Density (PHD) filter. In the presence of uncertainties brought about by clutter; decisions to retain a track, terminate it or initialise a new track are based on probability, rather than on distance criterion or estimation error. The visibility concept is introduced into a conventional data-association-oriented multitarget tracker, the GNN; and a random finite set based-tracker, the PHD filter, to take into account instances when targets become invisible or occluded by obstacles. We employ the natural logarithmof the Dynamic Error Spectrum to assess the performance of the trackers with and without probability of visibility incorporated. Simulation results show that the performance of the GNN tracker with visibility concept incorporated is significantly enhanced.

  7. Investigation of Beamforming Patterns from Volumetric Randomly Distributed Phased Arrays

    Science.gov (United States)

    2017-03-01

    Introduction Modern wireless technologies, such as ad-hoc networking, require agile and controllable antennas on their frontends. These networks often...Traditionally, these antennas are designed as periodic structures, where each element is placed in a lattice. The elements constructively add in

  8. Stimulated luminescence emission from localized recombination in randomly distributed defects

    DEFF Research Database (Denmark)

    Jain, Mayank; Guralnik, Benny; Andersen, Martin Thalbitzer

    2012-01-01

    results in a highly asymmetric TL peak; this peak can be understood to derive from a continuum of several first-order TL peaks. Our model also shows an extended power law behaviour for OSL (or prompt luminescence), which is expected from localized recombination mechanisms in materials with random...

  9. Frozen spin targets

    CERN Document Server

    Parsons, A S L

    1976-01-01

    Describes six projects which use the frozen-spin principle: Helium-3 R.M.S. and longitudinally polarized frozen spin targets at Rutherford Laboratory, and the frozen spin targets at KEK, Saclay and the one used by the CERN-Helsinki collaboration. (7 refs).

  10. 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...

  11. Strategic Targeted Advertising

    NARCIS (Netherlands)

    A. Galeotti; J.L. Moraga-Gonzalez (José Luis)

    2003-01-01

    textabstractWe present a strategic game of pricing and targeted-advertising. Firms can simultaneously target price advertisements to different groups of customers, or to the entire market. Pure strategy equilibria do not exist and thus market segmentation cannot occur surely. Equilibria exhibit

  12. Segmented Target Design

    Science.gov (United States)

    Merhi, Abdul Rahman; Frank, Nathan; Gueye, Paul; Thoennessen, Michael; MoNA Collaboration

    2013-10-01

    A proposed segmented target would improve decay energy measurements of neutron-unbound nuclei. Experiments like this have been performed at the National Superconducting Cyclotron Laboratory (NSCL) located at Michigan State University. Many different nuclei are produced in such experiments, some of which immediately decay into a charged particle and neutron. The charged particles are bent by a large magnet and measured by a suite of charged particle detectors. The neutrons are measured by the Modular Neutron Array (MoNA) and Large Multi-Institutional Scintillation Array (LISA). With the current target setup, a nucleus in a neutron-unbound state is produced with a radioactive beam impinged upon a beryllium target. The resolution of these measurements is very dependent on the target thickness since the nuclear interaction point is unknown. In a segmented target using alternating layers of silicon detectors and Be-targets, the Be-target in which the nuclear reaction takes place would be determined. Thus the experimental resolution would improve. This poster will describe the improvement over the current target along with the status of the design. Work supported by Augustana College and the National Science Foundation grant #0969173.

  13. The CNGS target

    CERN Multimedia

    Patrice Loïez

    2005-01-01

    The CERN Neutrinos to Gran Sasso (CNGS) target ‘magazine’ of five target units. Each unit contains a series of 10-cm long graphite rods distributed over a length of 2 m. It is designed to maximize the number of secondary particles produced and hence the number of neutrinos. One unit is used at a time to prevent over heating.

  14. Targeting vulnerable households in urban Burkina Faso: effectiveness of geographical criteria but not of proxy-means testing.

    Science.gov (United States)

    Fortin, Sonia; Kameli, Yves; Ouattara, Ali; Castan, Florence; Perenze, Maria L; Kankouan, Justine; Traore, Alladari; Kouanda, Seni; Conte, Annalisa; Martin-Prével, Yves

    2016-06-01

    The 2007/2008 food prices hike has increased the interest in social safety nets programmes to fight food insecurity. Targeting the most in need is central to achieve effectiveness of such interventions. In 2009 in Ouagadougou, Burkina Faso, a food voucher (FV) programme targeted the 25 000 most vulnerable households (8.3% of the population). Targeting used a two-stage process: first geographical selection of poorest districts (∼90 000 households); then, in those districts, identification of the most vulnerable households according to a proxy-means test (PMT). Targeted households were entitled to receive FV for 1 year. A first survey was conducted at the beginning of the FV distribution on a representative sample of 2273 households drawn from the poorest districts. One year later a second survey, conducted on a subsample of same households (n = 901), identified those who actually received FV (beneficiary). The performance of the whole process was assessed against household food expenditure, used as the reference measure for vulnerability with a cut-off point of 1513 FCFA (corresponding to the 8.3th percentile of the distribution of expenditure). The 'normalized share of transfers going to vulnerable households' (NSTVH), i.e. proportion of FVs allocated to households below the cut-point, was the main criteria of judgement. Almost twice as many FV were allocated to vulnerable households as compared with a theoretical random distribution all over Ouagadougou (NSTVH = 1.85). When considering the sole targeted districts the NSTVH was only 0.84 (i.e. no more effective than a random distribution), meaning that the geographical stage was effective to select vulnerable districts while the PMT did not perform well to identify the most vulnerable households in those districts. Results could have been improved if only targeted households had received FV (NSTVH = 2.61 and 1.18 for the whole Ouagadougou and targeted districts, respectively). Improved targeting

  15. Site environmental programs

    Energy Technology Data Exchange (ETDEWEB)

    Schmidt, J.W.; Hanf, R.W.

    1995-06-01

    This section of the 1994 Hanford Site Environmental Report summarizes the site environmental programs. Effluent monitoring and environmental surveillance programs monitor for impacts from operations in several areas. The first area consists of the point of possible release into the environment. The second area consists of possible contamination adjacent to DOE facilities, and the third area is the general environment both on and off the site.

  16. Targeted therapy in lymphoma

    Directory of Open Access Journals (Sweden)

    Cavalli Franco

    2010-11-01

    Full Text Available Abstract Discovery of new treatments for lymphoma that prolong survival and are less toxic than currently available agents represents an urgent unmet need. We now have a better understanding of the molecular pathogenesis of lymphoma, such as aberrant signal transduction pathways, which have led to the discovery and development of targeted therapeutics. The ubiquitin-proteasome and the Akt/mammalian target of rapamycin (mTOR pathways are examples of pathological mechanisms that are being targeted in drug development efforts. Bortezomib (a small molecule protease inhibitor and the mTOR inhibitors temsirolimus, everolimus, and ridaforolimus are some of the targeted therapies currently being studied in the treatment of aggressive, relapsed/refractory lymphoma. This review will discuss the rationale for and summarize the reported findings of initial and ongoing investigations of mTOR inhibitors and other small molecule targeted therapies in the treatment of lymphoma.

  17. Targets and teamwork

    DEFF Research Database (Denmark)

    Skinner, Timothy C; Lange, Karin S; Hoey, Hilary

    2017-01-01

    with less disagreement about recommended targets. Multiple regression analysis indicated that teams reporting higher HbA1c targets and more target disagreement had parents reporting higher treatment targets. This seemed to partially account for center differences in Hb1Ac. Conclusions: The diabetes care....... Research Design and Methods: Children, under the age of 11 with type 1 diabetes and their parents treated at the study centers participated. Clinical, medical, and demographic data were obtained, along with blood sample for centralized assay. Parents and all members of the diabetes care team completed...... questionnaires on treatment targets for hemoglobin A1c (HbA1c) and recommended frequency of blood glucose monitoring. Results: Totally 1113 (53% male) children (mean age 8.0±2.1years) from 18 centers in 17 countries, along with parents and 113 health-care professionals, participated. There were substantial...

  18. 1994 Site environmental report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-07-01

    The Fernald site is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the site in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the site. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1994 SER provides the general public as well as scientists and engineers with the results from the site`s ongoing Environmental Monitoring Program. Also included in this report is information concerning the site`s progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (USEPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish to read more detailed descriptions of the information than those which are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  19. Explaining the effects of targeted online advertising on children's cognitive, affective, and behavioral brand responses

    NARCIS (Netherlands)

    van Reijmersdal, E.; Rozendaal, E.; Smink, N.; van Noort, G.; Buijzen, M.

    2013-01-01

    Increasingly, information from children's profile pages on social network sites is used to target online advertising. This practice has raised concerns in society and academia, however, effects of profile targeting on children remained unstudied. Therefore, this study focused on children's

  20. Midcourse Guidance Law Based on High Target Acquisition Probability Considering Angular Constraint and Line-of-Sight Angle Rate Control

    Directory of Open Access Journals (Sweden)

    Xiao Liu

    2016-01-01

    Full Text Available Random disturbance factors would lead to the variation of target acquisition point during the long distance flight. To acquire a high target acquisition probability and improve the impact precision, missiles should be guided to an appropriate target acquisition position with certain attitude angles and line-of-sight (LOS angle rate. This paper has presented a new midcourse guidance law considering the influences of random disturbances, detection distance restraint, and target acquisition probability with Monte Carlo simulation. Detailed analyses of the impact points on the ground and the random distribution of the target acquisition position in the 3D space are given to get the appropriate attitude angles and the end position for the midcourse guidance. Then, a new formulation biased proportional navigation (BPN guidance law with angular constraint and LOS angle rate control has been derived to ensure the tracking ability when attacking the maneuvering target. Numerical simulations demonstrates that, compared with the proportional navigation guidance (PNG law and the near-optimal spatial midcourse guidance (NSMG law, BPN guidance law demonstrates satisfactory performances and can meet both the midcourse terminal angular constraint and the LOS angle rate requirement.

  1. 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

  2. Preliminary Site Characterization Report, Rulsion Site, Colorado

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-08-01

    This report is a summary of environmental information gathered during a review of the documents pertaining to Project Rulison and interviews with personnel who worked on the project. Project Rulison was part of Operation Plowshare (a program designed to explore peaceful uses for nuclear devices). The project consisted of detonating a 43-kiloton nuclear device on September 10, 1969, in western Colorado to stimulate natural gas production. Following the detonation, a reentry well was drilled and several gas production tests were conducted. The reentry well was shut-in after the last gas production test and was held in standby condition until the general cleanup was undertaken in 1972. A final cleanup was conducted after the emplacement and testing wells were plugged in 1976. However, some surface radiologic contamination resulted from decontamination of the drilling equipment and fallout from the gas flaring during drilling operations. With the exception of the drilling effluent pond, all surface contamination at the Rulison Site was removed during the cleanup operations. All mudpits and other excavations were backfilled, and both upper and lower drilling pads were leveled and dressed. This report provides information regarding known or suspected areas of contamination, previous cleanup activities, analytical results, a review of the regulatory status, the site`s physical environment, and future recommendations for Project Ruhson. Based on this research, several potential areas of contamination have been identified. These include the drilling effluent pond and mudpits used during drilling operations. In addition, contamination could migrate in the gas horizon.

  3. Subcellular drug targeting, pharmacokinetics and bioavailability.

    Science.gov (United States)

    Leucuta, Sorin Emilian

    2014-02-01

    Effective treatment of diseases at the molecular level is possible by directing the drug substance (micromolecular, protein or peptide drugs, DNA, oligonucleotides, siRNA) with the aid of a specialized nanoparticulate carrier, for safe and effective transport to the specific site of action in the cytosol and its organelles including nuclear targeting. To achieve efficient cytosolic delivery of therapeutics or nuclear targeting, different drug delivery systems (DDS) have been developed (macromolecular drug conjugates, chemically or genetically modified proteins, and particulate drug carriers) capable of subcellular internalization overcoming the biological barriers, by passive targeting and especially by active targeting (receptor-targeted delivery). The success depends on the physicochemical nature of DDS, intracellular barriers that these systems need to overcome, the bioavailability of the bioactive drug, biodistribution, the intracellular pharmacokinetics and its influence on the pharmacodynamic effect. Models necessary for this purpose exist but they need to be more developed especially with quantitative treatments, after the development of the means of highlighting the evolution of the drug substance in biophase or at the level of the target cellular organelle by quantitative assays. It is expected that intracellularly targeted drug delivery approaches will be clinically useful using specialized DDSs belonging to the pharmaceutical nanotechnologies.

  4. Cisplatin Targeting of Bacterial Ribosomal RNA Hairpins

    Directory of Open Access Journals (Sweden)

    Gayani N. P. Dedduwa-Mudalige

    2015-09-01

    Full Text Available Cisplatin is a clinically important chemotherapeutic agent known to target purine bases in nucleic acids. In addition to major deoxyribonucleic acid (DNA intrastrand cross-links, cisplatin also forms stable adducts with many types of ribonucleic acid (RNA including siRNA, spliceosomal RNAs, tRNA, and rRNA. All of these RNAs play vital roles in the cell, such as catalysis of protein synthesis by rRNA, and therefore serve as potential drug targets. This work focused on platination of two highly conserved RNA hairpins from E. coli ribosomes, namely pseudouridine-modified helix 69 from 23S rRNA and the 790 loop of helix 24 from 16S rRNA. RNase T1 probing, MALDI mass spectrometry, and dimethyl sulfate mapping revealed platination at GpG sites. Chemical probing results also showed platination-induced RNA structural changes. These findings reveal solvent and structural accessibility of sites within bacterial RNA secondary structures that are functionally significant and therefore viable targets for cisplatin as well as other classes of small molecules. Identifying target preferences at the nucleotide level, as well as determining cisplatin-induced RNA conformational changes, is important for the design of more potent drug molecules. Furthermore, the knowledge gained through studies of RNA-targeting by cisplatin is applicable to a broad range of organisms from bacteria to human.

  5. Site-Specific Innovation

    DEFF Research Database (Denmark)

    Reeh, Henrik; Hemmersam, Peter

    2015-01-01

    Currently, cities across the Northern European region are actively redeveloping their former industrial harbours. Indeed, harbours areas are essential in the long-term transition from industrial to information and experience societies; harbours are becoming sites for new businesses and residences...... question is how innovation may contribute to urban life and site-specific qualities....

  6. The Greenland Ramsar Sites

    DEFF Research Database (Denmark)

    Egevang, C.; Boertmann, D.

    The eleven Ramsar sites in Greenland are reviewed in terms of their status as habitats for waterbirds and other fauna. Management and monitoring is proposed, as well as revisions of their boundaries. A number of potential new Ramsar sites are described...

  7. Site characterization handbook

    Energy Technology Data Exchange (ETDEWEB)

    1988-06-01

    This Handbook discusses both management and technical elements that should be considered in developing a comprehensive site characterization program. Management elements typical of any project of a comparable magnitude and complexity are combined with a discussion of strategies specific to site characterization. Information specific to the technical elements involved in site characterization is based on guidance published by the Nuclear Regulatory Commission (NRC) with respect to licensing requirements for LLW disposal facilities. The objective of this Handbook is to provide a reference for both NRC Agreement States and non-Agreement States for use in developing a comprehensive site characterization program that meets the specific objectives of the State and/or site developer/licensee. Each site characterization program will vary depending on the objectives, licensing requirements, schedules/budgets, physical characteristics of the site, proposed facility design, and the specific concerns raised by government agencies and the public. Therefore, the Handbook is not a prescriptive guide to site characterization. 18 refs., 6 figs.

  8. Horus Web Site Evaluation

    OpenAIRE

    Atef Qattan Ben Mohamed Qattan

    2005-01-01

    An Evaluative study for the children web site Horus, it begins with general description for the web site and its components, then it evaluates it according to 6 criteria ; Authority, Coverage, Contents, Accuracy, Design, and pictures and Multimedia. Finally it summarizes its results.

  9. AA antiproton production target

    CERN Multimedia

    CERN PhotoLab

    1979-01-01

    The first version of the antiproton production target was a tungsten rod, 11 cm long and 3 mm in diameter. The rod was embedded in graphite, pressure-seated into an outer casing of stainless steel. At the entrance to the target assembly was a scintillator screen, imprinted with circles every 5 mm in radius, which allowed to precisely aim the 26 GeV high-intensity proton beam from the PS onto the centre of the target rod. The scintillator screen was a 1 mm thick plate of Cr-doped alumina. See also 7903034 and 7905091.

  10. Targeting determinants of dosage compensation in Drosophila.

    Directory of Open Access Journals (Sweden)

    2006-02-01

    Full Text Available The dosage compensation complex (DCC in Drosophila melanogaster is responsible for up-regulating transcription from the single male X chromosome to equal the transcription from the two X chromosomes in females. Visualization of the DCC, a large ribonucleoprotein complex, on male larval polytene chromosomes reveals that the complex binds selectively to many interbands on the X chromosome. The targeting of the DCC is thought to be in part determined by DNA sequences that are enriched on the X. So far, lack of knowledge about DCC binding sites has prevented the identification of sequence determinants. Only three binding sites have been identified to date, but analysis of their DNA sequence did not allow the prediction of further binding sites. We have used chromatin immunoprecipitation to identify a number of new DCC binding fragments and characterized them in vivo by visualizing DCC binding to autosomal insertions of these fragments, and we have demonstrated that they possess a wide range of potential to recruit the DCC. By varying the in vivo concentration of the DCC, we provide evidence that this range of recruitment potential is due to differences in affinity of the complex to these sites. We were also able to establish that DCC binding to ectopic high-affinity sites can allow nearby low-affinity sites to recruit the complex. Using the sequences of the newly identified and previously characterized binding fragments, we have uncovered a number of short sequence motifs, which in combination may contribute to DCC recruitment. Our findings suggest that the DCC is recruited to the X via a number of binding sites of decreasing affinities, and that the presence of high- and moderate-affinity sites on the X may ensure that lower-affinity sites are occupied in a context-dependent manner. Our bioinformatics analysis suggests that DCC binding sites may be composed of variable combinations of degenerate motifs.

  11. Site decommissioning management plan

    Energy Technology Data Exchange (ETDEWEB)

    Fauver, D.N.; Austin, J.H.; Johnson, T.C.; Weber, M.F.; Cardile, F.P.; Martin, D.E.; Caniano, R.J.; Kinneman, J.D.

    1993-10-01

    The Nuclear Regulatory Commission (NRC) staff has identified 48 sites contaminated with radioactive material that require special attention to ensure timely decommissioning. While none of these sites represent an immediate threat to public health and safety they have contamination that exceeds existing NRC criteria for unrestricted use. All of these sites require some degree of remediation, and several involve regulatory issues that must be addressed by the Commission before they can be released for unrestricted use and the applicable licenses terminated. This report contains the NRC staff`s strategy for addressing the technical, legal, and policy issues affecting the timely decommissioning of the 48 sites and describes the status of decommissioning activities at the sites.

  12. Site Calibration report

    DEFF Research Database (Denmark)

    Yordanova, Ginka; Vesth, Allan

    The report describes site calibration measurements carried out on a site in Denmark. The measurements are carried out in accordance to Ref. [1]. The site calibration is carried out before a power performance measurement on a given turbine to clarify the influence from the terrain on the ratio...... between the wind speed at the center of the turbine hub and at the met mast. The wind speed at the turbine is measured by a temporary mast placed at the foundation for the turbine. The site and measurement equipment is detailed described in [2]. The possible measurement sector for power performance...... according to [1] is also described in [2] and no results from the site calibration have shown any necessary exclusion from this sector. All parts of the sensors and the measurement system have been installed by DTU....

  13. Site directed recombination

    Science.gov (United States)

    Jurka, Jerzy W.

    1997-01-01

    Enhanced homologous recombination is obtained by employing a consensus sequence which has been found to be associated with integration of repeat sequences, such as Alu and ID. The consensus sequence or sequence having a single transition mutation determines one site of a double break which allows for high efficiency of integration at the site. By introducing single or double stranded DNA having the consensus sequence flanking region joined to a sequence of interest, one can reproducibly direct integration of the sequence of interest at one or a limited number of sites. In this way, specific sites can be identified and homologous recombination achieved at the site by employing a second flanking sequence associated with a sequence proximal to the 3'-nick.

  14. New Methods for Targeted Alpha Radiotherapy

    Science.gov (United States)

    Robertson, J. David

    2014-03-01

    Targeted radiotherapies based on alpha emitters are a promising alternative to beta emitting radionuclides. Because of their much shorter range, targeted α-radiotherapy (TAT) agents have great potential for application to small, disseminated tumors and micro metastases and treatment of hematological malignancies consisting of individual, circulating neoplastic cells. A promising approach to TAT is the use of the in vivo α-generator radionuclides 223 = 11.4 d) and 225Ac 1/2 = 10.0 d). In addition to their longer half-lives, these two isotopes have the potential of dramatically increasing the therapeutic efficacy of TAT as they each emit four α particles in their decay chain. This principle has recently been exploited in the development of Xofigo®, the first TAT agent approved for clinical use by the U.S. FDA. Xofigo, formulated as 223RaCl2, is used for treatment of metastatic bone cancer in men with castration-resistant prostate cancer. TAT with 223Ra works, however, only in the case of bone cancer because radium, as a chemical analogue of calcium, efficiently targets bone. In order to bring the benefits of TAT with 223Ra or 225Ac to other tumor types, a new delivery method must be devised. Retaining the in vivo α generator radionuclides at the target site through the decay process is one of the major challenges associated with the development of TAT. Because the recoil energy of the daughter radionuclides from the α-emission is ~ 100 keV - a value which is four orders of magnitude greater than the energy of a covalent bond - the daughters will not remain bound to the bioconjugate at the targeting site. Various approaches have been attempted to achieve retention of the α-generator daughter radionuclides at the target site, including incorporation of the in vivo generator into liposomes and fullerenes. Unfortunately, to date single wall liposomes and fullerenes are able to retain less than 10% of the daughter radionuclides. We have recently demonstrated that a

  15. Strategies for targeted antimicrobial photodynamic therapy

    Science.gov (United States)

    Verma, Sarika; Sallum, Ulysses; Zheng, Xiang; Hasan, Tayyaba

    2009-06-01

    The photophysics and mechanisms of cell killing by photodynamic therapy (PDT) have been extensively studied in recent years, and PDT has received regulatory approval for the treatment of a number of diseases worldwide. As the application of this treatment modality expands with regard to both anatomical sites and diseases, it is important to develop strategies for enhancing PDT outcomes. Our group has focused on developing targeting strategies to enhance PDT for both cancerous as well as anti-microbial applications. In this article, we will discuss photosensitizer modification and conjugation strategies for targeted antimicrobial photodynamic therapy.

  16. Slugs as target or non-target organisms for environmental chemicals

    OpenAIRE

    Triebskorn, R.; Henderson, I. F.; Martin, A.; Köhler, H.-R.

    1996-01-01

    The ability of slugs (Deroceras reticulatum) to survive exposure to various chemical stressors such as molluscicides ( carbamates, metaldehyde, ironchelates) or other environmental pollutants (heavy metals, pesticides) was investigated using x-ray analyses, autoradiography, filter electron microscopy, enzyme histochemistry, enzymatics, electron microscopy, and stress protein analyses. Uptake pathways, target sites, modes of action and general responses in the animals were studied, and the res...

  17. Target Price Accuracy

    Directory of Open Access Journals (Sweden)

    Alexander G. Kerl

    2011-04-01

    Full Text Available This study analyzes the accuracy of forecasted target prices within analysts’ reports. We compute a measure for target price forecast accuracy that evaluates the ability of analysts to exactly forecast the ex-ante (unknown 12-month stock price. Furthermore, we determine factors that explain this accuracy. Target price accuracy is negatively related to analyst-specific optimism and stock-specific risk (measured by volatility and price-to-book ratio. However, target price accuracy is positively related to the level of detail of each report, company size and the reputation of the investment bank. The potential conflicts of interests between an analyst and a covered company do not bias forecast accuracy.

  18. Optimal exploration target zones

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2008-09-01

    Full Text Available This research describes a quantitative methodology for deriving optimal exploration target zones based on a probabilistic mineral prospectivity map. In order to arrive at out objective, we provide a plausible answer to the following question: "Which...

  19. Delays in thick targets

    CERN Document Server

    Bennett, J R J

    2002-01-01

    The delays in the emission of radioactive particles from a thick target bombarded by high-energy protons is discussed in relation to the basic physical processes of diffusion and effusion through the target and ioniser. The delay time, relative to the decay time, is crucial to the efficiency of particle release at the exit of the ioniser. The principles of minimizing the delay times are discussed with reference to a mathematical model of the process, and some experimental examples are given.

  20. An ISOLDE target unit

    CERN Multimedia

    Maximilien Brice

    2002-01-01

    A good dozen different targets are available for ISOLDE, made of different materials and equipped with different kinds of ion-sources, according to the needs of the experiments. Each separator (GPS: general purpose; HRS: high resolution) has its own target. Because of the high radiation levels, robots effect the target changes, about 80 times per year. In the standard unit shown in picture _01, the target is the cylindrical object in the front. It contains uranium-carbide kept at a temperature of 2200 deg C, necessary for the isotopes to be able to escape. At either end, one sees the heater current leads, carrying 700 A. The Booster beam, some 3E13 protons per pulse, enters the target from left. The evaporated isotope atoms enter a hot-plasma ion source (the black object behind the target). The whole unit sits at 60 kV potential (pulsed in synchronism with the arrival of the Booster beam) which accelerates the ions (away from the viewer) towards one of the 2 separators.

  1. The CRISPR-Cas9 technology: Closer to the ultimate toolkit for targeted genome editing.

    Science.gov (United States)

    Quétier, Francis

    2016-01-01

    The first period of plant genome editing was based on Agrobacterium; chemical mutagenesis by EMS (ethyl methanesulfonate) and ionizing radiations; each of these technologies led to randomly distributed genome modifications. The second period is associated with the discoveries of homing and meganuclease enzymes during the 80s and 90s, which were then engineered to provide efficient tools for targeted editing. From 2006 to 2012, a few crop plants were successfully and precisely modified using zinc-finger nucleases. A third wave of improvement in genome editing, which led to a dramatic decrease in off-target events, was achieved in 2009-2011 with the TALEN technology. The latest revolution surfaced in 2013 with the CRISPR-Cas9 system, whose high efficiency and technical ease of use is really impressive; scientists can use in-house kits or commercially available kits; the only two requirements are to carefully choose the location of the DNA double strand breaks to be induced and then to order an oligonucleotide. While this close-to- ultimate toolkit for targeted editing of genomes represents dramatic scientific progress which allows the development of more complex useful agronomic traits through synthetic biology, the social acceptance of genome editing remains regularly questioned by anti-GMO citizens and organizations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  2. Multi-Chromatic Analysis of SAR Images for Coherent Target Detection

    Directory of Open Access Journals (Sweden)

    Fabio Bovenga

    2014-09-01

    Full Text Available This work investigates the possibility of performing target analysis through the Multi-Chromatic Analysis (MCA, a technique that basically explores the information content of sub-band images obtained by processing portions of the range spectrum of a synthetic aperture radar (SAR image. According to the behavior of the SAR signal at the different sub-bands, MCA allows target classification. Two strategies have been experimented by processing TerraSAR-X images acquired over the Venice Lagoon, Italy: one exploiting the phase of interferometric sub-band pairs, the other using the spectral coherence derived by computing the coherence between sub-band images of a single SAR acquisition. The first approach introduces the concept of frequency-persistent scatterers (FPS, which is complementary to that of the time-persistent scatterers (PS. FPS and PS populations have been derived and analyzed to evaluate the respective characteristics and the physical nature of the targets. Spectral coherence analysis has been applied to vessel detection, according to the property that, in presence of a random distribution of surface scatterers, as for open sea surfaces, spectral coherence is expected to be proportional to sub-band intersection, while in presence of manmade structures it is preserved anyhow. First results show that spectral coherence is well preserved even for very small vessels, and can be used as a complementary information channel to constrain vessel detection in addition to classical Constant False Alarm Rate techniques based on the sole intensity channel.

  3. Financial costs of meeting global biodiversity conservation targets

    DEFF Research Database (Denmark)

    McCarthy, Donal P.; Donald, Paul F.; Scharlemann, Jörn P.W.

    2012-01-01

    World governments have committed to halting human-induced extinctions and safeguarding important sites for biodiversity by 2020, but the financial costs of meeting these targets are largely unknown. We estimate the cost of reducing the extinction risk of all globally threatened bird species (by ≥1...... and effectively managing all terrestrial sites of global avian conservation significance (11,731 Important Bird Areas) would cost U.S. $65.1 billion annually. Adding sites for other taxa increases this to U.S. $76.1 billion annually. Meeting these targets will require conservation funding to increase by at least...

  4. Colon cancer targeting using conjugates biomaterial 5-flurouracil.

    Science.gov (United States)

    Jaferian, Soleiman; Negahdari, Babak; Eatemadi, Ali

    2016-12-01

    There has been several research works on the development of an oral delivery system to deliver cytotoxic and chemo preventive agents directly at the targeted site of action with reduced unwanted side effects. The efficacy of the site-specific delivery system of a drug to colon has been proven to increase the drugs concentration at the target site, and thus requires a reduced dose of the drug with minimized side effects. This review includes discussion of the delivery systems of 5-FU using biodegradable materials and some significant outcomes in the pre-clinical development of 5-fluorouracil carriers for the colon cancer. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

  5. A Modified phosphate-carrier protein theory is proposed as a non-target site mechanism For glyphosate resistance in weeds Teoria das proteínas carregadoras fosfato modificadas proposta como mecanismo de resistência ao herbicida glyphosate em plantas daninhas

    Directory of Open Access Journals (Sweden)

    A.C. Roso

    2010-01-01

    Full Text Available Glyphosate is an herbicide that inhibits the enzyme 5-enolpyruvyl-shikimate-3-phosphate synthase (EPSPs (EC 2.5.1.19. EPSPs is the sixth enzyme of the shikimate pathway, by which plants synthesize the aromatic amino acids phenylalanine, tyrosine, and tryptophan and many compounds used in secondary metabolism pathways. About fifteen years ago it was hypothesized that it was unlikely weeds would evolve resistance to this herbicide because of the limited degree of glyphosate metabolism observed in plants, the low resistance level attained to EPSPs gene overexpression, and because of the lower fitness in plants with an altered EPSPs enzyme. However, today 20 weed species have been described with glyphosate resistant biotypes that are found in all five continents of the world and exploit several different resistant mechanisms. The survival and adaptation of these glyphosate resistant weeds are related toresistance mechanisms that occur in plants selected through the intense selection pressure from repeated and exclusive use of glyphosate as the only control measure. In this paper the physiological, biochemical, and genetic basis of glyphosate resistance mechanisms in weed species are reviewed and a novel and innovative theory that integrates all the mechanisms of non-target site glyphosate resistance in plants is presented.Glyphosate é uma glicina fosfonada e inibe a enzima 5-enolpiruvil-shikimato-3-fosfato sintase (EPSPS (EC 2.5.1.19. EPSPS é a sexta enzima da rota do shikimato, na qual são sintetizados os compostos do metabolismo secundário e os aminoácidos aromáticos fenilalanina, tirosina e triptofano. Alguns autores hipotetizaram que seria improvável a evolução de plantas daninhas resistentes a este herbicida. As justificativas estariam relacionadas à limitada metabolização de glyphosate nas plantas, ao baixo nível de resistência obtido com a superexpressão do gene EPSPS e à alta penalidade de adaptação oriunda de mutações no

  6. Degradable Polymersomes for Targeted Drug Delivery

    Science.gov (United States)

    Petersen, Matthew Alan

    Chemotherapy today is often accompanied by major side effects due to delivery of toxic drugs to healthy tissue in addition to diseased cells. Targeted drug delivery offers the possibility of minimizing these side effects by specific delivery to cancer cells using targeted nanocarriers that enhance drug accumulation in tumors and facilitate target-specific cellular uptake. Polymersomes, vesicles self-assembled from polymeric amphiphiles, are an attractive targeted vehicle, as they are capable of encapsulating both hydrophobic and hydrophilic drugs, have lengthy circulation times in vivo, and can employ degradable functionality for triggered release of payload and clearance from the body. This thesis reports on efforts to enhance the capabilities of degradable polymersomes for targeted delivery. First, targeting functionality is incorporated into polymersomes of the block copolymer poly(ethylene oxide)-b-poly(gamma-methyl-epsilon-caprolactone) by incorporating the reactive vinyl sulfone group into the amphiphile's hydrophilic terminus, allowing site-selective reaction with cysteine-functionalized targeting peptides following self-assembly. The performance of targeted delivery using this polymersome is then evaluated in vitro. Binding and delivery to model cell lines for targeted and bystander cells is tracked using nontargeted polymersomes and compared to that for polymersomes using a high- or low-affinity ligand. Polymer degradation is also tracked both in simple media and during cellular delivery. Finally, a new monomer is developed incorporating acid-labile acetal functionality into a cyclic polyester. The polymerization of this monomer to two distinct polymers is also characterized and the degradation behavior of both polymers evaluated.

  7. Protein search for multiple targets on DNA

    Energy Technology Data Exchange (ETDEWEB)

    Lange, Martin [Johannes Gutenberg University, Mainz 55122 (Germany); Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Kochugaeva, Maria [Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Kolomeisky, Anatoly B., E-mail: tolya@rice.edu [Department of Chemistry, Rice University, Houston, Texas 77005 (United States); Center for Theoretical Biological Physics, Rice University, Houston, Texas 77005 (United States)

    2015-09-14

    Protein-DNA interactions are crucial for all biological processes. One of the most important fundamental aspects of these interactions is the process of protein searching and recognizing specific binding sites on DNA. A large number of experimental and theoretical investigations have been devoted to uncovering the molecular description of these phenomena, but many aspects of the mechanisms of protein search for the targets on DNA remain not well understood. One of the most intriguing problems is the role of multiple targets in protein search dynamics. Using a recently developed theoretical framework we analyze this question in detail. Our method is based on a discrete-state stochastic approach that takes into account most relevant physical-chemical processes and leads to fully analytical description of all dynamic properties. Specifically, systems with two and three targets have been explicitly investigated. It is found that multiple targets in most cases accelerate the search in comparison with a single target situation. However, the acceleration is not always proportional to the number of targets. Surprisingly, there are even situations when it takes longer to find one of the multiple targets in comparison with the single target. It depends on the spatial position of the targets, distances between them, average scanning lengths of protein molecules on DNA, and the total DNA lengths. Physical-chemical explanations of observed results are presented. Our predictions are compared with experimental observations as well as with results from a continuum theory for the protein search. Extensive Monte Carlo computer simulations fully support our theoretical calculations.

  8. Superfund Site Information

    Data.gov (United States)

    U.S. Environmental Protection Agency — This asset includes a number of individual data sets related to site-specific information for Superfund, which is governed under the Comprehensive Environmental...

  9. Outdoor Recreation Sites Inventory

    Data.gov (United States)

    Vermont Center for Geographic Information — The RECSITES data layer contains a wide range of recreational sites in Vermont. This point data layer includes parks, ski areas, boat access points, and many other...

  10. Water Quality Monitoring Sites

    Data.gov (United States)

    Vermont Center for Geographic Information — Water Quality Monitoring Site identifies locations across the state of Vermont where water quality data has been collected, including habitat, chemistry, fish and/or...

  11. Summer Meal Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — Information pertaining to Summer Meal Sites, as collected by Citiparks in the City of Pittsburgh Department of Parks and Recreation. This dataset includes the...

  12. Coal mine site reclamation

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    2013-02-15

    Coal mine sites can have significant effects on local environments. In addition to the physical disruption of land forms and ecosystems, mining can also leave behind a legacy of secondary detrimental effects due to leaching of acid and trace elements from discarded materials. This report looks at the remediation of both deep mine and opencast mine sites, covering reclamation methods, back-filling issues, drainage and restoration. Examples of national variations in the applicable legislation and in the definition of rehabilitation are compared. Ultimately, mine site rehabilitation should return sites to conditions where land forms, soils, hydrology, and flora and fauna are self-sustaining and compatible with surrounding land uses. Case studies are given to show what can be achieved and how some landscapes can actually be improved as a result of mining activity.

  13. Sites and Enactments

    DEFF Research Database (Denmark)

    Korsgaard, Steffen; Neergaard, Helle

    2010-01-01

    This paper develops a framework for researching entrepreneurial opportunities. We argue that these can best be understood as dynamic and fluid effects of entrepreneurial processes that are enacted differently across different sites. On this basis we develop a framework for studying entrepreneurial...... opportunities that is suited to track those opportunities across enactments and sites. The framework is demonstrated through an analysis of the genesis of the company The Republic ofTea, as portrayed in the book of the same name...

  14. Burglar Target Selection

    Science.gov (United States)

    Townsley, Michael; Bernasco, Wim; Ruiter, Stijn; Johnson, Shane D.; White, Gentry; Baum, Scott

    2015-01-01

    Objectives: This study builds on research undertaken by Bernasco and Nieuwbeerta and explores the generalizability of a theoretically derived offender target selection model in three cross-national study regions. Methods: Taking a discrete spatial choice approach, we estimate the impact of both environment- and offender-level factors on residential burglary placement in the Netherlands, the United Kingdom, and Australia. Combining cleared burglary data from all study regions in a single statistical model, we make statistical comparisons between environments. Results: In all three study regions, the likelihood an offender selects an area for burglary is positively influenced by proximity to their home, the proportion of easily accessible targets, and the total number of targets available. Furthermore, in two of the three study regions, juvenile offenders under the legal driving age are significantly more influenced by target proximity than adult offenders. Post hoc tests indicate the magnitudes of these impacts vary significantly between study regions. Conclusions: While burglary target selection strategies are consistent with opportunity-based explanations of offending, the impact of environmental context is significant. As such, the approach undertaken in combining observations from multiple study regions may aid criminology scholars in assessing the generalizability of observed findings across multiple environments. PMID:25866418

  15. The Sinuous Target

    Energy Technology Data Exchange (ETDEWEB)

    Zwaska, R. [Fermilab

    2015-06-01

    We report on the concept for a target material comprised of a multitude of interlaced wires of small dimension. This target material concept is primarily directed at high-power neutrino targets where the thermal shock is large due to small beam sizes and short durations; it also has applications to other high-power targets, particularly where the energy deposition is great or a high surface area is preferred. This approach ameliorates the problem of thermal shock by engineering a material with high strength on the micro-scale, but a very low modulus of elasticity on the meso-scale. The low modulus of elasticity is achieved by constructing the material of spring-like wire segments much smaller than the beam dimension. The intrinsic bends of the wires will allow them to absorb the strain of thermal shock with minimal stress. Furthermore, the interlaced nature of the wires provides containment of any segment that might become loose. We will discuss the progress on studies of analogue materials and fabrication techniques for sinuous target materials.

  16. The cytoplasmic face of cell contact sites.

    Science.gov (United States)

    Pokutta, Sabine; Weis, William I

    2002-04-01

    The cytoplasmic face of cell contact sites comprises large macromolecular assemblies that link transmembrane cell adhesion molecules to the cytoskeleton. These assemblies are dynamic structures that are the targets of regulatory signals that control cell adhesiveness. Recent studies of the biochemistry and structure of the cadherin-catenin complex, vinculin and proteins of the ezrin/radixin/moesin family have begun to reveal the architecture of these assemblies and the mechanisms that are involved in their regulation.

  17. Chemical, target, and bioactive properties of allosteric modulation.

    Science.gov (United States)

    van Westen, Gerard J P; Gaulton, Anna; Overington, John P

    2014-04-01

    Allosteric modulators are ligands for proteins that exert their effects via a different binding site than the natural (orthosteric) ligand site and hence form a conceptually distinct class of ligands for a target of interest. Here, the physicochemical and structural features of a large set of allosteric and non-allosteric ligands from the ChEMBL database of bioactive molecules are analyzed. In general allosteric modulators are relatively smaller, more lipophilic and more rigid compounds, though large differences exist between different targets and target classes. Furthermore, there are differences in the distribution of targets that bind these allosteric modulators. Allosteric modulators are over-represented in membrane receptors, ligand-gated ion channels and nuclear receptor targets, but are underrepresented in enzymes (primarily proteases and kinases). Moreover, allosteric modulators tend to bind to their targets with a slightly lower potency (5.96 log units versus 6.66 log units, pweight and more lipophilic nature, leading to similar binding efficiency and surface efficiency indices. Subsequently a series of classifier models are trained, initially target class independent models followed by finer-grained target (architecture/functional class) based models using the target hierarchy of the ChEMBL database. Applications of these insights include the selection of likely allosteric modulators from existing compound collections, the design of novel chemical libraries biased towards allosteric regulators and the selection of targets potentially likely to yield allosteric modulators on screening. All data sets used in the paper are available for download.

  18. Exopaleontology at The Pathfinder Landing Site

    Science.gov (United States)

    Farmer, Jack D.; DesMarais, David J.; Greeley, Ronald; DeVincenzi, Donald L. (Technical Monitor)

    1995-01-01

    The Mars Pathfinder Mission is a Discovery Class mission that will place a small lander and rover on the surface of Mars in July of 1997. It is primarily a technology demonstration to test the feasibility of a direct entry-delivery system, but carries a nominal scientific payload that includes rover-lander and instrumentation for limited mineralogical analysis. The nominal landing site was selected by the Pathfinder Team under the leadership of Dr. Matthew Golombek (JPL) based input from 60 participants at a Landing Site Workshop held last Spring at the Lunar Planetary Institute in Houston. The mission constraints for the landing site were 0-30 deg. N latitude, and below the 0.0 elevation datum. Over 20 landing sites were proposed and a nominal site was selected on southern Chryse Planitia near the terminae of the Ares and Tui outflow channels. In part, the decision to land at this location was based on the opportunity to sample a potentially large number lithologies in a small area (the rover will have a range of a few tens of meters from the lander). The purpose here is to review the general geological context of the landing site and the rationale for Exobiology's recommendation of the Ares site given at the workshop last spring. Because Ares and Tui Valles are sourced within terranes that may have originated by thermokarst processes, hydrothermal processes could have operated there for some time. Hydrothermal systems are presently regarded as important sites for a fossil record on Mars. Models for the formation of the outflow channels suggest that thermal spring sinters and associated aqueous mineral deposits, high priority targets for Mars Exopaleontology, could have formed in association with thermokarst processes and subsequently been delivered to the landing site in large quantities during the periodic cataclysmic outflows that created the channels.

  19. Stable Targets for Spaceborne Microwave Radiometer Calibration

    Science.gov (United States)

    Njoku, Eni G.; Chan, S. K.; Armstrong, R. L.; Brodzik, M. J.; Savoie, M. H.; Knowles, K.

    2006-01-01

    Beginning in the 1970s, continuous observations of the Earth have been made by spaceborne microwave radiometers. Since these instruments have different observational characteristics, care must be taken in combining their data to form consistent long term records of brightness temperatures and derived geophysical quantities. To be useful for climate studies, data from different instruments must be calibrated relative to each other and to reference targets on the ground whose characteristics are stable and can be monitored continuously. Identifying such targets over land is not straightforward due to the heterogeneity and complexity of the land surface and cover. In this work, we provide an analysis of multi-sensor brightness temperature statistics over ocean, tropical forest, and ice sheet locations, spanning the period from 1978 to the present, and indicate the potential of these sites as continuous calibration monitoring targets.

  20. Targeting Specific Immunologic Pathways in Crohn's Disease.

    Science.gov (United States)

    Ramos, Guilherme Piovezani; Faubion, William A; Papadakis, Konstantinos A

    2017-09-01

    Understanding the immunologic pathways in intestinal inflammation is crucial for the development of new therapies that can maximize patient response and minimize toxicity. Targeting integrins and cytokines is intended to control leukocyte migration to effector sites or inhibit the action of proinflammatory cytokines. New approaches to preventing leukocyte migration may target integrin receptors expressed on the intestinal vascular endothelium. The interleukin (IL)-12/IL-23 pathway has been a therapeutic target of interest in controlling active Crohn's disease (CD). New therapeutic approaches in CD may involve the enhancement of anti-inflammatory cytokine pathways and modulation of cellular responses and intranuclear signals associated with intestinal inflammation. Copyright © 2017 Elsevier Inc. All rights reserved.

  1. Will nanotechnology influence targeted cancer therapy?

    Science.gov (United States)

    Grimm, Jan; Scheinberg, David A

    2011-04-01

    The rapid development of techniques that enable synthesis (and manipulation) of matter on the nanometer scale and the development of new nanomaterials will play a large role in disease diagnosis and treatment, specifically in targeted cancer therapy. Targeted nanocarriers are an intriguing means to selectively deliver high concentrations of cytotoxic agents or imaging labels directly to the cancer site. Often, solubility issues and an unfavorable biodistribution can result in a suboptimal response of novel agents even though they are very potent. New nanoparticulate formulations allow simultaneous imaging and therapy ("theranostics"), which can provide a realistic means for the clinical implementation of such otherwise suboptimal formulations. In this review, we did not attempt to provide a complete overview of the rapidly enlarging field of nanotechnology in cancer; rather, we presented properties specific to nanoparticles and examples of their uses, which show their importance for targeted cancer therapy. Copyright © 2011 Elsevier Inc. All rights reserved.

  2. Novel advances in targeted drug delivery.

    Science.gov (United States)

    Öztürk-Atar, Kıvılcım; Eroğlu, Hakan; Çalış, Sema

    2017-11-23

    Developing a new drug molecule is not only time-consuming and expensive, but also mostly a failing process. However, improving bioavailability, targetability, efficacy or safety of old drugs could be more effective way to use them in clinic. For these purposes, so many strategies including individualising drug therapy, nanoparticle-based drug delivery systems, drug conjugates, therapeutic drug monitoring, stimuli-sensitive targeted therapy are investigated intensely. Depending on the desired application or targeted site, nanoparticles can be administrated as orally, locally, topically and systemically. Currently, the Food and Drug Administration and the European Medicines Agency approved nanoparticles are mostly aimed to treat cancer. Although some of these formulations were approved by Food and Drug Administration and/or European Medicines Agency to use in clinic, most of them have fell down to pass either pre-clinical or clinical trials. To have high approval rate, failure reasons need to be better understand.

  3. Saccade target selection in Chinese reading.

    Science.gov (United States)

    Li, Xingshan; Liu, Pingping; Rayner, Keith

    2015-04-01

    In Chinese reading, there are no spaces to mark the word boundaries, so Chinese readers cannot target their saccades to the center of a word. In this study, we investigated how Chinese readers decide where to move their eyes during reading. To do so, we introduced a variant of the boundary paradigm in which only the target stimulus remained on the screen, displayed at the saccade landing site, after the participant's eyes crossed an invisible boundary. We found that when the saccade target was a word, reaction times in a lexical decision task were shorter when the saccade landing position was closer to the end of that word. These results are consistent with the predictions of a processing-based strategy to determine where to move the eyes. Specifically, this hypothesis assumes that Chinese readers estimate how much information is processed in parafoveal vision and saccade to a location that will carry novel information.

  4. Setting reference targets

    Energy Technology Data Exchange (ETDEWEB)

    Ruland, R.E.

    1997-04-01

    Reference Targets are used to represent virtual quantities like the magnetic axis of a magnet or the definition of a coordinate system. To explain the function of reference targets in the sequence of the alignment process, this paper will first briefly discuss the geometry of the trajectory design space and of the surveying space, then continue with an overview of a typical alignment process. This is followed by a discussion on magnet fiducialization. While the magnetic measurement methods to determine the magnetic centerline are only listed (they will be discussed in detail in a subsequent talk), emphasis is given to the optical/mechanical methods and to the task of transferring the centerline position to reference targets.

  5. Targeted Therapy of CLL.

    Science.gov (United States)

    Al-Sawaf, Othman; Fischer, Kirsten; Eichhorst, Barbara; Hallek, Michael

    2016-01-01

    The landscape of chronic lymphocytic leukemia (CLL) has undergone profound changes in the past years. First, the addition of CD20-targeting antibodies to conventional chemotherapy has improved the therapeutic outcome in the majority of CLL patients. Since the establishment of the critical role of the B cell receptor signaling pathway in the pathogenesis of CLL, several agents have been developed to target this pathway. Ibrutinib and idelalisib, 2 potent kinase inhibitors, have both become available for CLL therapy in the first and second line. Additionally, the observation of high expression levels of the anti-apoptotic mitochondrial protein Bcl-2 in CLL has led to the development of venetoclax, a BH3 mimetic compound that inhibits Bcl-2 and has shown high efficacy in CLL. This short review summarizes preclinical and clinical data on currently available agents in CLL and provides an outlook on upcoming new challenges in the targeted therapy of CLL. © 2016 S. Karger GmbH, Freiburg.

  6. Modelling Recycling Targets

    DEFF Research Database (Denmark)

    Hill, Amanda Louise; Leinikka Dall, Ole; Andersen, Frits M.

    2014-01-01

    Within the European Union (EU) a paradigm shift is currently occurring in the waste sector, where EU waste directives and national waste strategies are placing emphasis on resource efficiency and recycling targets. The most recent Danish resource strategy calculates a national recycling rate of 22......% for household waste, and sets an ambitious goal of a 50% recycling rate by 2020. This study integrates the recycling target into the FRIDA model to project how much waste and from which streams should be diverted from incineration to recycling in order to achieve the target. Furthermore, it discusses how...... the existing technological, organizational and legislative frameworks may affect recycling activities. The results of the analysis show that with current best practice recycling rates, the 50% recycling rate cannot be reached without recycling of household biowaste. It also shows that all Danish municipalities...

  7. psRNATarget: a plant small RNA target analysis server.

    Science.gov (United States)

    Dai, Xinbin; Zhao, Patrick Xuechun

    2011-07-01

    Plant endogenous non-coding short small RNAs (20-24 nt), including microRNAs (miRNAs) and a subset of small interfering RNAs (ta-siRNAs), play important role in gene expression regulatory networks (GRNs). For example, many transcription factors and development-related genes have been reported as targets of these regulatory small RNAs. Although a number of miRNA target prediction algorithms and programs have been developed, most of them were designed for animal miRNAs which are significantly different from plant miRNAs in the target recognition process. These differences demand the development of separate plant miRNA (and ta-siRNA) target analysis tool(s). We present psRNATarget, a plant small RNA target analysis server, which features two important analysis functions: (i) reverse complementary matching between small RNA and target transcript using a proven scoring schema, and (ii) target-site accessibility evaluation by calculating unpaired energy (UPE) required to 'open' secondary structure around small RNA's target site on mRNA. The psRNATarget incorporates recent discoveries in plant miRNA target recognition, e.g. it distinguishes translational and post-transcriptional inhibition, and it reports the number of small RNA/target site pairs that may affect small RNA binding activity to target transcript. The psRNATarget server is designed for high-throughput analysis of next-generation data with an efficient distributed computing back-end pipeline that runs on a Linux cluster. The server front-end integrates three simplified user-friendly interfaces to accept user-submitted or preloaded small RNAs and transcript sequences; and outputs a comprehensive list of small RNA/target pairs along with the online tools for batch downloading, key word searching and results sorting. The psRNATarget server is freely available at http://plantgrn.noble.org/psRNATarget/.

  8. Optimal exploration target zones

    CSIR Research Space (South Africa)

    Debba, Pravesh

    2008-09-01

    Full Text Available , Carranza, Stein, van der Meer Introduction to Remote Sensing Background and Objective of the study Methodology Results Optimal Exploration Target Zones Pravesh Debba1, Emmanual M.J. Carranza2, Alfred Stein2, Freek D. van der Meer2 1CSIR, Logistics... and Quantitative Methods, CSIR Built Environment 2International Institute for Geo-Information Science and Earth Observation (ITC), Hengelosestraat 99, P.O. Box 6, 7500AA Enschede, The Netherlands Optimal Exploration Target Zones Debba, Carranza, Stein, van der Meer...

  9. AA antiproton production target

    CERN Multimedia

    CERN PhotoLab

    1979-01-01

    The first version of the antiproton production target was a tungsten rod, 11 cm long (actually a row of 11 rods, each 1 cm long) and 3 mm in diameter. The rod was embedded in graphite, pressure-seated into an outer casing made of stainless steel. The casing had fins for forced-air cooling. In this picture, the 26 GeV high-intensity beam from the PS enters from the right, where a scintillator screen, with circles every 5 mm in radius, permits precise aim at the target centre. See also 7903034 and 7905094.

  10. Site clearance working group

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-03-01

    The Gulf of Mexico and Louisiana continue to be areas with a high level of facility removal, and the pace of removal is projected to increase. Regulations were promulgated for the Gulf of Mexico and Louisiana requiring that abandoned sites be cleared of debris that could interfere with fishing and shrimping activities. The site clearance regulations also required verification that the sites were clear. Additionally, government programs were established to compensate fishermen for losses associated with snagging their equipment on oil and gas related objects that remained on the water bottoms in areas other than active producing sites and sites that had been verified as clear of obstructions and snags. The oil and gas industry funds the compensation programs. This paper reviews the regulations and evolving operating practices in the Gulf of Mexico and Louisiana where site clearance and fisherman`s gear compensation regulations have been in place for a number of years. Although regulations and guidelines may be in place elsewhere in the world, this paper focuses on the Gulf of Mexico and Louisiana. Workshop participants are encouraged to bring up international issues during the course of the workshop. Additionally, this paper raises questions and focuses on issues that are of concern to the various Gulf of Mexico and Louisiana water surface and water bottom stakeholders. This paper does not have answers to the questions or issues. During the workshop participants will debate the questions and issues in an attempt to develop consensus opinions and/or make suggestions that can be provided to the appropriate organizations, both private and government, for possible future research or policy adjustments. Site clearance and facility removal are different activities. Facility removal deals with removal of the structures used to produce oil and gas including platforms, wells, casing, piles, pipelines, well protection structures, etc.

  11. Site 300 SPCC Plan

    Energy Technology Data Exchange (ETDEWEB)

    Griffin, D. [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)

    2016-11-23

    This Spill Prevention, Control, and Countermeasure (SPCC) Plan describes the measures that are taken at Lawrence Livermore National Laboratory’s (LLNL) Experimental Test Site (Site 300) near Tracy, California, to prevent, control, and handle potential spills from aboveground containers that can contain 55 gallons or more of oil. This SPCC Plan complies with the Oil Pollution Prevention regulation in Title 40 of the Code of Federal Regulations, Part 112 (40 CFR 112) and with 40 CFR 761.65(b) and (c), which regulates the temporary storage of polychlorinated biphenyls (PCBs). This Plan has also been prepared in accordance with Division 20, Chapter 6.67 of the California Health and Safety Code (HSC 6.67) requirements for oil pollution prevention (referred to as the Aboveground Petroleum Storage Act [APSA]), and the United States Department of Energy (DOE) Order No. 436.1. This SPCC Plan establishes procedures, methods, equipment, and other requirements to prevent the discharge of oil into or upon the navigable waters of the United States or adjoining shorelines for aboveground oil storage and use at Site 300. This SPCC Plan has been prepared for the entire Site 300 facility and replaces the three previous plans prepared for Site 300: LLNL SPCC for Electrical Substations Near Buildings 846 and 865 (LLNL 2015), LLNL SPCC for Building 883 (LLNL 2015), and LLNL SPCC for Building 801 (LLNL 2014).

  12. Cleavage site analysis in picornaviral polyproteins

    DEFF Research Database (Denmark)

    Blom, Nikolaj; Hansen, Jan; Blaas, Dieter

    1996-01-01

    Picornaviral proteinases are responsible for maturation cleavages of the viral polyprotein, but also catalyze the degradation of cellular targets. Using graphical visualization techniques and neural network algorithms, we have investigated the sequence specificity of the two proteinases 2Apro and 3......Cpro. The cleavage of VP0 (giving rise to VP2 and VP4), which is carried out by a so-far unknown proteinase, was also examined. In combination with a novel surface exposure prediction algorithm, our neural network approach successfully distinguishes known cleavage sites from nocleavage sites and yields...... are indeed cleaved awaits experimental verification. Additionally, we report several errors detected in the protein databases. A computer server for prediction of cleavage sites by picornaviral proteinases is publicly available at the e-mail address NetPicoRNA@cbs.dtu.dk or via WWW at http://www.cbs.dtu.dk/services/NetPicoRNA...

  13. Aquaporin-2 membrane targeting

    DEFF Research Database (Denmark)

    Olesen, Emma T B; Fenton, Robert A

    2017-01-01

    The targeting of the water channel aquaporin-2 (AQP2) to the apical plasma membrane of kidney collecting duct principal cells is regulated mainly by the antidiuretic peptide hormone arginine vasopressin (AVP). This process is of crucial importance for the maintenance of body water homeostasis...

  14. ISOLDE back on target

    CERN Multimedia

    Anaïs Schaeffer

    2014-01-01

    Today, Friday 1 August, the ISOLDE installation, supplied by the beams of the PS Booster, restarted its physics programme. After a shutdown of almost a year and a half, there was a real buzz in the air as the first beam of protons hit the target of the first post-LS1 ISOLDE experiment.   One of the new target-handling robots installed by ISOLDE during LS1. Many improvements have been made to the ISOLDE installation during LS1. One of the main projects was the installation of new robots for handling the targets (see photo 1). “Our targets are bombarded by protons from the PS Booster’s beams and become very radioactive,” explains Maria Jose Garcia Borge, spokesperson for the ISOLDE collaboration. “They therefore need to be handled carefully, which is where the robots come in. The robots we had until now were already over 20 years old and were starting to suffer from the effects of radiation. So LS1 was a perfect opportunity to replace them with more moder...

  15. Microenvironmental targets in sarcoma

    Directory of Open Access Journals (Sweden)

    Monika eEhnman

    2015-11-01

    Full Text Available Sarcomas are rare malignant tumors affecting all age groups. They are typically classified according to their resemblance to corresponding normal tissue. Their heterogeneous features, for example in terms of disease-driving genetic aberrations and body location, complicate both disease classification and development of novel treatment regimens. Many years of failure of improved patient outcome in clinical trials has lead to the conclusion that novel targeted therapies are likely needed in combination with current multimodality regimens. Sarcomas have not, in contrast to the common carcinomas, been the subject for larger systematic studies on how tumor behavior relates to characteristics of the tumor microenvironment. There is consequently an urgent need for identifying suitable molecular targets, not only in tumor cells, but also in the tumor microenvironment. This review discusses preclinical and clinical data about potential molecular targets in sarcomas. Studies on targeted therapies involving the tumor microenvironment are prioritized. A greater understanding of the biological context is expected to facilitate more successful design of future clinical trials in sarcoma.

  16. Target Heart Rates

    Science.gov (United States)

    ... is your level of intensity? When is the best time of day to work out? Target Heart Rates Warm Up, Cool Down See More >> Getting Active Getting Started - Tips for Long-term Exercise Success Get Moving: Easy Tips to Get Active! ...

  17. Targeted Therapy for Melanoma

    Energy Technology Data Exchange (ETDEWEB)

    Quinn, Thomas [Alphamed, Jackson, TN (United States); Moore, Herbert [Alphamed, Jackson, TN (United States)

    2016-12-05

    The research project, entitled ”Targeted Therapy for Melanoma,” was focused on investigating the use of kidney protection measures to lower the non-specific kidney uptake of the radiolabeled Pb-DOTA-ReCCMSH peptide. Previous published work demonstrated that the kidney exhibited the highest non-target tissue uptake of the 212Pb/203Pb radiolabeled melanoma targeting peptide DOTA-ReCCMSH. The radiolabeled alpha-melanocyte stimulating hormone (α-MSH) peptide analog DOTA-Re(Arg11)CCMSH, which binds the melanocortin-1 receptor over-expressed on melanoma tumor cells, has shown promise as a PRRT agent in pre-clinical studies. High tumor uptake of 212Pb labeled DOTA-Re(Arg11)CCMSH resulted in tumor reduction or eradication in melanoma therapy studies. Of particular note was the 20-50% cure rate observed when melanoma mice were treated with alpha particle emitter 212Pb. However, as with most PRRT agents, high radiation doses to the kidneys where observed. To optimize tumor treatment efficacy and reduce nephrotoxicity, the tumor to kidney uptake ratio must be improved. Strategies to reduce kidney retention of the radiolabeled peptide, while not effecting tumor uptake and retention, can be broken into several categories including modification of the targeting peptide sequence and reducing proximal tubule reabsorption.

  18. Target Chamber Manipulator

    Science.gov (United States)

    Tantillo, Anthony; Watson, Matthew

    2015-11-01

    A system has been developed to allow remote actuation of sensors in a high vacuum target chamber used with a particle accelerator. Typically, sensors of various types are placed into the target chamber at specific radial and angular positions relative to the beam line and target. The chamber is then evacuated and the experiments are performed for those sensor positions. Then, the chamber is opened, the sensors are repositioned to new angles or radii, and the process is repeated, with a separate pump-down cycle for each set of sensor positions. The new sensor positioning system allows scientists to pre-set the radii of up to a dozen sensors, and then remotely actuate their angular positions without breaking the vacuum of the target chamber. This reduces the time required to reposition sensors from 6 hours to 1 minute. The sensors are placed into one of two tracks that are separately actuated using vacuum-grade stepping motors. The positions of the sensors are verified using absolute optical rotary encoders, and the positions are accurate to 0.5 degrees. The positions of the sensors are electronically recorded and time-stamped after every change. User control is through a GUI using LabVIEW.

  19. Active Target Simulation

    Science.gov (United States)

    Smith, Nathan; Draznik, Peter; Frank, Nathan

    2012-10-01

    We have simulated an existing experimental design to determine the resolution improvement upon energy measurements of neutron unbound nuclei. A number of experiments of this type have been performed at the National Superconducting Cyclotron Laboratory (NSCL), located at Michigan State University. An excited nucleus is typically produced with a radioactive beam interacting with a passive Beryllium target. Many different nuclei are produced in experiment, each of which immediately decays into a charged particle and neutron. The charged particles are detected and the neutrons interact in scintillation detectors such as the Modular Neutron Array (MoNA) and Large Multi-Institutional Scintillation Array (LISA). In our simulation, we have constructed an active target that provides additional information such that the point of nuclear interaction within the target may be determined. This information improves the resolution in decay energy measurements of neutron unbound isotopes. This presentation will cover some aspects of the simulation process, as well as showing some of the results that demonstrate the simulated improvement over a passive target.

  20. Intracellular delivery of nanocarriers and targeting to subcellular organelles.

    Science.gov (United States)

    Jhaveri, Aditi; Torchilin, Vladimir

    2016-01-01

    Recent trends in drug delivery indicate a steady increase in the use of targeted therapeutics to enhance the specific delivery of biologically active payloads to diseased tissues while avoiding their off-target effects. However, in most cases, the distribution of therapeutics inside cells and their targeting to intracellular targets still presents a formidable challenge. The main barrier to intracellular delivery is the translocation of therapeutic molecules across the cell membrane, and ultimately through the membrane of their intracellular target organelles. Another prerequisite for an efficient intracellular localization of active molecules is their escape from the endocytic pathway. Pharmaceutical nanocarriers have demonstrated substantial advantages for the delivery of therapeutics and offer elegant platforms for intracellular delivery. They can be engineered with both intracellular and organelle-specific targeting moieties to deliver encapsulated or conjugated cargoes to specific sub-cellular targets. In this review, we discuss important aspects of intracellular drug targeting and delivery with a focus on nanocarriers modified with various ligands to specifically target intracellular organelles. Intracellular delivery affords selective localization of molecules to their target site, thus maximizing their efficacy and safety. The advent of novel nanocarriers and targeting ligands as well as exploration of alternate routes for the intracellular delivery and targeting has prompted extensive research, and promises an exciting future for this field.

  1. Superfund and Toxic Release Inventory Sites - MDC_ContaminatedSite

    Data.gov (United States)

    NSGIC Local Govt | GIS Inventory — A point feature class of open DERM Contaminated sites - see phase code for status of site. Contaminated sites identifies properties where environmental contamination...

  2. YUCCA MOUNTAIN SITE DESCRIPTION

    Energy Technology Data Exchange (ETDEWEB)

    A.M. Simmons

    2004-04-16

    The ''Yucca Mountain Site Description'' summarizes, in a single document, the current state of knowledge and understanding of the natural system at Yucca Mountain. It describes the geology; geochemistry; past, present, and projected future climate; regional hydrologic system; and flow and transport within the unsaturated and saturated zones at the site. In addition, it discusses factors affecting radionuclide transport, the effect of thermal loading on the natural system, and tectonic hazards. The ''Yucca Mountain Site Description'' is broad in nature. It summarizes investigations carried out as part of the Yucca Mountain Project since 1988, but it also includes work done at the site in earlier years, as well as studies performed by others. The document has been prepared under the Office of Civilian Radioactive Waste Management quality assurance program for the Yucca Mountain Project. Yucca Mountain is located in Nye County in southern Nevada. The site lies in the north-central part of the Basin and Range physiographic province, within the northernmost subprovince commonly referred to as the Great Basin. The basin and range physiography reflects the extensional tectonic regime that has affected the region during the middle and late Cenozoic Era. Yucca Mountain was initially selected for characterization, in part, because of its thick unsaturated zone, its arid to semiarid climate, and the existence of a rock type that would support excavation of stable openings. In 1987, the United States Congress directed that Yucca Mountain be the only site characterized to evaluate its suitability for development of a geologic repository for high-level radioactive waste and spent nuclear fuel.

  3. Targeted Genome Regulation and Editing in Plants

    KAUST Repository

    Piatek, Agnieszka

    2016-03-01

    The ability to precisely regulate gene expression patterns and to modify genome sequence in a site-specific manner holds much promise in determining gene function and linking genotype to phenotype. DNA-binding modules have been harnessed to generate customizable and programmable chimeric proteins capable of binding to site-specific DNA sequences and regulating the genome and epigenome. Modular DNA-binding domains from zinc fingers (ZFs) and transcriptional activator-like effectors (TALEs) are amenable to engineering to bind any DNA target sequence of interest. Deciphering the code of TALE repeat binding to DNA has helped to engineer customizable TALE proteins capable of binding to any sequence of interest. Therefore TALE repeats provide a rich resource for bioengineering applications. However, the TALE system is limited by the requirement to re-engineer one or two proteins for each new target sequence. Recently, the clustered regularly interspaced palindromic repeats (CRISPR)/ CRISPR associated 9 (Cas9) has been used as a versatile genome editing tool. This machinery has been also repurposed for targeted transcriptional regulation. Due to the facile engineering, simplicity and precision, the CRISPR/Cas9 system is poised to revolutionize the functional genomics studies across diverse eukaryotic species. In this dissertation I employed transcription activator-like effectors and CRISPR/Cas9 systems for targeted genome regulation and editing and my achievements include: 1) I deciphered and extended the DNA-binding code of Ralstonia TAL effectors providing new opportunities for bioengineering of customizable proteins; 2) I repurposed the CRISPR/Cas9 system for site-specific regulation of genes in plant genome; 3) I harnessed the power of CRISPR/Cas9 gene editing tool to study the function of the serine/arginine-rich (SR) proteins.

  4. Vision-Based Target Finding and Inspection of a Ground Target Using a Multirotor UAV System

    Directory of Open Access Journals (Sweden)

    Ajmal Hinas

    2017-12-01

    Full Text Available In this paper, a system that uses an algorithm for target detection and navigation and a multirotor Unmanned Aerial Vehicle (UAV for finding a ground target and inspecting it closely is presented. The system can also be used for accurate and safe delivery of payloads or spot spraying applications in site-specific crop management. A downward-looking camera attached to a multirotor is used to find the target on the ground. The UAV descends to the target and hovers above the target for a few seconds to inspect the target. A high-level decision algorithm based on an OODA (observe, orient, decide, and act loop was developed as a solution to address the problem. Navigation of the UAV was achieved by continuously sending local position messages to the autopilot via Mavros. The proposed system performed hovering above the target in three different stages: locate, descend, and hover. The system was tested in multiple trials, in simulations and outdoor tests, from heights of 10 m to 40 m. Results show that the system is highly reliable and robust to sensor errors, drift, and external disturbance.

  5. Targeted inactivation and identification of targets of the Gli2a transcription factor in the zebrafish

    Directory of Open Access Journals (Sweden)

    Xingang Wang

    2013-09-01

    Hedgehog (Hh signaling is mediated by the Gli transcription factors and, in the zebrafish, plays an important role in patterning both the neural tube and myotome. Using a null allele of the gli2a gene induced by targeted mutagenesis, we show that Gli2a is completely dispensable in the fish but acts redundantly with Gli1 to regulate expression of known Hh targets, such as ptch2, prdm1a and eng2a, in the myotome and neural tube. To identify novel targets of Hh signaling, we performed chromatin immunoprecipitation sequencing (ChIP-seq of whole embryo extracts. Samples were significantly enriched for 192 genomic regions, some of which are associated with four known Hh target genes, ptch1, ptch2, gli1 and olig2. Sequence analysis of these regions reveals a high level of conservation of Gli-binding sites from fish to mammals in some, but not all, cases. Expression analysis of other transcription units that are closely associated with peaks identified several putative targets not previously implicated as Hh targets, including myl10, hnmt, lrp4, efemp2, fras1, quo, and lamc1. Each of these genes shows loss of, or reduced expression in, embryos homozygous for an antimorphic allele of gli2a, you-too (yot, consistent with their being direct targets of Gli2a.

  6. Vision-Based Target Finding and Inspection of a Ground Target Using a Multirotor UAV System.

    Science.gov (United States)

    Hinas, Ajmal; Roberts, Jonathan M; Gonzalez, Felipe

    2017-12-17

    In this paper, a system that uses an algorithm for target detection and navigation and a multirotor Unmanned Aerial Vehicle (UAV) for finding a ground target and inspecting it closely is presented. The system can also be used for accurate and safe delivery of payloads or spot spraying applications in site-specific crop management. A downward-looking camera attached to a multirotor is used to find the target on the ground. The UAV descends to the target and hovers above the target for a few seconds to inspect the target. A high-level decision algorithm based on an OODA (observe, orient, decide, and act) loop was developed as a solution to address the problem. Navigation of the UAV was achieved by continuously sending local position messages to the autopilot via Mavros. The proposed system performed hovering above the target in three different stages: locate, descend, and hover. The system was tested in multiple trials, in simulations and outdoor tests, from heights of 10 m to 40 m. Results show that the system is highly reliable and robust to sensor errors, drift, and external disturbance.

  7. Drug Promiscuity in PDB: Protein Binding Site Similarity Is Key.

    Science.gov (United States)

    Haupt, V Joachim; Daminelli, Simone; Schroeder, Michael

    2013-01-01

    Drug repositioning applies established drugs to new disease indications with increasing success. A pre-requisite for drug repurposing is drug promiscuity (polypharmacology) - a drug's ability to bind to several targets. There is a long standing debate on the reasons for drug promiscuity. Based on large compound screens, hydrophobicity and molecular weight have been suggested as key reasons. However, the results are sometimes contradictory and leave space for further analysis. Protein structures offer a structural dimension to explain promiscuity: Can a drug bind multiple targets because the drug is flexible or because the targets are structurally similar or even share similar binding sites? We present a systematic study of drug promiscuity based on structural data of PDB target proteins with a set of 164 promiscuous drugs. We show that there is no correlation between the degree of promiscuity and ligand properties such as hydrophobicity or molecular weight but a weak correlation to conformational flexibility. However, we do find a correlation between promiscuity and structural similarity as well as binding site similarity of protein targets. In particular, 71% of the drugs have at least two targets with similar binding sites. In order to overcome issues in detection of remotely similar binding sites, we employed a score for binding site similarity: LigandRMSD measures the similarity of the aligned ligands and uncovers remote local similarities in proteins. It can be applied to arbitrary structural binding site alignments. Three representative examples, namely the anti-cancer drug methotrexate, the natural product quercetin and the anti-diabetic drug acarbose are discussed in detail. Our findings suggest that global structural and binding site similarity play a more important role to explain the observed drug promiscuity in the PDB than physicochemical drug properties like hydrophobicity or molecular weight. Additionally, we find ligand flexibility to have a minor

  8. Allegheny County Illegal Dump Sites

    Data.gov (United States)

    Allegheny County / City of Pittsburgh / Western PA Regional Data Center — The Illegal Dump Site dataset includes information on illegal dump sites, their type of trash, and the estimate tons of trash at each site. The information was...

  9. 2014 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    Paquette, Douglas [Brookhaven National Lab. (BNL), Upton, NY (United States); Remien, Jason [Brookhaven National Lab. (BNL), Upton, NY (United States); Foley, Brian [Brookhaven National Lab. (BNL), Upton, NY (United States); Burke, John [Brookhaven National Lab. (BNL), Upton, NY (United States); Dorsch, William [Brookhaven National Lab. (BNL), Upton, NY (United States); Ratel, Karen [Brookhaven National Lab. (BNL), Upton, NY (United States); Howe, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Welty, Tim [Brookhaven National Lab. (BNL), Upton, NY (United States); Williams, Jeffrey [Brookhaven National Lab. (BNL), Upton, NY (United States); Pohlpt, Peter [Brookhaven National Lab. (BNL), Upton, NY (United States); Lagattolla, Richard [Brookhaven National Lab. (BNL), Upton, NY (United States); Metz, Robert [Brookhaven National Lab. (BNL), Upton, NY (United States); Milligan, James [Brookhaven National Lab. (BNL), Upton, NY (United States); Lettieri, Lawrence [Brookhaven National Lab. (BNL), Upton, NY (United States)

    2015-10-01

    BNL prepares an annual Site Environmental Report (SER) in accordance with DOE Order 231.1B, Environment, Safety and Health Reporting. The report is written to inform the public, regulators, employees, and other stakeholders of the Laboratory’s environmental performance during the calendar year in review.

  10. Surgical site infections

    African Journals Online (AJOL)

    Organ space SSI. • Infection occurs within 30 days if no implant, or within a year if implant and the infection seems to be related to the operation and infection occurs in any anatomical site ... Diagnosis of an organ/space SSI made by the surgeon or ..... selected projects ”enlist the best academic researchers and industry to.

  11. Sites and Enactments

    DEFF Research Database (Denmark)

    Korsgaard, Steffen T.; Neergaard, Helle

    2008-01-01

    is formulated where opportunities are seen as dynamic in the sense that they are enacted in different social practices at different sites. The method is illustrated through an analysis of the birth of The Republic of Tea, a very successful tea company, as presented in the book "The Republic of Tea"....

  12. Surveying Lab II site

    CERN Document Server

    1974-01-01

    The network of survey reference points on the Lab II site was extended to meet the geodetic needs of the SPS and its North Experimental Area. The work was greatly eased by a geodolite, a measuring instrument on loan from the Fermi Laboratory, which uses a modulated laser beam. (See CERN Courier 14 (1974) p. 247.)

  13. Surgical site infections

    African Journals Online (AJOL)

    Surgical site infections (SSIs) are a worldwide problem that has far reaching implications on patient morbidity and ... was complicated by a SSI had a 2-11% higher risk of death. In those patients who died, 75% was directly .... genital and uninfected urinary tract is not entered. In addition, clean wounds are primarily closed ...

  14. Power plant siting

    Energy Technology Data Exchange (ETDEWEB)

    Winter, J.V.; Conner, D.A.

    1978-01-01

    Just to keep up with expected demand, the US will need over 500 new power generation units by 1985. Where these power plants will be located is the subject of heated debate among utility officials, government leaders, conservationists, concerned citizens and a multitude of special interest groups. This book offers a balanced review of all of the salient factors that must be taken into consideration in selecting power plant locations. To deal with this enormously complex subject, the authors (1) offer a general overview of the history and reasoning behind present legislation on the state and national levels; (2) describe the many different agencies that have jurisdiction in power plant location, from local water authorities and city councils to state conservation boards and the Nuclear Regulatory Commission; and (3) include a state-by-state breakdown of siting laws, regulations and present licensing procedures. Architects, engineers, contractors, and others involved in plant construction and site evaluation will learn of the trade-offs that must be made in balancing the engineering, economic, and environmental impacts of plant location. The book covers such areas as availability of water supplies for generation or cooling; geology, typography, and demography of the proposed site; and even the selection of the fuel best suited for the area. Finally, the authors examine the numerous environmental aspects of power plant siting.

  15. Visit our Site

    NARCIS (Netherlands)

    Jos de Haan; Renée Mast; Marleen Varekamp; Susanne Janssen

    2006-01-01

    Original title: Bezoek onze site. More and more cultural organisations are digitising content and making this cultural treasure chest available to a wider public via the Internet. International comparison shows that the Netherlands is one of the leaders in this regard. This report summarises

  16. Physics of polarized targets

    CERN Document Server

    Niinikoski, Tapio

    2014-01-01

    For developing, building and operating solid polarized targets we need to understand several fields of physics that have seen sub stantial advances during the last 50 years. W e shall briefly review a selection of those that are important today. These are: 1) quantum statistical methods to describe saturation and relaxation in magnetic resonance; 2) equal spin temperature model for dy namic nuclear polarization; 3 ) weak saturation during NMR polarization measurement; 4 ) refrigeration using the quantum fluid properties of helium isotopes. These, combined with superconducting magnet technologies, permit today to reach nearly complete pola rization of almost any nuclear spins. Targets can be operated in frozen spin mode in rather low and inhomogeneous field of any orientation, and in DNP mode in beams of high intensity. Beyond such experiments of nuclear and particle physics, applications a re also emerging in macromolecular chemistry and in magnetic resonance imaging. This talk is a tribute to Michel Borghini...

  17. Emerging Targets in Photopharmacology.

    Science.gov (United States)

    Lerch, Michael M; Hansen, Mickel J; van Dam, Gooitzen M; Szymanski, Wiktor; Feringa, Ben L

    2016-09-05

    The field of photopharmacology uses molecular photoswitches to establish control over the action of bioactive molecules. It aims to reduce systemic drug toxicity and the emergence of resistance, while achieving unprecedented precision in treatment. By using small molecules, photopharmacology provides a viable alternative to optogenetics. We present here a critical overview of the different pharmacological targets in various organs and a survey of organ systems in the human body that can be addressed in a non-invasive manner. We discuss the prospects for the selective delivery of light to these organs and the specific requirements for light-activatable drugs. We also aim to illustrate the druggability of medicinal targets with recent findings and emphasize where conceptually new approaches have to be explored to provide photopharmacology with future opportunities to bring "smart" molecular design ultimately to the realm of clinical use. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Inflation Targeting: Provisional Results

    Directory of Open Access Journals (Sweden)

    Cerna, Silviu

    2010-06-01

    Full Text Available Inflation targeting monetary policy framework that requires the central bank to achieve a low inflation has contributed to price stability in industrialized countries. As well as the other developing countries, ex communist countries have also tried to apply this strategy, which was susceptible to increase monetary policy transparency and to determine authorities to make necessary reforms in order to pass from a planned to a market economy. In Romania, inflation targeting has contributed, to a large extent, to price increase smoothening, without affecting economic growth. Knowing the factors that have determined this unquestionable success allows for not only understanding the Romanian transition process, but also draw some useful conclusions in view of the necessary actions for adopting the euro.

  19. Foucault on targets.

    Science.gov (United States)

    Lynch, John

    2004-01-01

    This paper seeks to gain an insight into the behavior of a large NHS trust, in its attempt to meet a 90 percent patient access target, in a week long national audit in March 2003. Why did individuals act in dramatically different ways to their norm over this period. The work of Michel Foucault is used to explore these issues. The discourses of power, knowledge, discipline and governmentality are identified as key foucaudian themes that offer an alternative interpretation of how individuals behave in their place of work. The importance of the historical context of discourse within the NHS cannot be underestimated in shaping the behavior of individuals and groups today. Power and knowledge permeate NHS organizations through disciplinary practices and dressage. Governmentality seeks to maintain the status quo through disciplinary processes such as national healthcare targets. The natural response of NHS organizations is therefore, to seek order and conformity rather than disorder and conflict.

  20. Small Wind Site Assessment Guidelines

    Energy Technology Data Exchange (ETDEWEB)

    Olsen, Tim [Advanced Energy Systems LLC, Eugene, OR (United States); Preus, Robert [National Renewable Energy Lab. (NREL), Golden, CO (United States)

    2015-09-01

    Site assessment for small wind energy systems is one of the key factors in the successful installation, operation, and performance of a small wind turbine. A proper site assessment is a difficult process that includes wind resource assessment and the evaluation of site characteristics. These guidelines address many of the relevant parts of a site assessment with an emphasis on wind resource assessment, using methods other than on-site data collection and creating a small wind site assessment report.

  1. Antibodies Targeting EMT

    Science.gov (United States)

    2017-10-01

    VLDL uptake and redistribution of lipids to cells for energy metabolism and cell signaling. ApoE overexpression has shown to be associated with a...involved in testosterone and estradiol biosynthesis, as well as prostaglandin F synthesis and has previously been implicated in cancer progression, AKR1C2...is involved in androgen metabolism and is a potential drug target for prostate cancer. AKR1C4 is involved in bile acid synthesis but has not yet

  2. Explosive Target Balances

    OpenAIRE

    Potrafke, Niklas; Reischmann, Markus

    2013-01-01

    Using the new unit root test by Phillips et al. (2011) we show that the Target balances of the German Bundesbank have been exploding from the beginning of 2009 to the beginning of 2013. By implementing a full-allotment policy and reducing the required minimum quality of collaterals in October 2008, the European Central Bank (ECB) refinanced credits in the GIIPS countries to a large extent. Private capital flowed out of the GIIPS countries (Greece, Italy, Ireland, Portugal and Spain), and the ...

  3. Implementing Target Value Design.

    Science.gov (United States)

    Alves, Thais da C L; Lichtig, Will; Rybkowski, Zofia K

    2017-04-01

    An alternative to the traditional way of designing projects is the process of target value design (TVD), which takes different departure points to start the design process. The TVD process starts with the client defining an allowable cost that needs to be met by the design and construction teams. An expected cost in the TVD process is defined through multiple interactions between multiple stakeholders who define wishes and others who define ways of achieving these wishes. Finally, a target cost is defined based on the expected profit the design and construction teams are expecting to make. TVD follows a series of continuous improvement efforts aimed at reaching the desired goals for the project and its associated target value cost. The process takes advantage of rapid cycles of suggestions, analyses, and implementation that starts with the definition of value for the client. In the traditional design process, the goal is to identify user preferences and find solutions that meet the needs of the client's expressed preferences. In the lean design process, the goal is to educate users about their values and advocate for a better facility over the long run; this way owners can help contractors and designers to identify better solutions. This article aims to inform the healthcare community about tools and techniques commonly used during the TVD process and how they can be used to educate and support project participants in developing better solutions to meet their needs now as well as in the future.

  4. Standardized UXO Technology Demonstration Site

    National Research Council Canada - National Science Library

    Overbay, Larry

    2004-01-01

    ...) utilizing the APG Standardized UXO Technology Demonstration Site Blind Grid. The scoring record was coordinated by Larry Overbay and by the Standardized UXO Technology Demonstration Site Scoring Committee...

  5. True perylene epitaxy on Ag(110) driven by site recognition effect.

    Science.gov (United States)

    Bobrov, K; Kalashnyk, N; Guillemot, L

    2015-03-14

    We present a STM study of room temperature perylene adsorption on the Ag(110) surface. We have found a 2D perylene crystalline phase coexisting with the perylene liquid phase under thermal equilibrium. The reversible precipitation of the liquid phase at sub-monolayer coverage reveals the well ordered chiral crystalline phase existing in two enantiomorphic configurations of the ((-2)(3) (5)(2)) and ((2)(3) (5)(-2)) symmetry. This chiral phase is spatially separated into the 2D enantiopure islands of tens of nanometers size randomly distributed on the substrate and surrounded by the liquid medium. Analysis of surface registry of the crystalline phase combined with modeling of the intermolecular interactions indicates that its structure and symmetry is determined by a specific balance between the intermolecular attraction and intrinsic ability of the perylene aromatic board to recognize adsorption sites. The recognition effect was found to be strong enough to pin half of the perylene molecules into defined adsorption sites providing the structure skeleton. The attractive intermolecular interaction was found to be strong enough to bind another half of the molecules to the perylene skeleton shaping the true epitaxial structure.

  6. True perylene epitaxy on Ag(110) driven by site recognition effect

    Science.gov (United States)

    Bobrov, K.; Kalashnyk, N.; Guillemot, L.

    2015-03-01

    We present a STM study of room temperature perylene adsorption on the Ag(110) surface. We have found a 2D perylene crystalline phase coexisting with the perylene liquid phase under thermal equilibrium. The reversible precipitation of the liquid phase at sub-monolayer coverage reveals the well ordered chiral crystalline phase existing in two enantiomorphic configurations of the (- 2 5 3 2 ) and (2 5 3 -2 ) symmetry. This chiral phase is spatially separated into the 2D enantiopure islands of tens of nanometers size randomly distributed on the substrate and surrounded by the liquid medium. Analysis of surface registry of the crystalline phase combined with modeling of the intermolecular interactions indicates that its structure and symmetry is determined by a specific balance between the intermolecular attraction and intrinsic ability of the perylene aromatic board to recognize adsorption sites. The recognition effect was found to be strong enough to pin half of the perylene molecules into defined adsorption sites providing the structure skeleton. The attractive intermolecular interaction was found to be strong enough to bind another half of the molecules to the perylene skeleton shaping the true epitaxial structure.

  7. Inflation targeting and core inflation

    OpenAIRE

    Julie Smith

    2005-01-01

    This paper examines the interaction of core inflation and inflation targeting as a monetary policy regime. Interest in core inflation has grown because of inflation targeting. Core inflation is defined in numerous ways giving rise to many potential measures; this paper defines core inflation as the best forecaster of inflation. A cross-country study finds before the start of inflation targeting, but not after, core inflation differs between non-inflation targeters and inflation targeters. Thr...

  8. Is Privacy at Risk when Commercial Websites Target Primary School Children? A Case Study in Korea

    Science.gov (United States)

    Kim, Sora; Yi, Soon-Hyung

    2010-01-01

    This study discusses privacy risk factors when commercial web sites target primary school children in Korea. Specifically, the authors examined types of personal information required for membership subscriptions and whether privacy policies at commercial sites for children abide by privacy guidelines. A total of 159 commercial sites targeting…

  9. Towards targeted cancer therapy: Aptamer or oncolytic virus?

    Science.gov (United States)

    Tan, Kei X; Danquah, Michael K; Sidhu, Amandeep; Ongkudon, Clarence M; Lau, Sie Yon

    2017-01-01

    Cancer is a leading cause of global mortality. Whilst anticancer awareness programs have increased significantly over the years, scientific research into the development of efficient and specific drugs to target cancerous cells for enhanced therapeutic effects has not received much clinical success. Chemotherapeutic agents are incapable of acting specifically on cancerous cells, thus causing low therapeutic effects accompanied by toxicity to surrounding normal tissues. The search for smart, highly specific and efficient cancer treatments and delivery systems continues to be a significant research endeavor. Targeted cancer therapy is an evolving treatment approach with great promise in enhancing the efficacy of cancer therapies via the delivery of therapeutic agents specifically to and into desired tumor cells using viral or non-viral targeting elements. Viral oncotherapy is an advanced cancer therapy based on the use of oncolytic viruses (OV) as elements to specifically target, replicate and kill malignant cancer cells selectively without affecting surrounding healthy cells. Aptamers, on the other hand, are non-viral targeting elements that are single-stranded nucleic acids with high specificity, selectivity and binding affinity towards their cognate targets. Aptamers have emerged as a new class of bioaffinity targeting elements can be generated and molecularly engineered to selectively bind to diverse targets including proteins, cells and tissues. This article discusses, comparatively, the potentials and impacts of both viral and aptamer-mediated targeted cancer therapies in advancing conventional drug delivery systems through enhanced target specificity, therapeutic payload, bioavailability of the therapeutic agents at the target sites whilst minimizing systemic cytotoxicity. This article emphasizes on effective site-directed targeting mechanisms and efficacy issues that impact on clinical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  10. PhosphoSiteAnalyzer

    DEFF Research Database (Denmark)

    Bennetzen, Martin V; Cox, Jürgen; Mann, Matthias

    2012-01-01

    Phosphoproteomic experiments are routinely conducted in laboratories worldwide, and because of the fast development of mass spectrometric techniques and efficient phosphopeptide enrichment methods, researchers frequently end up having lists with tens of thousands of phosphorylation sites...... for further interrogation. To answer biologically relevant questions from these complex data sets, it becomes essential to apply computational, statistical, and predictive analytical methods. Here we provide an advanced bioinformatic platform termed "PhosphoSiteAnalyzer" to explore large phosphoproteomic data...... an algorithm to retrieve kinase predictions from the public NetworKIN webpage in a semiautomated way and applies hereafter advanced statistics to facilitate a user-tailored in-depth analysis of the phosphoproteomic data sets. The interface of the software provides a high degree of analytical flexibility...

  11. Large scale RNAi screen in Tribolium reveals novel target genes for pest control and the proteasome as prime target.

    Science.gov (United States)

    Ulrich, Julia; Dao, Van Anh; Majumdar, Upalparna; Schmitt-Engel, Christian; Schwirz, Jonas; Schultheis, Dorothea; Ströhlein, Nadi; Troelenberg, Nicole; Grossmann, Daniela; Richter, Tobias; Dönitz, Jürgen; Gerischer, Lizzy; Leboulle, Gérard; Vilcinskas, Andreas; Stanke, Mario; Bucher, Gregor

    2015-09-03

    Insect pest control is challenged by insecticide resistance and negative impact on ecology and health. One promising pest specific alternative is the generation of transgenic plants, which express double stranded RNAs targeting essential genes of a pest species. Upon feeding, the dsRNA induces gene silencing in the pest resulting in its death. However, the identification of efficient RNAi target genes remains a major challenge as genomic tools and breeding capacity is limited in most pest insects impeding whole-animal-high-throughput-screening. We use the red flour beetle Tribolium castaneum as a screening platform in order to identify the most efficient RNAi target genes. From about 5,000 randomly screened genes of the iBeetle RNAi screen we identify 11 novel and highly efficient RNAi targets. Our data allowed us to determine GO term combinations that are predictive for efficient RNAi target genes with proteasomal genes being most predictive. Finally, we show that RNAi target genes do not appear to act synergistically and that protein sequence conservation does not correlate with the number of potential off target sites. Our results will aid the identification of RNAi target genes in many pest species by providing a manageable number of excellent candidate genes to be tested and the proteasome as prime target. Further, the identified GO term combinations will help to identify efficient target genes from organ specific transcriptomes. Our off target analysis is relevant for the sequence selection used in transgenic plants.

  12. MicroRNA target prediction using thermodynamic and sequence curves.

    Science.gov (United States)

    Ghoshal, Asish; Shankar, Raghavendran; Bagchi, Saurabh; Grama, Ananth; Chaterji, Somali

    2015-11-25

    MicroRNAs (miRNAs) are small regulatory RNA that mediate RNA interference by binding to various mRNA target regions. There have been several computational methods for the identification of target mRNAs for miRNAs. However, these have considered all contributory features as scalar representations, primarily, as thermodynamic or sequence-based features. Further, a majority of these methods solely target canonical sites, which are sites with "seed" complementarity. Here, we present a machine-learning classification scheme, titled Avishkar, which captures the spatial profile of miRNA-mRNA interactions via smooth B-spline curves, separately for various input features, such as thermodynamic and sequence features. Further, we use a principled approach to uniformly model canonical and non-canonical seed matches, using a novel seed enrichment metric. We demonstrate that large number of seed-match patterns have high enrichment values, conserved across species, and that majority of miRNA binding sites involve non-canonical matches, corroborating recent findings. Using spatial curves and popular categorical features, such as target site length and location, we train a linear SVM model, utilizing experimental CLIP-seq data. Our model significantly outperforms all established methods, for both canonical and non-canonical sites. We achieve this while using a much larger candidate miRNA-mRNA interaction set than prior work. We have developed an efficient SVM-based model for miRNA target prediction using recent CLIP-seq data, demonstrating superior performance, evaluated using ROC curves, specifically about 20% better than the state-of-the-art, for different species (human or mouse), or different target types (canonical or non-canonical). To the best of our knowledge we provide the first distributed framework for microRNA target prediction based on Apache Hadoop and Spark. All source code and data is publicly available at https://bitbucket.org/cellsandmachines/avishkar.

  13. Placental site trophoblastic tumor

    Directory of Open Access Journals (Sweden)

    Jean eBouquet De Jolinière

    2014-08-01

    Full Text Available Trophoblastic tumors of placental site (PSTT are rare. They represent a rare form of gestational trophoblastic disease. (GTD. They occur mainly in women who have a history of miscarriage, termination of pregnancy, or even a normal or pathological ongoing pregnancy. The clinical course is unpredictable. This malignancy has different characteristics from other gestational trophoblastic tumors.Following a clinical case that we encountered and treated, we conducted a literary research and review, focusing primarily on prognostic factors and treatment.

  14. Web site for GAIN

    OpenAIRE

    Brænden, Stig; Gjerde, Stian; Hansen, Terje, TAR

    2001-01-01

    The project started with an inquiry from GAIN, Graphic Arts Intelligence Network, on the September 26. 2000. GAIN currently has a website that is static, and is not functioning in a satisfying way. The desire is therefore to establish a new dynamic web site with the possibility for the GAIN members to update the page via a browser interface, and maintain their own profiles. In addition to this they would like a brand new and more functional design. GAIN also wants to e...

  15. 1999 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    ENGEL-COX,J.; ZIMMERMAN,E.; LEE,R.; WILLIAMS,J.; GREEN,T.; PAQUETTE,D.; HOODA,B.; SCARPITTA,S.; GENZER,P.; ET AL

    2000-09-01

    Throughout the scientific community, Brookhaven National Laboratory (BNL) is renowned for its leading-edge research in physics, medicine, chemistry, biology, materials, and the environment. BNL is committed to supporting its world-class scientific research with an internationally recognized environmental protection program. The 1999 Site Environmental Report (SER) summarizes the status of the Laboratory's environmental programs and performance, including the steady progress towards cleaning up the site and fully integrating environmental stewardship into all facets of the Laboratory's mission. BNL is located on 5,265 acres of pine barrens in Suffolk County in the center of Long Island, New York. The Laboratory is situated above a sole source aquifer at the headwaters of the Peconic River; therefore, protecting ground and surface water quality is a special concern. Approximately 3,600 acres of the site are undeveloped and serve as habitat for a wide variety of animals and plants, including one New York State endangered species, the tiger salamander, and two New York State threatened species, the banded sunfish and the stiff goldenrod. Monitoring, preserving, and restoring these ecological resources is a high priority for the Laboratory.

  16. Targeted therapy for sarcomas

    Directory of Open Access Journals (Sweden)

    Forscher C

    2014-03-01

    Full Text Available Charles Forscher,1 Monica Mita,2 Robert Figlin3 1Sarcoma Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; 2Experimental Therapeutics Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA; 3Academic Development Program, Samuel Oschin Comprehensive Cancer Institute, and Division of Hematology/Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA Abstract: Sarcomas are tumors of mesenchymal origin that make up approximately 1% of human cancers. They may arise as primary tumors in either bone or soft tissue, with approximately 11,280 soft tissue tumors and 2,650 bone tumors diagnosed each year in the United States. There are at least 50 different subtypes of soft tissue sarcoma, with new ones described with ever-increasing frequency. One way to look at sarcomas is to divide them into categories on the basis of their genetic make-up. One group of sarcomas has an identifiable, relatively simple genetic signature, such as the X:18 translocation seen in synovial sarcoma or the 11:22 translocation seen in Ewing's sarcoma. These specific abnormalities often lead to the presence of fusion proteins, such as EWS-FLI1 in Ewing's sarcoma, which are helpful as diagnostic tools and may become therapeutic targets in the future. Another group of sarcomas is characterized by complex genetic abnormalities as seen in leiomyosarcoma, osteosarcoma, and undifferentiated sarcoma. It is important to keep these distinctions in mind when contemplating the development of targeted agents for sarcomas. Different abnormalities in sarcoma could be divided by tumor subtype or by the molecular or pathway abnormality. However, some existing drugs or drugs in development may interfere with or alter more than one of the presented pathways. Keywords: sarcoma, targeted agents, tyrosine kinase inhibitors, mTor inhibition

  17. Identification of genomic sites for CRISPR/Cas9-based genome editing in the Vitis vinifera genome

    National Research Council Canada - National Science Library

    Wang, Yi; Liu, Xianju; Ren, Chong; Zhong, Gan-Yuan; Yang, Long; Li, Shaohua; Liang, Zhenchang

    2016-01-01

    .... Many specific target sites for CRISPR/Cas9 have been computationally identified for several annual model and crop species, but such sites have not been reported for perennial, woody fruit species...

  18. Heterocyclic inhibitors of AChE acylation and peripheral sites.

    Science.gov (United States)

    Bolognesi, Maria Laura; Andrisano, Vincenza; Bartolini, Manuela; Cavalli, Andrea; Minarini, Anna; Recanatini, Maurizio; Rosini, Michela; Tumiatti, Vincenzo; Melchiorre, Carlo

    2005-01-01

    Notwithstanding the criticism to the so called " cholinergic hypothesis", the therapeutic strategies for the treatment of Alzheimer's disease (AD) have been mainly centered on the restoration of cholinergic functionality and, until the last year, the only drugs licensed for the management of AD were the acetycholinesterase (AChE) inhibitors. Target enzyme AChE consists of a narrow gorge with two separate ligand binding sites: an acylation site at the bottom of the gorge containing the catalytic triad and a peripheral site located at the gorge rim, which encompasses binding sites for allosteric ligands. The aim of this short review is to update the knowledge on heterocyclic AChE inhibitors able to interact with the two sites of enzymes, structurally related to the well known inhibitors physostigmine, rivastigmine and propidium. The therapeutic potential of the dual site inhibithors in inhibiting amyloid-beta aggregatrion and deposition is also briefly summarised.

  19. Polarized scintillator targets

    Science.gov (United States)

    van den Brandt, B.; Bunyatova, E. I.; Hautle, P.; Konter, J. A.; Mango, S.

    2000-05-01

    The hydrogen nuclei in an organic scintillator have been polarized to more than 80% and the deuterons in its fully deuterated version to 24%. The scintillator, doped with TEMPO, has been polarized dynamically in a field of 2.5 T in a vertical dilution refrigerator in which a plastic lightguide transports the scintillation light from the sample in the mixing chamber to a photomultiplier outside the cryostat. Sizeable solid samples with acceptable optical properties and light output have been prepared and successfully operated as "live" polarized targets in nuclear physics experiments.

  20. Polarized scintillator targets

    Energy Technology Data Exchange (ETDEWEB)

    Brandt, B. van den E-mail: vandenbrandt@psi.ch; Bunyatova, E.I.; Hautle, P.; Konter, J.A.; Mango, S

    2000-05-21

    The hydrogen nuclei in an organic scintillator have been polarized to more than 80% and the deuterons in its fully deuterated version to 24%. The scintillator, doped with TEMPO, has been polarized dynamically in a field of 2.5 T in a vertical dilution refrigerator in which a plastic lightguide transports the scintillation light from the sample in the mixing chamber to a photomultiplier outside the cryostat. Sizeable solid samples with acceptable optical properties and light output have been prepared and successfully operated as 'live' polarized targets in nuclear physics experiments.

  1. Targeting Prostate Cancer Metastasis

    Science.gov (United States)

    2015-09-01

    achieve this goal, we cultured high-invasive prostate cancer PC3 cells and treated them with the drugs/inhibitors that were proposed to target WASF3...groups (treated by DMSO), either treated by 100 μM CYT997 or 10 μM Dasatinib suppressed the cells to spread throughout the fish body (Fig. 4). As...have scr eened t he e f fect s o f mor e t han 40 drugs on invasion using cul tur ed prost ate cancer cells and f ound t hat tar geting multiple

  2. Gene manipulation to enhance MIBG-targeted radionuclide therapy

    Energy Technology Data Exchange (ETDEWEB)

    Mairs, Robert J. [Targeted Therapy Group, Centre for Oncology and Applied Pharmacology, Cancer Research UK Beatson Laboratories, University of Glasgow, G61 1BD Glasgow (United Kingdom)]. E-mail: r.mairs@beatson.gla.ac.uk; Fullerton, Natasha E. [Targeted Therapy Group, Centre for Oncology and Applied Pharmacology, Cancer Research UK Beatson Laboratories, University of Glasgow, G61 1BD Glasgow (United Kingdom); Department of Urology, Gartnavel General Hospital, Glasgow G12 0NY (United Kingdom); Cosimo, Emilio [Targeted Therapy Group, Centre for Oncology and Applied Pharmacology, Cancer Research UK Beatson Laboratories, University of Glasgow, G61 1BD Glasgow (United Kingdom); Boyd, Marie [Targeted Therapy Group, Centre for Oncology and Applied Pharmacology, Cancer Research UK Beatson Laboratories, University of Glasgow, G61 1BD Glasgow (United Kingdom)

    2005-10-01

    The goal of targeted radionuclide therapy is the deposition in malignant cells of sterilizing doses of radiation without damaging normal tissue. The radiopharmaceutical [{sup 131}I]meta-iodobenzylguanidine ([{sup 131}I]MIBG) is an effective single agent for the treatment of neuroblastoma. However, uptake of the drug in malignant sites is insufficient to cure disease. A growing body of experimental evidence indicates exciting possibilities for the integration of gene transfer with [{sup 131}I]MIBG-targeted radiotherapy.

  3. Assessing the Impact of Tissue Target Concentration Data on Uncertainty in In Vivo Target Coverage Predictions.

    Science.gov (United States)

    Tiwari, A; Luo, H; Chen, X; Singh, P; Bhattacharya, I; Jasper, P; Tolsma, J E; Jones, H M; Zutshi, A; Abraham, A K

    2016-10-01

    Understanding pharmacological target coverage is fundamental in drug discovery and development as it helps establish a sequence of research activities, from laboratory objectives to clinical doses. To this end, we evaluated the impact of tissue target concentration data on the level of confidence in tissue coverage predictions using a site of action (SoA) model for antibodies. By fitting the model to increasing amounts of synthetic tissue data and comparing the uncertainty in SoA coverage predictions, we confirmed that, in general, uncertainty decreases with longitudinal tissue data. Furthermore, a global sensitivity analysis showed that coverage is sensitive to experimentally identifiable parameters, such as baseline target concentration in plasma and target turnover half-life and fixing them reduces uncertainty in coverage predictions. Overall, our computational analysis indicates that measurement of baseline tissue target concentration reduces the uncertainty in coverage predictions and identifies target-related parameters that greatly impact the confidence in coverage predictions. © 2016 The Authors CPT: Pharmacometrics & Systems Pharmacology published by Wiley Periodicals, Inc. on behalf of American Society for Clinical Pharmacology and Therapeutics.

  4. Enhancing RGI lyase thermostability by targeted single point mutations

    DEFF Research Database (Denmark)

    Silva, Inês R.; Larsen, Dorte Møller; Jers, Carsten

    2013-01-01

    approach involving single amino acid substitution. Nine individual amino acids were selected as targets for site-saturated mutagenesis by the use of a predictive consensus approach in combination with prediction of protein mutant stability changes and B-factor iteration testing. After extensive...... the applicability of a combinatorial predictive approach for designing a small site saturation library for improving enzyme thermostability. In addition, new thermostable RGI lyases suitable for enzymatic upgrading of pectinaceous plant biomass materials at elevated temperatures were produced....

  5. 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

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

    National Research Council Canada - National Science Library

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

    2014-01-01

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

  7. Targeting Nuclear Thymidylate Biosynthesis

    Science.gov (United States)

    Chon, James; Stover, Patrick J.; Field, Martha S.

    2016-01-01

    Thymidylate (dTMP) biosynthesis plays an essential and exclusive function in DNA synthesis and proper cell division, and therefore has been an attractive therapeutic target. Folate analogues, known as antifolates, and nucleotide analogs that inhibit the enzymatic action of the de novo thymidylate biosynthesis pathway and are commonly used in cancer treatment. In this review, we examine the mechanisms by which the antifolate 5-fluorouracil, as well as other dTMP synthesis inhibitors, function in cancer treatment in light of emerging evidence that dTMP synthesis occurs in the nucleus. Nuclear localization of the de novo dTMP synthesis pathway requires modification of the pathway enzymes by the small ubiquitin-like modifier (SUMO) protein. SUMOylation is required for nuclear localization of the de novo dTMP biosynthesis pathway, and disruption in the SUMO pathway inhibits cell proliferation in several cancer models. We summarize evidence that the nuclear localization of the dTMP biosynthesis pathway is a critical factor in the efficacy of antifolate-based therapies that target dTMP synthesis. PMID:27876557

  8. Targeted corneal transplantation.

    Science.gov (United States)

    Jhanji, Vishal; Mehta, Jod S; Sharma, Namrata; Sharma, Bhavana; Vajpayee, Rasik B

    2012-07-01

    Corneal transplantation surgery has moved from an era of conventional penetrating keratoplasty to selective replacement of the diseased corneal layer with complementary healthy donor corneal tissue. Anterior lamellar transplantation surgeries do not involve replacement of corneal endothelium, consequently eliminating the occurrence of endothelial rejection. Similarly, in diseases affecting the corneal endothelium, selective replacement with a lamellar lenticule bearing healthy endothelium provides better outcomes in terms of ocular surface, lesser astigmatism and quick visual recovery. In addition to the advantages of enhanced surgical outcomes, targeted corneal transplantation allows the use of one donor cornea for more than one recipient, thereby offering a viable solution to the problem of paucity of donor corneas. Evolving techniques of corneal transplantation have enabled better utilization of donor corneal tissue. Anterior lamellar as well as endothelial keratoplasty surgeries have become first-choice surgeries in appropriately selected cases. This review briefly discusses some of these novel surgical techniques. A better understanding of targeted corneal transplantation would lead to adaptation of the concept of component corneal surgery. This would further enable the corneal surgeons to circumvent the problem of donor corneal shortage especially in the developing world.

  9. Fixed target beams

    CERN Document Server

    Kain, V; Cettour-Cave, S; Cornelis, K; Fraser, M A; Gatignon, L; Goddard, B; Velotti, F

    2017-01-01

    The CERN SPS (Super Proton Synchrotron) serves asLHC injector and provides beam for the North Area fixedtarget experiments. At low energy, the vertical acceptancebecomes critical with high intensity large emittance fixed tar-get beams. Optimizing the vertical available aperture is a keyingredient to optimize transmission and reduce activationaround the ring. During the 2016 run a tool was developed toprovide an automated local aperture scan around the entirering.The flux of particles slow extracted with the1/3inte-ger resonance from the Super Proton Synchrotron at CERNshould ideally be constant over the length of the extractionplateau, for optimum use of the beam by the fixed target ex-periments in the North Area. The extracted intensity is con-trolled in feed-forward correction of the horizontal tune viathe main SPS quadrupoles. The Mains power supply noiseat 50 Hz and harmonics is also corrected in feed-forwardby small amplitude tune modulation at the respective fre-quencies with a dedicated additional quad...

  10. Old Drug, New Target

    Science.gov (United States)

    Andrews, William J.; Panova, Tatiana; Normand, Christophe; Gadal, Olivier; Tikhonova, Irina G.; Panov, Konstantin I.

    2013-01-01

    Transcription by RNA polymerase I (Pol-I) is the main driving force behind ribosome biogenesis, a fundamental cellular process that requires the coordinated transcription of all three nuclear polymerases. Increased Pol-I transcription and the concurrent increase in ribosome biogenesis has been linked to the high rates of proliferation in cancers. The ellipticine family contains a number of potent anticancer therapeutic agents, some having progressed to stage I and II clinical trials; however, the mechanism by which many of the compounds work remains unclear. It has long been thought that inhibition of Top2 is the main reason behind the drugs antiproliferative effects. Here we report that a number of the ellipticines, including 9-hydroxyellipticine, are potent and specific inhibitors of Pol-I transcription, with IC50 in vitro and in cells in the nanomolar range. Essentially, the drugs did not affect Pol-II and Pol-III transcription, demonstrating a high selectivity. We have shown that Pol-I inhibition occurs by a p53-, ATM/ATR-, and Top2-independent mechanism. We discovered that the drug influences the assembly and stability of preinitiation complexes by targeting the interaction between promoter recognition factor SL1 and the rRNA promoter. Our findings will have an impact on the design and development of novel therapeutic agents specifically targeting ribosome biogenesis. PMID:23293027

  11. Quantum state targeting

    Science.gov (United States)

    Rudolph, Terry; Spekkens, Robert W.

    2004-11-01

    We introduce a primitive for quantum cryptography that we term “state targeting.” We show that increasing one’s probability of success in this task above a minimum amount implies an unavoidable increase in the probability of a particular kind of failure. This is analogous to the unavoidable disturbance to a quantum state that results from gaining information about its identity, and can be shown to be a purely quantum effect. We solve various optimization problems for state targeting that are useful for the security analysis of two-party cryptographic tasks implemented between remote antagonistic parties. Although we focus on weak coin flipping, the results are significant for other two-party protocols, such as strong coin flipping, partially binding and concealing bit commitment, and bit escrow. Furthermore, the results have significance not only for the traditional notion of security in cryptography, that of restricting a cheater’s ability to bias the outcome of the protocol, but also for a different notion of security that arises only in the quantum context, that of cheat sensitivity. Finally, our analysis leads to some interesting secondary results, namely, a generalization of Uhlmann’s theorem and an operational interpretation of the fidelity between two mixed states.

  12. Target Housing Material Options

    Energy Technology Data Exchange (ETDEWEB)

    Woloshun, Keith Albert [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2016-02-11

    With gas cooling, heat transfer coefficients are low compared to water. The benefit of gas from a heat transfer point of view is that there is really no upper temperature limit for the coolant, as compared to water, which is limited ultimately by the critical point, and in practice the critical heat flux. In our case with parallel flow channels, water is limited to even lower operating limits by nucleate boiling. So gas can get as hot as the containment material will allow, but to get the density and heat transfer up to something reasonable, we must also increase pressure, thus increasing stress on the containment, namely the front and back faces. We are designing to ASME BPVC, which, for most materials allows a maximum stress of UTS/3. So we want the highest possible UTS. For reference, the front face stress in the 12 mm target at 300 psi was about 90 MPa. The inconel 718 allowable stress at 900°C is 1/3 of 517 or 172 MPa. So we are in a very safe place, but the uTS is dropping rapidly with temperature above 900°C. As we increase target diameter, the challenge will be to keep the stress down. We are probably looking at keeping the allowable at or above the present value, and at as high a temperature as possible.

  13. Targeting adipose tissue

    Directory of Open Access Journals (Sweden)

    Haas Bodo

    2012-10-01

    Full Text Available Abstract Two different types of adipose tissues can be found in humans enabling them to respond to starvation and cold: white adipose tissue (WAT is generally known and stores excess energy in the form of triacylglycerol (TG, insulates against cold, and serves as a mechanical cushion. Brown adipose tissue (BAT helps newborns to cope with cold. BAT has the capacity to uncouple the mitochondrial respiratory chain, thereby generating heat rather than adenosine triphosphate (ATP. The previously widely held view was that BAT disappears rapidly after birth and is no longer present in adult humans. Using positron emission tomography (PET, however, it was recently shown that metabolically active BAT occurs in defined regions and scattered in WAT of the adult and possibly has an influence on whole-body energy homeostasis. In obese individuals adipose tissue is at the center of metabolic syndrome. Targeting of WAT by thiazolidinediones (TZDs, activators of peroxisome proliferator-activated receptor γ (PPARγ a ‘master’ regulator of fat cell biology, is a current therapy for the treatment of type 2 diabetes. Since its unique capacity to increase energy consumption of the body and to dissipate surplus energy as heat, BAT offers new perspectives as a therapeutic target for the treatment of obesity and associated diseases such as type 2 diabetes and metabolic syndrome. Recent discoveries of new signaling pathways of BAT development give rise to new therapeutic possibilities in order to influence BAT content and activity.

  14. Targeting adipose tissue.

    Science.gov (United States)

    Haas, Bodo; Schlinkert, Paul; Mayer, Peter; Eckstein, Niels

    2012-10-27

    Two different types of adipose tissues can be found in humans enabling them to respond to starvation and cold: white adipose tissue (WAT) is generally known and stores excess energy in the form of triacylglycerol (TG), insulates against cold, and serves as a mechanical cushion. Brown adipose tissue (BAT) helps newborns to cope with cold. BAT has the capacity to uncouple the mitochondrial respiratory chain, thereby generating heat rather than adenosine triphosphate (ATP). The previously widely held view was that BAT disappears rapidly after birth and is no longer present in adult humans. Using positron emission tomography (PET), however, it was recently shown that metabolically active BAT occurs in defined regions and scattered in WAT of the adult and possibly has an influence on whole-body energy homeostasis. In obese individuals adipose tissue is at the center of metabolic syndrome. Targeting of WAT by thiazolidinediones (TZDs), activators of peroxisome proliferator-activated receptor γ (PPARγ) a 'master' regulator of fat cell biology, is a current therapy for the treatment of type 2 diabetes. Since its unique capacity to increase energy consumption of the body and to dissipate surplus energy as heat, BAT offers new perspectives as a therapeutic target for the treatment of obesity and associated diseases such as type 2 diabetes and metabolic syndrome. Recent discoveries of new signaling pathways of BAT development give rise to new therapeutic possibilities in order to influence BAT content and activity.

  15. ExoMars 2018: the four final candidate Landing Sites

    Science.gov (United States)

    Loizeau, Damien; Flahaut, Jessica; Vago, Jorge L.; Hauber, Ernst; Bridges, John C.

    2015-04-01

    The ExoMars 2018 mission will land a rover on Mars, its scientific objectives are to search for signs of past and present life on Mars and to investigate the water/geochemical environment as a function of depth in the shallow subsurface. The rover will be able to travel several kilometres, analyzing surface and subsurface samples, down to a 2 meter depth. The very powerful combination of mobility with the ability to access in-depth locations, where organic molecules can be well preserved, is unique to this mission [1]. An invitation has been sent to the community to propose scientifically compelling sites for the mission [2], which comply to the main engineering constraints for landing and operation safety. Scientifically interesting sites include locations with evidence for long duration or frequently recurring aqueous activity, low energy transport and deposition, fined-grained, recently exposed sediments, and/or hydrated minerals such as clays or evaporites. The outcrops of interest must be distributed over the landing ellipse to ensure that the rover can access some of them over a short distance [2]. The received proposals have been reviewed by the Landing Site Selection Working Group (LSSWG) and at first eight sites were found to be compliant with the science, engineering, and planetary protection requirements [3]. These sites were presented by their proposers and discussed at the first landing site workshop that took place in ESAC, Spain, 26-28 March 2014. Following that workshop, four sites were selected for further investigation, on the base of their higher potential for long lived water activity, the presence of fine grained sediments, and also importantly on the high concentration of potential targets of interest over the whole landing ellipse [3]. The analysis of these sites, both in term of scientific relevance and engineering safety, is still on-going. Latest findings were presented during a second workshop that took place in ALTEC, Torino, Italy, 11

  16. Generation of Modified Pestiviruses by Targeted Recombination

    DEFF Research Database (Denmark)

    Rasmussen, Thomas Bruun; Friis, Martin Barfred; Risager, Peter Christian

    Infectious cDNA clones are a prerequisite for directed genetic manipulation of pestivirus RNA genomes. We have developed a novel strategy to facilitate manipulation and rescue of modified pestiviruses from infectious cDNA clones based on bacterial artificial chromosomes (BACs). The strategy...... involves targeted modification of viral cDNA genomes, cloned within BACs, by Red/ET recombination-mediated mutagenesis in E.coli DH10B cells. Using recombination-mediated mutagenesis for the targeted design, the work can be expedited and focused in principal on any sequence within the viral genome...... and hence is not limited to the use of internal restriction sites. Rescue of modified pestiviruses can be obtained by electroporation of cell cultures with full-length RNA transcripts in vitro transcribed from the recombined BAC clones. We have used this approach to generate a series of new pestivirus BACs...

  17. STARS MDT-II targets mission

    Energy Technology Data Exchange (ETDEWEB)

    Sims, B.A.; White, J.E.

    1997-08-01

    The Strategic Target System (STARS) was launched successfully on August 31, 1996 from the Kauai Test Facility (KTF) at the Pacific Missile Range Facility (PMRF). The STARS II booster delivered a payload complement of 26 vehicles atop a post boost vehicle. These targets were designed and the mission planning was achieved to provide for a dedicated mission for view by the Midcourse Space Experiment (MSX) Satellite Sensor Suite. Along with the MSX Satellite, other corollary sensors were involved. Included in these were the Airborne Surveillance Test Bed (AST) aircraft, the Cobra Judy sea based radar platform, Kwajalein Missile Range (KMR), and the Kiernan Reentry Measurements Site (KREMS). The launch was a huge success from all aspects. The STARS Booster flew a perfect mission from hardware, software and mission planning respects. The payload complement achieved its desired goals. All sensors (space, air, ship, and ground) attained excellent coverage and data recording.

  18. Injected nanocrystals for targeted drug delivery

    Science.gov (United States)

    Lu, Yi; Li, Ye; Wu, Wei

    2016-01-01

    Nanocrystals are pure drug crystals with sizes in the nanometer range. Due to the advantages of high drug loading, platform stability, and ease of scaling-up, nanocrystals have been widely used to deliver poorly water-soluble drugs. Nanocrystals in the blood stream can be recognized and sequestered as exogenous materials by mononuclear phagocytic system (MPS) cells, leading to passive accumulation in MPS-rich organs, such as liver, spleen and lung. Particle size, morphology and surface modification affect the biodistribution of nanocrystals. Ligand conjugation and stimuli-responsive polymers can also be used to target nanocrystals to specific pathogenic sites. In this review, the progress on injected nanocrystals for targeted drug delivery is discussed following a brief introduction to nanocrystal preparation methods, i.e., top-down and bottom-up technologies. PMID:27006893

  19. Targeted delivery of colloids by swimming bacteria

    Science.gov (United States)

    Koumakis, N.; Lepore, A.; Maggi, C.; Di Leonardo, R.

    2013-01-01

    The possibility of exploiting motile microorganisms as tiny propellers represents a fascinating strategy for the transport of colloidal cargoes. However, delivery on target sites usually requires external control fields to steer propellers and trigger cargo release. The need for a constant feedback mechanism prevents the design of compact devices where biopropellers could perform their tasks autonomously. Here we show that properly designed three-dimensional (3D) microstructures can define accumulation areas where bacteria spontaneously and efficiently store colloidal beads. The process is stochastic in nature and results from the rectifying action of an asymmetric energy landscape over the fluctuating forces arising from collisions with swimming bacteria. As a result, the concentration of colloids over target areas can be strongly increased or depleted according to the topography of the underlying structures. Besides the significance to technological applications, our experiments pose some important questions regarding the structure of stationary probability distributions in non-equilibrium systems. PMID:24100868

  20. Targeted Sister Chromatid Cohesion by Sir2

    Science.gov (United States)

    Wu, Ching-Shyi; Chen, Yu-Fan; Gartenberg, Marc R.

    2011-01-01

    The protein complex known as cohesin binds pericentric regions and other sites of eukaryotic genomes to mediate cohesion of sister chromatids. In budding yeast Saccharomyces cerevisiae, cohesin also binds silent chromatin, a repressive chromatin structure that functionally resembles heterochromatin of higher eukaryotes. We developed a protein-targeting assay to investigate the mechanistic basis for cohesion of silent chromatin domains. Individual silencing factors were tethered to sites where pairing of sister chromatids could be evaluated by fluorescence microscopy. We report that the evolutionarily conserved Sir2 histone deacetylase, an essential silent chromatin component, was both necessary and sufficient for cohesion. The cohesin genes were required, but the Sir2 deacetylase activity and other silencing factors were not. Binding of cohesin to silent chromatin was achieved with a small carboxyl terminal fragment of Sir2. Taken together, these data define a unique role for Sir2 in cohesion of silent chromatin that is distinct from the enzyme's role as a histone deacetylase. PMID:21304892

  1. Low intensity beam target unit

    CERN Multimedia

    CERN PhotoLab

    1976-01-01

    This is a wheel fitted with many targets around its periphery (each with three longitudinally arranged thin rods) of which one is placed into the beam via a rotation of the wheel. Upstream of each target is placed a luminescent screen, aligbed on each target axis and viewed with a TV camera, to make sure that one is hitting the target. This target unit was probably used to study target's behaviour (like beam heating). Gualtiero Del Torre stands on the left, Pierre Gerdil on the right.

  2. Risk-targeted maps for Romania

    Science.gov (United States)

    Vacareanu, Radu; Pavel, Florin; Craciun, Ionut; Coliba, Veronica; Arion, Cristian; Aldea, Alexandru; Neagu, Cristian

    2017-11-01

    Romania has one of the highest seismic hazard levels in Europe. The seismic hazard is due to a combination of local crustal seismic sources, situated mainly in the western part of the country and the Vrancea intermediate-depth seismic source, which can be found at the bend of the Carpathian Mountains. Recent seismic hazard studies have shown that there are consistent differences between the slopes of the seismic hazard curves for sites situated in the fore-arc and back-arc of the Carpathian Mountains. Consequently, in this study we extend this finding to the evaluation of the probability of collapse of buildings and finally to the development of uniform risk-targeted maps. The main advantage of uniform risk approach is that the target probability of collapse will be uniform throughout the country. Finally, the results obtained are discussed in the light of a recent study with the same focus performed at European level using the hazard data from SHARE project. The analyses performed in this study have pointed out to a dominant influence of the quantile of peak ground acceleration used for anchoring the fragility function. This parameter basically alters the shape of the risk-targeted maps shifting the areas which have higher collapse probabilities from eastern Romania to western Romania, as its exceedance probability increases. Consequently, a uniform procedure for deriving risk-targeted maps appears as more than necessary.

  3. Targeted anticancer therapy: overexpressed receptors and nanotechnology.

    Science.gov (United States)

    Akhtar, Mohd Javed; Ahamed, Maqusood; Alhadlaq, Hisham A; Alrokayan, Salman A; Kumar, Sudhir

    2014-09-25

    Targeted delivery of anticancer drugs to cancer cells and tissues is a promising field due to its potential to spare unaffected cells and tissues, but it has been a major challenge to achieve success in these therapeutic approaches. Several innovative approaches to targeted drug delivery have been devised based on available knowledge in cancer biology and on technological advancements. To achieve the desired selectivity of drug delivery, nanotechnology has enabled researchers to design nanoparticles (NPs) to incorporate anticancer drugs and act as nanocarriers. Recently, many receptor molecules known to be overexpressed in cancer have been explored as docking sites for the targeting of anticancer drugs. In principle, anticancer drugs can be concentrated specifically in cancer cells and tissues by conjugating drug-containing nanocarriers with ligands against these receptors. Several mechanisms can be employed to induce triggered drug release in response to either endogenous trigger or exogenous trigger so that the anticancer drug is only released upon reaching and preferentially accumulating in the tumor tissue. This review focuses on overexpressed receptors exploited in targeting drugs to cancerous tissues and the tumor microenvironment. We briefly evaluate the structure and function of these receptor molecules, emphasizing the elegant mechanisms by which certain characteristics of cancer can be exploited in cancer treatment. After this discussion of receptors, we review their respective ligands and then the anticancer drugs delivered by nanotechnology in preclinical models of cancer. Ligand-functionalized nanocarriers have delivered significantly higher amounts of anticancer drugs in many in vitro and in vivo models of cancer compared to cancer models lacking such receptors or drug carrying nanocarriers devoid of ligand. This increased concentration of anticancer drug in the tumor site enabled by nanotechnology could have a major impact on the efficiency of cancer

  4. Quilting suture in the donor site of the transverse rectus abdominis musculocutaneous flap in breast reconstruction.

    Science.gov (United States)

    Rossetto, Luís A; Garcia, Elvio B; Abla, Luis F; Neto, Miguel S; Ferreira, Lydia M

    2009-03-01

    The purpose of this study was to evaluate the effects of quilting suture (placement of stitches between the superficial fascia in the supraumbilical remaining flap and the musculoaponeurotic layer of the anterior abdominal wall) at the donor site of the transverse rectus abdominis musculocutaneous flap in breast reconstruction. There is a theory that the use of quilting suture, during the closure of the donor site with the abdominal flap, causes collapse of the dead space and enables the flap to rest, thus diminishing factors that may interfere in its adherence and help to reduce complications. Between January 2004 and March 2005, we performed 30 breast reconstructions using a unipedicled transverse rectus abdominis musculocutaneous flap. The sample was randomly distributed in 2 groups: 15 patients with quilting suture (group A) and 15 patients without quilting suture (group B). The study focused on daily drain output (mL), time to drain removal (days), and possible donor site complications (%). Group A presented an average of 4.2 days for removal of the drain and group B, 6.93 days, with a statistically significant difference (P < 0.001). Concerning the total volume upon removal of the drain, group A presented an average of 434.7 mL and group B, 620.7 mL, with a statistically significant difference (P = 0.002). Group A presented 13.3% complications at the donor site and group B, 53.3%, with a statistically significant difference (P = 0.05). The quilting suture in this study reduces the permanence of drains, total volume of tissue fluids upon drain removal, and complication rates.

  5. 1994 Site Environmental Report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1995-05-01

    The 1994 Site Environmental Report summarizes environmental activities at Lawrence Berkeley Laboratory (LBL) for the calendar year (CY) 1994. The report strives to present environmental data in a manner that characterizes the performance and compliance status of the Laboratory`s environmental management programs when measured against regulatory standards and DOE requirements. The report also discusses significant highlight and planning efforts of these programs. The format and content of the report are consistent with the requirements of the US Department of Energy (DOE) Order 5400.1, General Environmental Protection Program.

  6. Windows Azure web sites

    CERN Document Server

    Chambers, James

    2013-01-01

    A no-nonsense guide to maintaining websites in Windows Azure If you're looking for a straightforward, practical guide to get Azure websites up and running, then this is the book for you. This to-the-point guide provides you with the tools you need to move and maintain a website in the cloud. You'll discover the features that most affect developers and learn how they can be leveraged to work to your advantage. Accompanying projects enhance your learning experience and help you to walk away with a thorough understanding of Azure's supported technologies, site deployment, and manageme

  7. Present on Site

    DEFF Research Database (Denmark)

    Ingemann, Bruno

    Why are exhibitions and museums so important? What can they be used for? Who determines relevance in a transformative process? Transforming exhibitions is not just something you do, it is something that gets better the more you do it. This book looks at the intersection of the visitor or user, who...... gets personal and cultural meaning from their visit and the museum as it appears in the design of the exhibition. It examines on-site communication for intentional and hidden content and messages, and reveals possible relations to the visitor, his or her world and society in general. This investigation...

  8. Issues in Target Tracking

    Science.gov (United States)

    2010-05-01

    simulations we take as ground truth that the target moves at 10m/s heading west and 5m/s heading north, starting from ( 5000m , 35000m). The emitted frequency is... runs , the estimated initial and final positions fall into the 99% confidence region. −1 −0.8 −0.6 −0.4 −0.2 0 0.2 0.4 0.6 0.8 1 x 10 4 0 0.5 1 1.5 2 2.5...position of trajectories. “F”: final position of trajectories. Right: The true and estimated trajectories from 100 Monte Carlo runs for Johnson noise

  9. LCA of contaminated site remediation - integration of site-specific impact assessment of local toxic impacts

    DEFF Research Database (Denmark)

    Lemming, Gitte; Hauschild, Michael Zwicky; Chambon, Julie Claire Claudia

    2011-01-01

    of bioremediation scenarios (86-98 % of the human toxicity impacts at Site 1). The inclusion of primary impacts in the environmental assessment of remediation alternatives gives a more complete basis for comparison of technologies with substantially different timeframes and efficiencies........ Although two different remediation methods reach the same remedial target with time, their timeframes can be substantially different and lead to a difference in the local toxic impacts over time. By including primary impacts in the LCA of remediation this quality difference is accounted for. Primary...... impacts have typically been assessed using site-generic characterization models representing a continental scale and excluding the groundwater compartment. Soil contaminants have therefore generally been assigned as emissions to surface soil or surface water compartments. However, such site...

  10. HANFORD SITE SUSTAINABILITY PROGRAM RICHLAND WASHINGTON - 12464

    Energy Technology Data Exchange (ETDEWEB)

    FRITZ LL

    2012-01-12

    In support of implementation of Executive Order (EO) 13514, Federal Leadership in Environmental, Energy and Economic Performance, the Hanford Site Sustainability Plan was developed to implement strategies and activities required to achieve the prescribed goals in the EO as well as demonstrate measurable progress in environmental stewardship at the Hanford Site. The Hanford Site Sustainability Program was developed to demonstrate progress towards sustainability goals as defined and established in Executive Order (EO) 13514, Federal Leadership in Environmental, Energy and Economic Performance; EO 13423, Strengthening Federal Environmental, Energy and Transportation Management, and several applicable Energy Acts. Multiple initiatives were undertaken in Fiscal Year (FY) 2011 to implement the Program and poise the Hanford Site as a leader in environmental stewardship. In order to implement the Hanford Site Sustainability Program, a Sustainability Plan was developed in conjunction with prime contractors, two U.S. Department of Energy (DOE) Offices, and key stakeholders to serve as the framework for measuring progress towards sustainability goals. Based on the review of these metrics and future plans, several activities were initiated to proactively improve performance or provide alternatives for future consideration contingent on available funding. A review of the key metric associated with energy consumption for the Hanford Site in FY 2010 and 2011 indicated an increase over the target reduction of 3 percent annually from a baseline established in FY 2003 as illustrated in Figure 1. This slight increase was attributed primarily from the increased energy demand from the cleanup projects funded by the American Recovery and Reinvestment Act (ARRA) in FY 2010 and 2011. Although it is forecasted that the energy demand will decrease commensurate with the completion of ARRA projects, several major initiatives were launched to improve energy efficiency.

  11. Bradycardia During Targeted Temperature Management

    DEFF Research Database (Denmark)

    Thomsen, Jakob Hartvig; Nielsen, Niklas; Hassager, Christian

    2016-01-01

    OBJECTIVES: Bradycardia is common during targeted temperature management, likely being a physiologic response to lower body temperature, and has recently been associated with favorable outcome following out-of-hospital cardiac arrest in smaller observational studies. The present study sought...... to confirm this finding in a large multicenter cohort of patients treated with targeted temperature management at 33°C and explore the response to targeted temperature management targeting 36°C. DESIGN: Post hoc analysis of a prospective randomized study. SETTING: Thirty-six ICUs in 10 countries. PATIENTS......: We studied 447 (targeted temperature management = 33°C) and 430 (targeted temperature management = 36°C) comatose out-of-hospital cardiac arrest patients with available heart rate data, randomly assigned in the targeted temperature management trial from 2010 to 2013. INTERVENTIONS: Targeted...

  12. 2003 SITE ENVIRONMENTAL REPORT

    Energy Technology Data Exchange (ETDEWEB)

    ENVIRONMENT AND WASTE MANAGMENT SERVICES DIVISION; ET AL.

    2004-10-01

    Each year, Brookhaven National Laboratory (BNL), a multi-program national laboratory, prepares an annual Site Environmental Report (SER) in accordance with Order 231.1A, Environment, Safety and Health Reporting, of the U.S. Department of Energy (DOE). The SER is written to inform outside regulators, the public, and Laboratory employees of BNL's environmental performance during the calendar year in review, and to summarize BNL's on-site environmental data; environmental management performance; compliance with applicable DOE, Environmental Protection Agency (EPA), state, and local regulations; and environmental, restoration, and surveillance monitoring programs. BNL has prepared annual SERs since 1971 and has documented nearly all of its environmental history since the Laboratory's inception in 1947. This report is intended to be a technical document. It is available in print and as a downloadable file on the BNL web page at http://www.bnl.ser.htm. A summary of the SER is also prepared each year to provide a general overview, and is distributed with a CD version of the full-length SER. The summary supports BNL's educational and community outreach program.

  13. AMF 1 Site Science

    Energy Technology Data Exchange (ETDEWEB)

    Miller, Mark Alan [Rutgers Univ., New Brunswick, NJ (United States)

    2016-08-18

    This report documents progress on DOE Grant# DE-FG02-08ER64531 funded by the Department of Energy’s Atmospheric Systems Research (ASR) program covering the period between its inception in 2008 and its conclusion in 2014. The Atmospheric Radiation Measurement (ARM) Program’s Mobile Facility #1 (AMF#1) is a collection of state-of-the art atmospheric sensing systems including remote and in situ instrumentation designed to characterize the atmospheric column above and in the immediate vicinity of the deployment location. The grant discussed in this report funded the activities of the AMF#1 Site Scientist Team. Broad responsibilities of this team included examining new deployment sites and recommending instrument deployment configurations; data quality control during the early stages of deployments and for certain instruments through the course of the deployment; scientific outreach in the host country or location (particularly international deployments); scientific research oriented toward basic questions about cloud physics and radiation transfer in the deployment region; and training of Ph.D. students to conduct future research relevant to the Atmospheric Systems Research (ASR) program.

  14. 1996 Site environmental report

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-06-01

    The FEMP is a Department of Energy (DOE)-owned facility that produced high-quality uranium metals for military defense for nearly 40 years. DOE suspended production at the FEMP in 1989 and formally ended production in 1991. Although production activities have ceased, the site continues to examine the air and liquid pathways as possible routes through which pollutants from past operations and current remedial activities may leave the FEMP. The Site Environmental Report (SER) is prepared annually in accordance with DOE Order 5400.1, General Environmental Protection Program. This 1996 SER provides the general public as well as scientists and engineers with the results from the ongoing Environmental Monitoring Program. Also included in this report is information concerning the FEMP progress toward achieving full compliance with requirements set forth by DOE, U.S. Environmental Protection Agency (EPA), and Ohio EPA (OEPA). For some readers, the highlights provided in this Executive Summary may provide sufficient information. Many readers, however, may wish are presented here. All information presented in this summary is discussed more fully in the main body of this report.

  15. Site-specific

    Directory of Open Access Journals (Sweden)

    Adel M.E. Mohamed

    2013-06-01

    Full Text Available In order to quantify the near-surface seismic properties (P- and S-wave velocities, and the dynamic elastic properties with respect to the depth at a specific area (6th of October club, we conducted a non-invasive and low cost active seismic survey. The primary wave velocity is determined by conducting a P-wave shallow seismic refraction survey. The dispersive characteristics of Rayleigh type surface waves were utilized for imaging the shallow subsurface layers by estimating the 1D (depth and 2D (depth and surface location shear wave velocities. The reliability of the Multi-channel Analysis of Surface Waves (MASW depends on the accurate determination of phase velocities for horizontally traveling fundamental mode Rayleigh waves. Consequently, the elastic properties are evaluated empirically. The Vs30 (average shear wave velocity down to 30 m depth, which is obtained from the MASW technique, plays a critical role in evaluating the site response of the upper 30 m depth. The distribution of the obtained values of Vs30 through the studied area demonstrates site classes of C and D, according to the NEHRP (National Earthquake Hazard Reduction Program and IBC (International Building Code standards.

  16. Multi-Sited Resilience

    DEFF Research Database (Denmark)

    Olwig, Mette Fog

    2012-01-01

    Participatory methods to build local resilience often involve the organization of local community groups. When global organizations use such methods, it reflects a desire to incorporate local agency. They thereby acknowledge the ability of a society to be innovative and adapt when faced with natu......Participatory methods to build local resilience often involve the organization of local community groups. When global organizations use such methods, it reflects a desire to incorporate local agency. They thereby acknowledge the ability of a society to be innovative and adapt when faced...... with natural disasters and climate change. In a globalized world, however, it is hard to discern what is “local” as global organizations play an increasingly visible and powerful role. This paper will argue that local understandings and practices of resilience cannot be disentangled from global understandings...... flooding in northern Ghana, this paper examines the mutual construction of “local” and “global” notions and practices of resilience through multi-sited processes. It is based on interviews and participant observation in multiple sites at the “local,” “regional” and “global” levels....

  17. Highly Efficient Cpf1-Mediated Gene Targeting in Mice Following High Concentration Pronuclear Injection

    Directory of Open Access Journals (Sweden)

    Dawn E. Watkins-Chow

    2017-02-01

    Full Text Available Cpf1 has emerged as an alternative to the Cas9 RNA-guided nuclease. Here we show that gene targeting rates in mice using Cpf1 can meet, or even surpass, Cas9 targeting rates (approaching 100% targeting, but require higher concentrations of mRNA and guide. We also demonstrate that coinjecting two guides with close targeting sites can result in synergistic genomic cutting, even if one of the guides has minimal cutting activity.

  18. Efficient four fragment cloning for the construction of vectors for targeted gene replacement in filamentous fungi

    DEFF Research Database (Denmark)

    Frandsen, Rasmus John Normand; Andersson, Jens A.; Kristensen, Matilde Bylov

    2008-01-01

    Background: The rapid increase in whole genome fungal sequence information allows large scale functional analyses of target genes. Efficient transformation methods to obtain site-directed gene replacement, targeted over-expression by promoter replacement, in-frame epitope tagging or fusion of cod...... with an average efficiency of 84% for gene replacement and 80% for targeted overexpression. Conclusion: The new vectors designed for USER Friendly cloning provided a fast reliable method to construct vectors for targeted gene manipulations in fungi....

  19. Characterization of solid hydrogen targets

    Energy Technology Data Exchange (ETDEWEB)

    Fujiwara, M.C. [British Columbia Univ., Vancouver, BC (Canada); Bailey, J.M.; Mulhauser, F. [Chester Technology (United Kingdom); Beer, G.A.; Douglas, J.L.; Knowles, P.E.; Maier, M.; Mason, G.R.; Olin, A.; Porcelli, T.A. [Victoria Univ., BC (Canada); Beveridge, J.L.; Marshall, G.M. [British Columbia Univ., Vancouver, BC (Canada). TRIUMF Facility; Huber, T.M. [Gustavus Adolphus Coll., St. Peter, MN (United States); Jacot-Guillarmod, R. [Fribourg Univ. (Switzerland); Kammel, P. [Lawrence Berkeley Lab., CA (United States); Kim, S.K. [Jeonbuk National Univ., Jeonju City (Korea, Republic of); Kunselman, A.R. [Wyoming Univ., Laramie, WY (United States); Martoff, C.J. [Temple Univ., Philadelphia, PA (United States); Petitjean, C. [Paul Scherrer Inst. (PSI), Villigen (Switzerland); Zmeskal, J. [Oesterreichische Akademie der Wissenschaften, Vienna (Austria)

    1996-10-01

    In experiments using the TRIUMF solid hydrogen target system, the knowledge of the target thickness and uniformity is often essential in order to extract physical parameters from the data. We have characterized the thickness and uniformity of frozen targets using the energy loss of alpha particles. An accuracy of {approx}5% was achieved, a limit imposed by the uncertainty in the stopping powers. The details of the method are described, and the thickness calibration of the target is presented. (orig.). 11 refs.

  20. Usability Evaluation of Public Web Mapping Sites

    Science.gov (United States)

    Wang, C.

    2014-04-01

    Web mapping sites are interactive maps that are accessed via Webpages. With the rapid development of Internet and Geographic Information System (GIS) field, public web mapping sites are not foreign to people. Nowadays, people use these web mapping sites for various reasons, in that increasing maps and related map services of web mapping sites are freely available for end users. Thus, increased users of web mapping sites led to more usability studies. Usability Engineering (UE), for instance, is an approach for analyzing and improving the usability of websites through examining and evaluating an interface. In this research, UE method was employed to explore usability problems of four public web mapping sites, analyze the problems quantitatively and provide guidelines for future design based on the test results. Firstly, the development progress for usability studies were described, and simultaneously several usability evaluation methods such as Usability Engineering (UE), User-Centered Design (UCD) and Human-Computer Interaction (HCI) were generally introduced. Then the method and procedure of experiments for the usability test were presented in detail. In this usability evaluation experiment, four public web mapping sites (Google Maps, Bing maps, Mapquest, Yahoo Maps) were chosen as the testing websites. And 42 people, who having different GIS skills (test users or experts), gender (male or female), age and nationality, participated in this test to complete the several test tasks in different teams. The test comprised three parts: a pretest background information questionnaire, several test tasks for quantitative statistics and progress analysis, and a posttest questionnaire. The pretest and posttest questionnaires focused on gaining the verbal explanation of their actions qualitatively. And the design for test tasks targeted at gathering quantitative data for the errors and problems of the websites. Then, the results mainly from the test part were analyzed. The