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Sample records for template-directed rna polymerization

  1. Emergence of a code in the polymerization of amino acids along RNA templates.

    Directory of Open Access Journals (Sweden)

    Jean Lehmann

    2009-06-01

    Full Text Available The origin of the genetic code in the context of an RNA world is a major problem in the field of biophysical chemistry. In this paper, we describe how the polymerization of amino acids along RNA templates can be affected by the properties of both molecules. Considering a system without enzymes, in which the tRNAs (the translation adaptors are not loaded selectively with amino acids, we show that an elementary translation governed by a Michaelis-Menten type of kinetics can follow different polymerization regimes: random polymerization, homopolymerization and coded polymerization. The regime under which the system is running is set by the relative concentrations of the amino acids and the kinetic constants involved. We point out that the coding regime can naturally occur under prebiotic conditions. It generates partially coded proteins through a mechanism which is remarkably robust against non-specific interactions (mismatches between the adaptors and the RNA template. Features of the genetic code support the existence of this early translation system.

  2. Metal-ion catalyzed polymerization in the eutectic phase in water-ice

    DEFF Research Database (Denmark)

    Monnard, Pierre-Alain; Szostak, Jack W.

    2008-01-01

    The emergence of an RNA world requires among other processes the non-enzymatic, template-directed replication of genetic polymers such as RNA or related nucleic acids, possibly catalyzed by metal ions. The absence of uridilate derivative polymerization on adenine containing templates has been...... the main issue preventing an efficient template-directed RNA polymerization. We report here the investigation of template-directed RNA polymerization in the eutectic phase in water-ice. In particular, it was found that activated Uridilate monomers in the presence of metal-ion catalysts could efficiently......-pairing opportunities. These results suggest that a template-directed RNA polymerization catalyzed by metal-ions could be carried out under eutectic phase in water-ice conditions....

  3. The Role of Templating in the Emergence of RNA from the Prebiotic Chemical Mixture

    Directory of Open Access Journals (Sweden)

    Andrew S. Tupper

    2017-10-01

    Full Text Available Biological RNA is a uniform polymer in three senses: it uses nucleotides of a single chirality; it uses only ribose sugars and four nucleobases rather than a mixture of other sugars and bases; and it uses only 3′-5′ bonds rather than a mixture of different bond types. We suppose that prebiotic chemistry would generate a diverse mixture of potential monomers, and that random polymerization would generate non-uniform strands of mixed chirality, monomer composition, and bond type. We ask what factors lead to the emergence of RNA from this mixture. We show that template-directed replication can lead to the emergence of all the uniform properties of RNA by the same mechanism. We study a computational model in which nucleotides react via polymerization, hydrolysis, and template-directed ligation. Uniform strands act as templates for ligation of shorter oligomers of the same type, whereas mixed strands do not act as templates. The three uniform properties emerge naturally when the ligation rate is high. If there is an exact symmetry, as with the chase of chirality, the uniform property arises via a symmetry-breaking phase transition. If there is no exact symmetry, as with monomer selection and backbone regioselectivity, the uniform property emerges gradually as the rate of template-directed ligation is increased.

  4. Colloidal templating : a route towards controlled synthesis of functional polymeric nanoparticles

    NARCIS (Netherlands)

    Ali, S.I.

    2010-01-01

    Template-directed synthesis of polymeric nanoparticles offers better control over particle morphology, shape, structure, composition and properties compare to the conventional emulsion polymerization routes. For the production of anisotropic polymer-clay composite latex particles and polymeric

  5. Structure of Hepatitis C Virus Polymerase in Complex with Primer-Template RNA

    Energy Technology Data Exchange (ETDEWEB)

    Mosley, Ralph T.; Edwards, Thomas E.; Murakami, Eisuke; Lam, Angela M.; Grice, Rena L.; Du, Jinfa; Sofia, Michael J.; Furman, Philip A.; Otto, Michael J. (Pharmasset); (Emerald)

    2012-08-01

    The replication of the hepatitis C viral (HCV) genome is accomplished by the NS5B RNA-dependent RNA polymerase (RdRp), for which mechanistic understanding and structure-guided drug design efforts have been hampered by its propensity to crystallize in a closed, polymerization-incompetent state. The removal of an autoinhibitory {beta}-hairpin loop from genotype 2a HCV NS5B increases de novo RNA synthesis by >100-fold, promotes RNA binding, and facilitated the determination of the first crystallographic structures of HCV polymerase in complex with RNA primer-template pairs. These crystal structures demonstrate the structural realignment required for primer-template recognition and elongation, provide new insights into HCV RNA synthesis at the molecular level, and may prove useful in the structure-based design of novel antiviral compounds. Additionally, our approach for obtaining the RNA primer-template-bound structure of HCV polymerase may be generally applicable to solving RNA-bound complexes for other viral RdRps that contain similar regulatory {beta}-hairpin loops, including bovine viral diarrhea virus, dengue virus, and West Nile virus.

  6. Gamma Radiation-Induced Template Polymerization Technique

    International Nuclear Information System (INIS)

    Siyam, T.

    2005-01-01

    Gamma radiation induced copolymerization of acrylamide sodiumacrylate (AM-AANa) in the presence and absence of the polymer additive was studied at low monomer concentration(1.4M/l). The results showed that the exponents of the dose rate for the polymerization rate was found to be 1.3 and 1.4 in the absence and in the presence of the polymer additive respectively. The molecular weight of the formed polymer increased by addition of the polymer to the system. In the presence of the polymer the comonomers polymerize on the added polymer. In the absence of the added polymer the comonomers polymerize according to the copolymerization process at the initial stage of the copolymerization. While at high conversion the residual comonomers polymerize on the formed macromolecular chains of the produced polymer. These studies showed that the copolymerization in the presence of added polymer is completely template copolymerization while in the absence of the polymer the copolymerization process is only template process with a high conversion

  7. Template Synthesis of Nanostructured Polymeric Membranes by Inkjet Printing.

    Science.gov (United States)

    Gao, Peng; Hunter, Aaron; Benavides, Sherwood; Summe, Mark J; Gao, Feng; Phillip, William A

    2016-02-10

    The fabrication of functional nanomaterials with complex structures has been serving great scientific and practical interests, but current fabrication and patterning methods are generally costly and laborious. Here, we introduce a versatile, reliable, and rapid method for fabricating nanostructured polymeric materials. The novel method is based on a combination of inkjet printing and template synthesis, and its utility and advantages in the fabrication of polymeric nanomaterials is demonstrated through three examples: the generation of polymeric nanotubes, nanowires, and thin films. Layer-by-layer-assembled nanotubes can be synthesized in a polycarbonate track-etched (PCTE) membrane by printing poly(allylamine hydrochloride) and poly(styrenesulfonate) sequentially. This sequential deposition of polyelectrolyte ink enables control over the surface charge within the nanotubes. By a simple change of the printing conditions, polymeric nanotubes or nanowires were prepared by printing poly(vinyl alcohol) in a PCTE template. In this case, the high-throughput nature of the method enables functional nanomaterials to be generated in under 3 min. Furthermore, we demonstrate that inkjet printing paired with template synthesis can be used to generate patterns comprised of chemically distinct nanomaterials. Thin polymeric films of layer-by-layer-assembled poly(allylamine hydrochloride) and poly(styrenesulfonate) are printed on a PCTE membrane. Track-etched membranes covered with the deposited thin films reject ions and can potentially be utilized as nanofiltration membranes. When the fabrication of these different classes of nanostructured materials is demonstrated, the advantages of pairing template synthesis with inkjet printing, which include fast and reliable deposition, judicious use of the deposited materials, and the ability to design chemically patterned surfaces, are highlighted.

  8. Polymeric Bicontinuous Microemulsions as Templates for Nanostructured Materials

    Science.gov (United States)

    Jones, Brad Howard

    Ternary blends of two homopolymers and a diblock copolymer can self-assemble into interpenetrating, three dimensionally-continuous networks with a characteristic length scale of ˜ 100 nm. In this thesis, it is shown that these liquid phases, known as polymeric bicontinuous microemulsions (BμE), can be designed as versatile precursors to nanoporous materials having pores with uniform sizes of ˜ 100 nm. The model blends from which the porous materials are derived are composed of polyethylene (PE) and a sacrificial polyolefin. The liquid BμE structure is captured by crystallization of the PE, and a three-dimensionally continuous pore network with a narrow pore size distribution is generated by selective extraction of the sacrificial component. The original BμE structure is retained in the resultant nanoporous PE. This monolithic material is then used as a template in the synthesis of other nanoporous materials for which structural control at the nm scale has traditionally been difficult to achieve. These materials, which include a high-temperature ceramic, polymeric thermosets, and a conducting polymer, are produced by a simple nanocasting process, providing an inverse replica of the PE template. On account of the BμE structure of the template, the product materials also possess three-dimensionally continuous pore networks with narrow size distributions centered at ˜ 100 nm. The PE template is further used as a template for the production of hierarchically structured inorganic and polymeric materials by infiltration of mesostructured compounds into its pore network. In the former case, a hierarchically porous SiO2 material is demonstrated, simultaneously possessing two discrete, bicontinuous pore networks with sizes differing by over an order of magnitude. Finally, the templating procedures are extended to thin films supported on substrates and novel conductive polymer films are synthesized. The work described herein represents an unprecedented suite of

  9. Neutral Polymeric Micelles for RNA Delivery

    Science.gov (United States)

    Lundy, Brittany B.; Convertine, Anthony; Miteva, Martina; Stayton, Patrick S.

    2013-01-01

    RNA interference (RNAi) drugs have significant therapeutic potential but delivery systems with appropriate efficacy and toxicity profiles are still needed. Here, we describe a neutral, ampholytic polymeric delivery system based on conjugatable diblock polymer micelles. The diblock copolymer contains a hydrophilic poly[N-(2-hydroxypropyl) methacrylamide-co-N-(2-(pyridin-2- yldisulfanyl)ethyl)methacrylamide) (poly[HPMA-co-PDSMA]) segment to promote aqueous stability and facilitate thiol-disulfide exchange reactions, and a second ampholytic block composed of propyl acrylic acid (PAA), dimethylaminoethyl methacrylate (DMAEMA), and butyl methacrylate (BMA). The poly[(HPMA-co-PDSMA)-b-(PAA-co-DMAEMA-co-BMA)] was synthesized using Reversible Addition-Fragmentation chain Transfer (RAFT) polymerization with an overall molecular weight of 22,000 g/mol and a PDI of 1.88. Dynamic light scattering and fluorescence measurements indicated that the diblock copolymers self-assemble under aqueous conditions to form polymeric micelles with a hydrodynamic radius and critical micelle concentration of 25 nm and 25 μg/mL respectively. Red blood cell hemolysis experiments show that the neutral hydrophilic micelles have potent membrane destabilizing activity at endosomal pH values. Thiolated siRNA targeting glyceraldehyde 3-phosphate dehydrogenase (GAPDH) was directly conjugated to the polymeric micelles via thiol exchange reactions with the pyridal disulfide groups present in the micelle corona. Maximum silencing activity in HeLa cells was observed at a 1:10 molar ratio of siRNA to polymer following a 48 h incubation period. Under these conditions 90 % mRNA knockdown and 65 % and protein knockdown of at 48 h was achieved with negligible toxicity. In contrast the polymeric micelles lacking a pH-responsive endosomalytic segment demonstrated negligible mRNA and protein knockdown under these conditions. The potent mRNA knockdown and excellent biocompatibility of the neutral siRNA conjugates

  10. TEMPLATE POLYMERIZATION OF N-VINYLIMIDAZOLE ALONG POLY(METHACRYLIC ACID) IN WATER .2. KINETICS OF THE TEMPLATE POLYMERIZATION

    NARCIS (Netherlands)

    VANDEGRAMPEL, HT; TAN, YY; CHALLA, G

    1991-01-01

    The template polymerization of N-vinylimidazole (VIm) along poly(methacrylic acid) (PMAA) in water at 50-degrees-C with 2,2'-azobis(2-amidinopropane).2HCl (AAP) as initiator was studied by using variable initiator and monomer concentrations at constant [PMAA]/[VIm]0. From the order in [VIm] it was

  11. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions

    Science.gov (United States)

    Coari, Kristin M.; Martin, Rebecca C.; Jain, Kopal; McGown, Linda B.

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  12. Nucleotide Selectivity in Abiotic RNA Polymerization Reactions.

    Science.gov (United States)

    Coari, Kristin M; Martin, Rebecca C; Jain, Kopal; McGown, Linda B

    2017-09-01

    In order to establish an RNA world on early Earth, the nucleotides must form polymers through chemical rather than biochemical reactions. The polymerization products must be long enough to perform catalytic functions, including self-replication, and to preserve genetic information. These functions depend not only on the length of the polymers, but also on their sequences. To date, studies of abiotic RNA polymerization generally have focused on routes to polymerization of a single nucleotide and lengths of the homopolymer products. Less work has been done the selectivity of the reaction toward incorporation of some nucleotides over others in nucleotide mixtures. Such information is an essential step toward understanding the chemical evolution of RNA. To address this question, in the present work RNA polymerization reactions were performed in the presence of montmorillonite clay catalyst. The nucleotides included the monophosphates of adenosine, cytosine, guanosine, uridine and inosine. Experiments included reactions of mixtures of an imidazole-activated nucleotide (ImpX) with one or more unactivated nucleotides (XMP), of two or more ImpX, and of XMP that were activated in situ in the polymerization reaction itself. The reaction products were analyzed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) to identify the lengths and nucleotide compositions of the polymerization products. The results show that the extent of polymerization, the degree of heteropolymerization vs. homopolymerization, and the composition of the polymeric products all vary among the different nucleotides and depend upon which nucleotides and how many different nucleotides are present in the mixture.

  13. Fabrication of Defined Polydopamine Nanostructures by DNA Origami-Templated Polymerization.

    Science.gov (United States)

    Tokura, Yu; Harvey, Sean; Chen, Chaojian; Wu, Yuzhou; Ng, David Y W; Weil, Tanja

    2018-02-05

    A versatile, bottom-up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage-mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase-mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as "supramolecular glue" for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami-controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template. © 2018 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  14. An Approach to Detect and Study DNA Double-Strand Break Repair by Transcript RNA Using a Spliced-Antisense RNA Template.

    Science.gov (United States)

    Keskin, Havva; Storici, Francesca

    2018-01-01

    A double-strand break (DSB) is one of the most dangerous DNA lesion, and its repair is crucial for genome stability. Homologous recombination is considered the safest way to repair a DNA DSB and requires an identical or nearly identical DNA template, such as a sister chromatid or a homologous chromosome for accurate repair. Can transcript RNA serve as donor template for DSB repair? Here, we describe an approach that we developed to detect and study DNA repair by transcript RNA. Key features of the method are: (i) use of antisense (noncoding) RNA as template for DSB repair by RNA, (ii) use of intron splicing to distinguish the sequence of the RNA template from that of the DNA that generates the RNA template, and (iii) use of a trans and cis system to study how RNA repairs a DSB in homologous but distant DNA or in its own DNA, respectively. This chapter provides details on how to use a spliced-antisense RNA template to detect and study DSB repair by RNA in trans or cis in yeast cells. Our approach for detection of DSB repair by RNA in cells can be applied to cell types other than yeast, such as bacteria, mammalian cells, or other eukaryotic cells. © 2018 Elsevier Inc. All rights reserved.

  15. Colloid-templated multisectional porous polymeric fibers.

    Science.gov (United States)

    Song, Jung Hun; Kretzschmar, Ilona

    2008-10-07

    A fabrication method for porous polymeric fibers (PPFs) is reported. We show that a multisectional colloidal crystal can be assembled within a microcapillary by alternating dipping into colloidal solutions of varying size. Subsequent infiltration with curable polymer and washing with suitable solvents results in porous fibers with a cylindrical cross section. Along the length of the fiber, alternating sections of controlled length, pore size, and pore size distribution exist. These fibers present interesting materials for neural scaffolding, catalysis, and possibly photonics if produced with a high degree of crystallinity. The surface pores and bulk porosity of the fibers are characterized by variable-pressure scanning electron microscopy (vp-SEM). Careful analysis shows that the surface pores vary with the colloidal template diameter and polymer infiltration time.

  16. Fluctuations in protein synthesis from a single RNA template: stochastic kinetics of ribosomes.

    Science.gov (United States)

    Garai, Ashok; Chowdhury, Debashish; Ramakrishnan, T V

    2009-01-01

    Proteins are polymerized by cyclic machines called ribosomes, which use their messenger RNA (mRNA) track also as the corresponding template, and the process is called translation. We explore, in depth and detail, the stochastic nature of the translation. We compute various distributions associated with the translation process; one of them--namely, the dwell time distribution--has been measured in recent single-ribosome experiments. The form of the distribution, which fits best with our simulation data, is consistent with that extracted from the experimental data. For our computations, we use a model that captures both the mechanochemistry of each individual ribosome and their steric interactions. We also demonstrate the effects of the sequence inhomogeneities of real genes on the fluctuations and noise in translation. Finally, inspired by recent advances in the experimental techniques of manipulating single ribosomes, we make theoretical predictions on the force-velocity relation for individual ribosomes. In principle, all our predictions can be tested by carrying out in vitro experiments.

  17. Fabrication of polymeric nano-batteries array using anodic aluminum oxide templates.

    Science.gov (United States)

    Zhao, Qiang; Cui, Xiaoli; Chen, Ling; Liu, Ling; Sun, Zhenkun; Jiang, Zhiyu

    2009-02-01

    Rechargeable nano-batteries were fabricated in the array pores of anodic aluminum oxide (AAO) template, combining template method and electrochemical method. The battery consisted of electropolymerized PPy electrode, porous TiO2 separator, and chemically polymerized PAn electrode was fabricated in the array pores of two-step anodizing aluminum oxide (AAO) membrane, based on three-step assembling method. It performs typical electrochemical battery behavior with good charge-discharge ability, and presents a capacity of 25 nAs. AFM results show the hexagonal array of nano-batteries' top side. The nano-battery may be a promising device for the development of Micro-Electro-Mechanical Systems (MEMS), and Nano-Electro-Mechanical Systems (NEMS).

  18. Biocatalytic synthesis of polymeric nanowires by micellar templates of ionic surfactants

    Energy Technology Data Exchange (ETDEWEB)

    Nazari, K., E-mail: nazarikh@ripi.ir [Research Institute of Petroleum Industry, NIOC, P.O. Box 14665-137, Tehran (Iran, Islamic Republic of); Chemistry Dept., Shahr Rey Islamic Azad University, P.O. Box 18735-334, Tehran (Iran, Islamic Republic of); Adhami, F.; Najjar-Safari, A.; Salmani, S. [Chemistry Dept., Shahr Rey Islamic Azad University, P.O. Box 18735-334, Tehran (Iran, Islamic Republic of); Mahmoudi, A. [Chemistry Dept., Karaj Islamic Azad University, Karaj (Iran, Islamic Republic of)

    2011-07-15

    Highlights: {yields} Soft-template production of polyguaiacol nanowire was done by peroxidase enzyme. {yields} Main advantage of this simple method is producing soluble encapsulated nanowires. {yields} Nanowire can be easily precipitated and separated by dilution with distilled water. {yields} Size tuned templates of sodium decyl sulfate (d = 2.7 nm) gave nanowires with d = 2-4 nm. {yields} Dried surfactant-coated wires recover freshly on specified and desired applications. -- Abstract: Micelle-templated polyguaiacol nanowires were successfully prepared via polymerization oxidation of guaiacol (o-methoxy phenol) by peroxidase enzyme in the presence of hydrogen peroxide at mild reaction conditions. The dimensions of the prepared nanowires were controlled by tuning the size and shape of the micelle structure via changing and controlling the type, chain length and molar concentrations of the ionic surfactant. The progress of the reaction and estimation of the size of soft micellar templates were followed by UV-Vis spectroscopy and dynamic light scattering (DLS). The resulting micelle encapsulated or purified polyguaiacol nanowires were characterized using transmission electron microscopy (TEM).

  19. Biocatalytic synthesis of polymeric nanowires by micellar templates of ionic surfactants

    International Nuclear Information System (INIS)

    Nazari, K.; Adhami, F.; Najjar-Safari, A.; Salmani, S.; Mahmoudi, A.

    2011-01-01

    Highlights: → Soft-template production of polyguaiacol nanowire was done by peroxidase enzyme. → Main advantage of this simple method is producing soluble encapsulated nanowires. → Nanowire can be easily precipitated and separated by dilution with distilled water. → Size tuned templates of sodium decyl sulfate (d = 2.7 nm) gave nanowires with d = 2-4 nm. → Dried surfactant-coated wires recover freshly on specified and desired applications. -- Abstract: Micelle-templated polyguaiacol nanowires were successfully prepared via polymerization oxidation of guaiacol (o-methoxy phenol) by peroxidase enzyme in the presence of hydrogen peroxide at mild reaction conditions. The dimensions of the prepared nanowires were controlled by tuning the size and shape of the micelle structure via changing and controlling the type, chain length and molar concentrations of the ionic surfactant. The progress of the reaction and estimation of the size of soft micellar templates were followed by UV-Vis spectroscopy and dynamic light scattering (DLS). The resulting micelle encapsulated or purified polyguaiacol nanowires were characterized using transmission electron microscopy (TEM).

  20. A Two-Piece Derivative of a Group I Intron RNA as a Platform for Designing Self-Assembling RNA Templates to Promote Peptide Ligation

    Directory of Open Access Journals (Sweden)

    Takahiro Tanaka

    2012-01-01

    Full Text Available Multicomponent RNA-peptide complexes are attractive from the viewpoint of artificial design of functional biomacromolecular systems. We have developed self-folding and self-assembling RNAs that serve as templates to assist chemical ligation between two reactive peptides with RNA-binding capabilities. The design principle of previous templates, however, can be applied only to limited classes of RNA-binding peptides. In this study, we employed a two-piece derivative of a group I intron RNA from the Tetrahymena large subunit ribosomal RNA (LSU rRNA as a platform for new template RNAs. In this group I intron-based self-assembling platform, modules for the recognition of substrate peptides can be installed independently from modules holding the platform structure. The new self-assembling platform allows us to expand the repertoire of substrate peptides in template RNA design.

  1. Crosslinked polymeric nanocapsules with controllable structure via a 'self-templating' approach

    International Nuclear Information System (INIS)

    Liu Peng; Liu Guangfeng; Zhang Wei; Jiang Fan

    2010-01-01

    We developed a novel strategy for the near-monodispersed crosslinked polymeric nanocapsules with controllable structure via the 'self-templating' approach by the following four steps: (i) preparation of the PVAc lattices by the emulsion polymerization of VAc; (ii) surface hydrolysis of the PVAc lattices; (iii) crosslinking the PVA segments on the surface of the surface-hydrolyzed PVAc lattices and (iv) removal of the PVAc core of the core-shell structures by being dissolved by methanol. The strategy developed was confirmed with Fourier-transform infrared, transmission electron microscopy and dynamic light scattering techniques. In the strategy developed, the particle size, the thickness and the crosslinking degree of the nanocapsules could be controlled with the lattice's size, relative molecular weight of PVAc and the crosslinking degree of the crosslinked shell.

  2. Rate in template-directed polymer synthesis.

    Science.gov (United States)

    Saito, Takuya

    2014-06-01

    We discuss the temporal efficiency of template-directed polymer synthesis, such as DNA replication and transcription, under a given template string. To weigh the synthesis speed and accuracy on the same scale, we propose a template-directed synthesis (TDS) rate, which contains an expression analogous to that for the Shannon entropy. Increasing the synthesis speed accelerates the TDS rate, but the TDS rate is lowered if the produced sequences are diversified. We apply the TDS rate to some production system models and investigate how the balance between the speed and the accuracy is affected by changes in the system conditions.

  3. Nucleic Acid Templated Reactions for Chemical Biology.

    Science.gov (United States)

    Di Pisa, Margherita; Seitz, Oliver

    2017-06-21

    Nucleic acid directed bioorthogonal reactions offer the fascinating opportunity to unveil and redirect a plethora of intracellular mechanisms. Nano- to picomolar amounts of specific RNA molecules serve as templates and catalyze the selective formation of molecules that 1) exert biological effects, or 2) provide measurable signals for RNA detection. Turnover of reactants on the template is a valuable asset when concentrations of RNA templates are low. The idea is to use RNA-templated reactions to fully control the biodistribution of drugs and to push the detection limits of DNA or RNA analytes to extraordinary sensitivities. Herein we review recent and instructive examples of conditional synthesis or release of compounds for in cellulo protein interference and intracellular nucleic acid imaging. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

  4. Possible Role of Ice in the Synthesis of Polymeric Compounds

    Science.gov (United States)

    Monnard, Pierre-Alain; Doerr, Mark; Loeffler, Philipp, M. G.

    ) and a liquid phase containing most solutes. The role of water likely extends beyond that of a simple chemical liquid medium since the surfaces of ice crystals could act as a substrate on which other reactants can attach and/or become aligned. The emergence of a polymer-based genetic or/and catalytic system, as it for example according to the "RNA World hypothesis" states, initially requires the synthesis of monomers followed by three non-enzymatic processes: polymerization of monomers; elongation of existing polymers with monomers or short oligomers; and replication of existing polymers in a template-directed fashion. Ideally, these processes should take place efficiently, using simple metal ions as cat-alysts. However, in a dilute solution, even when using activated monomers, these chemical processes occur very slowly, if at all. We have been exploring the plausibility of chemical reactions, such as non-enzymatic nucleotide condensations forming RNA, under cold environmental conditions and found that the polymer-ization of RNA from imidazole-activated ribonucleotides can proceed efficiently in the eutectic phase in water-ice when metal ions are available as catalysts [4]. Starting from monomer mix-tures, polymers up to 30 monomeric units in length can be readily formed [5]. Longer polymers can be obtained by adding freshly activated monomers or short oligomers to a solution over several freeze-thawing cycles. Depending on their sequences, oligomers can be elongated using monomers to obtain up to a 45-mer. Furthermore, the decomposition of the longer chains remained low. By using activated short oligomers, even longer polymers can be formed [6]. Studying RNA template-directed RNA polymerization under these conditions, we established-discovered that the initial elongation rates depended on the complementarity of the monomers with the templating nucleobases. That is, the polymerization rates for all four nucleobases op-positepairing with their corresponding Watson

  5. Structure and morphology of magnetron sputter deposited ultrathin ZnO films on confined polymeric template

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Ajaib [Discipline of Metallurgy Engineering and Materials Science, Indian Institute of Technology Indore, Indore 453552 (India); Schipmann, Susanne [II. Insatitute of Physics and JARA-FIT, RWTH Aachen University, 52056 Aachen (Germany); Mathur, Aakash; Pal, Dipayan [Discipline of Metallurgy Engineering and Materials Science, Indian Institute of Technology Indore, Indore 453552 (India); Sengupta, Amartya [Department of Physics, Indian Institute of Technology Delhi, Delhi 110016 (India); Klemradt, Uwe [II. Insatitute of Physics and JARA-FIT, RWTH Aachen University, 52056 Aachen (Germany); Chattopadhyay, Sudeshna, E-mail: sudeshna@iiti.ac.in [Discipline of Metallurgy Engineering and Materials Science, Indian Institute of Technology Indore, Indore 453552 (India); Discipline of Physics, Indian Institute of Technology Indore, Indore 453552 (India); Centre for Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552 (India)

    2017-08-31

    Highlights: • Ultra-thin ZnO films grown on confined polymeric (polystyrene, PS) template. • XRR and GISAXS explore the surface/interfaces structure and morphology of ZnO/PS. • Insights into the growth mechanism of magnetron sputtered ZnO thin film on PS template. • Nucleated disk-like cylindrical particles are the basis of the formation of ZnO layers. • Effect of ZnO film thickness on room temperature PL spectra in ZnO/PS systems. - Abstract: The structure and morphology of ultra-thin zinc oxide (ZnO) films with different film thicknesses on confined polymer template were studied through X-ray reflectivity (XRR) and grazing incidence small angle X-ray scattering (GISAXS). Using magnetron sputter deposition technique ZnO thin films with different film thicknesses (<10 nm) were grown on confined polystyrene with ∼2R{sub g} film thickness, where R{sub g} ∼ 20 nm (R{sub g} is the unperturbed radius of gyration of polystyrene, defined by R{sub g} = 0.272 √M{sub 0}, and M{sub 0} is the molecular weight of polystyrene). The detailed internal structure, along the surface/interfaces and the growth direction of the system were explored in this study, which provides insight into the growth procedure of ZnO on confined polymer and reveals that a thin layer of ZnO, with very low surface and interface roughness, can be grown by DC magnetron sputtering technique, with approximately full coverage (with bulk like electron density) even in nm order of thickness, in 2–7 nm range on confined polymer template, without disturbing the structure of the underneath template. The resulting ZnO-polystyrene hybrid systems show strong ZnO near band edge (NBE) and deep-level (DLE) emissions in their room temperature photoluminescence spectra, where the contribution of DLE gets relatively stronger with decreasing ZnO film thickness, indicating a significant enhancement of surface defects because of the greater surface to volume ratio in thinner films.

  6. Template-Directed Fabrication of Anatase TiO2 Hollow Nanoparticles and Their Application in Photocatalytic Degradation of Methyl Orange

    Institute of Scientific and Technical Information of China (English)

    Jie Chang; Wenjian Zhang; Chunyan Hong

    2017-01-01

    Polymerization-induced self-assembly (PISA) was used to fabricate polymeric nanoparticles via reversible addition-fragmentation chain transfer (RAFT) dispersion polymerization of benzyl methacrylate (BzMA) using diblock copolymer poly(glycerol monomethacrylate)-block-poly(2-dimethylaminoethyl methacrylate) (PGMMA-PDMAEMA-CTA) as the macro RAFT agent.The dispersion of polymeric nanoparticles with a final concentration of about 210 mg/g (solid content of 21%) was obtained via this efficient method (PISA).The resultant polymeric nanoparticles consisting of corona-shell-core three layers with weak polyelectrolyte PDMAEMA as the shell were used as sacrificial template to fabricate TiO2 hollow nanoparticles.The negatively charged titanium precursor was absorbed into the PDMAEMA shell via the electrostatic interaction,and hydrolyzed to form polymer/TiO2 hybrid nanoparticles.Anatase TiO2 hollow nanoparticles were formed after removing the polymeric templates by calcination at 550 ℃.The experiments of photocatalytic degradation of methyl orange showed that the resultant anatase TiO2 hollow nanoparticles had high photocatalytic activity and good reusability.

  7. The RNA template channel of the RNA-dependent RNA polymerase as a target for development of antiviral therapy of multiple genera within a virus family.

    Directory of Open Access Journals (Sweden)

    Lonneke van der Linden

    2015-03-01

    Full Text Available The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71 for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy. Nucleoside-based inhibitors have broad-spectrum activity but often exhibit off-target effects. Most non-nucleoside inhibitors (NNIs target surface cavities, which are structurally more flexible than the nucleotide-binding pocket, and hence have a more narrow spectrum of activity and are more prone to resistance development. Here, we report a novel NNI, GPC-N114 (2,2'-[(4-chloro-1,2-phenylenebis(oxy]bis(5-nitro-benzonitrile with broad-spectrum activity against enteroviruses and cardioviruses (another genus in the picornavirus family. Surprisingly, coxsackievirus B3 (CVB3 and poliovirus displayed a high genetic barrier to resistance against GPC-N114. By contrast, EMCV, a cardiovirus, rapidly acquired resistance due to mutations in 3Dpol. In vitro polymerase activity assays showed that GPC-N114 i inhibited the elongation activity of recombinant CVB3 and EMCV 3Dpol, (ii had reduced activity against EMCV 3Dpol with the resistance mutations, and (iii was most efficient in inhibiting 3Dpol when added before the RNA template-primer duplex. Elucidation of a crystal structure of the inhibitor bound to CVB3 3Dpol confirmed the RNA-binding channel as the target for GPC-N114. Docking studies of the compound into the crystal structures of the compound-resistant EMCV 3Dpol mutants suggested that the resistant phenotype is due to subtle changes that interfere with the binding of GPC-N114 but not of the RNA template-primer. In conclusion, this study presents the first NNI that targets the RNA template channel of the picornavirus polymerase and identifies a new pocket that can be used for the design of broad-spectrum inhibitors. Moreover, this study provides important new insight

  8. Hollow inorganic nanospheres and nanotubes with tunable wall thicknesses by atomic layer deposition on self-assembled polymeric templates

    NARCIS (Netherlands)

    Ras, Robin H. A.; Kemell, Marianna; de Wit, Joost; Ritala, Mikko; ten Brinke, Gerrit; Leskela, Markku; Ikkala, Olli; Leskelä, Markku

    2007-01-01

    The construction of inorganic nanostructures with hollow interiors is demonstrated by coating self-assembled polymeric nano-objects with a thin Al2O3 layer by atomic layer deposition (ALD), followed by removal of the polymer template upon heating. The morphology of the nano-object (i.e., spherical

  9. Evidence for an RNA polymerization activity in axolotl and Xenopus egg extracts.

    Directory of Open Access Journals (Sweden)

    Hélène Pelczar

    2010-12-01

    Full Text Available We have previously reported a post-transcriptional RNA amplification observed in vivo following injection of in vitro synthesized transcripts into axolotl oocytes, unfertilized (UFE or fertilized eggs. To further characterize this phenomenon, low speed extracts (LSE from axolotl and Xenopus UFE were prepared and tested in an RNA polymerization assay. The major conclusions are: i the amphibian extracts catalyze the incorporation of radioactive ribonucleotide in RNase but not DNase sensitive products showing that these products correspond to RNA; ii the phenomenon is resistant to α-amanitin, an inhibitor of RNA polymerases II and III and to cordycepin (3'dAMP, but sensitive to cordycepin 5'-triphosphate, an RNA elongation inhibitor, which supports the existence of an RNA polymerase activity different from polymerases II and III; the detection of radiolabelled RNA comigrating at the same length as the exogenous transcript added to the extracts allowed us to show that iii the RNA polymerization is not a 3' end labelling and that iv the radiolabelled RNA is single rather than double stranded. In vitro cell-free systems derived from amphibian UFE therefore validate our previous in vivo results hypothesizing the existence of an evolutionary conserved enzymatic activity with the properties of an RNA dependent RNA polymerase (RdRp.

  10. Site-selective metallization of polymeric substrates by the hyperbranched polymer templates

    International Nuclear Information System (INIS)

    Li, Peiyuan; Yang, Fang; Li, Xiangcheng; He, Chunling; Su, Wei; Chen, Jinhao; Huo, Lini; Chen, Rui; Lu, Chensheng; Liang, Lifang

    2013-01-01

    We demonstrate a simple, cost-effective and universal technique for the fabrication of copper circuit pattern on flexible polymeric substrate. This method relies on a ternary polyethylenimine-poly(acrylic acid)-substrate film incorporating palladium catalysts, which are used as adhesive interlayers for the copper metallization of flexible polymeric substrates. We demonstrated the fabrication of patterned copper films on a variety of flexible polymers with minimum feature sizes of 200 μm. And the resulting copper circuit showed strong adhesion with underlying flexible polymeric substrates. The films were characterized by ATR FT-IR, contact angle, XPS, XRD, TEM and SEM. The direct patterning of metallic circuit on flexible polymeric substrate indicates great potential for the use in electronics industry.

  11. Site-selective metallization of polymeric substrates by the hyperbranched polymer templates

    Energy Technology Data Exchange (ETDEWEB)

    Li, Peiyuan, E-mail: lipearpear@163.com [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Yang, Fang [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Li, Xiangcheng [School of Computer, Electronics and Information, Guangxi University, Nanning 530001 (China); He, Chunling [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Su, Wei, E-mail: suwmail@163.com [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Chen, Jinhao [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Huo, Lini; Chen, Rui; Lu, Chensheng [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Liang, Lifang [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China)

    2013-09-01

    We demonstrate a simple, cost-effective and universal technique for the fabrication of copper circuit pattern on flexible polymeric substrate. This method relies on a ternary polyethylenimine-poly(acrylic acid)-substrate film incorporating palladium catalysts, which are used as adhesive interlayers for the copper metallization of flexible polymeric substrates. We demonstrated the fabrication of patterned copper films on a variety of flexible polymers with minimum feature sizes of 200 μm. And the resulting copper circuit showed strong adhesion with underlying flexible polymeric substrates. The films were characterized by ATR FT-IR, contact angle, XPS, XRD, TEM and SEM. The direct patterning of metallic circuit on flexible polymeric substrate indicates great potential for the use in electronics industry.

  12. Template Directed Oligomer Ligation in Eutectic Phases in Water-Ice

    DEFF Research Database (Denmark)

    Dörr, Mark; Löffler, Philipp M. G.; Wieczorek, Rafal

    2011-01-01

    achieved, if small, activated, oligonucleotides are ligated on a template. A template directed ligation can lead to autocatalytic or cross- catalytic replication and thus maintain a certain pool of catalyitc species. Important for these processes is a destabilization of the formed douplex....../multiplex to overcome product inhibition. The latest results of our template directed ligation experiments in the eutectic ice phase are presented. Different activation strategies are compared and an outlook towards applications in molecular evolution and artifical cell systems (« protocells ») will be given. Figure 1....... (a) Reaction scheme of the condensation reaction of two oligoribonucleotides : The leaving group in this example is imidazole. (b) Illustration of a possible spatial arrangement of a template (15nt) directed ligation. The 7-mer is activated with imidazole at the 5' phosphate (apical moiety...

  13. Ribozyme Activity of RNA Nonenzymatically Polymerized from 3 ',5 '-Cyclic GMP

    Czech Academy of Sciences Publication Activity Database

    Pino, S.; Costanzo, G.; Giorgi, A.; Šponer, Jiří; Šponer, Judit E.; Di Mauro, E.

    2013-01-01

    Roč. 15, č. 12 (2013), s. 5362-5383 ISSN 1099-4300 R&D Projects: GA ČR(CZ) GAP208/10/2302; GA MŠk(CZ) ED1.1.00/02.0068 Institutional support: RVO:68081707 Keywords : RNA polymerization * RNA origin * ribozymes Subject RIV: BO - Biophysics Impact factor: 1.564, year: 2013

  14. RNA Polymerase Structure, Function, Regulation, Dynamics, Fidelity, and Roles in GENE EXPRESSION | Center for Cancer Research

    Science.gov (United States)

    Multi-subunit RNA polymerases (RNAP) are ornate molecular machines that translocate on a DNA template as they generate a complementary RNA chain. RNAPs are highly conserved in evolution among eukarya, eubacteria, archaea, and some viruses. As such, multi-subunit RNAPs appear to be an irreplaceable advance in the evolution of complex life on earth. Because of their stepwise movement on DNA, RNAPs are considered to be molecular motors, and because RNAPs catalyze a templated polymerization reaction, they are central to biological information flow.

  15. Direct measurement of the poliovirus RNA polymerase error frequency in vitro

    International Nuclear Information System (INIS)

    Ward, C.D.; Stokes, M.A.M.; Flanegan, J.B.

    1988-01-01

    The fidelity of RNA replication by the poliovirus-RNA-dependent RNA polymerase was examined by copying homopolymeric RNA templates in vitro. The poliovirus RNA polymerase was extensively purified and used to copy poly(A), poly(C), or poly(I) templates with equimolar concentrations of noncomplementary and complementary ribonucleotides. The error frequency was expressed as the amount of a noncomplementary nucleotide incorporated divided by the total amount of complementary and noncomplementary nucleotide incorporated. The polymerase error frequencies were very high, depending on the specific reaction conditions. The activity of the polymerase on poly(U) and poly(G) was too low to measure error frequencies on these templates. A fivefold increase in the error frequency was observed when the reaction conditions were changed from 3.0 mM Mg 2+ (pH 7.0) to 7.0 mM Mg 2+ (pH 8.0). This increase in the error frequency correlates with an eightfold increase in the elongation rate that was observed under the same conditions in a previous study

  16. New insights into the promoterless transcription of DNA coligo templates by RNA polymerase III.

    Science.gov (United States)

    Lama, Lodoe; Seidl, Christine I; Ryan, Kevin

    2014-01-01

    Chemically synthesized DNA can carry small RNA sequence information but converting that information into small RNA is generally thought to require large double-stranded promoters in the context of plasmids, viruses and genes. We previously found evidence that circularized oligodeoxynucleotides (coligos) containing certain sequences and secondary structures can template the synthesis of small RNA by RNA polymerase III in vitro and in human cells. By using immunoprecipitated RNA polymerase III we now report corroborating evidence that this enzyme is the sole polymerase responsible for coligo transcription. The immobilized polymerase enabled experiments showing that coligo transcripts can be formed through transcription termination without subsequent 3' end trimming. To better define the determinants of productive transcription, a structure-activity relationship study was performed using over 20 new coligos. The results show that unpaired nucleotides in the coligo stem facilitate circumtranscription, but also that internal loops and bulges should be kept small to avoid secondary transcription initiation sites. A polymerase termination sequence embedded in the double-stranded region of a hairpin-encoding coligo stem can antagonize transcription. Using lessons learned from new and old coligos, we demonstrate how to convert poorly transcribed coligos into productive templates. Our findings support the possibility that coligos may prove useful as chemically synthesized vectors for the ectopic expression of small RNA in human cells.

  17. Stochastic model of template-directed elongation processes in biology.

    Science.gov (United States)

    Schilstra, Maria J; Nehaniv, Chrystopher L

    2010-10-01

    We present a novel modular, stochastic model for biological template-based linear chain elongation processes. In this model, elongation complexes (ECs; DNA polymerase, RNA polymerase, or ribosomes associated with nascent chains) that span a finite number of template units step along the template, one after another, with semaphore constructs preventing overtaking. The central elongation module is readily extended with modules that represent initiation and termination processes. The model was used to explore the effect of EC span on motor velocity and dispersion, and the effect of initiation activator and repressor binding kinetics on the overall elongation dynamics. The results demonstrate that (1) motors that move smoothly are able to travel at a greater velocity and closer together than motors that move more erratically, and (2) the rate at which completed chains are released is proportional to the occupancy or vacancy of activator or repressor binding sites only when initiation or activator/repressor dissociation is slow in comparison with elongation. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  18. Microporous polymeric 3D scaffolds templated by the layer-by-layer self-assembly.

    Science.gov (United States)

    Paulraj, Thomas; Feoktistova, Natalia; Velk, Natalia; Uhlig, Katja; Duschl, Claus; Volodkin, Dmitry

    2014-08-01

    Polymeric scaffolds serve as valuable supports for biological cells since they offer essential features for guiding cellular organization and tissue development. The main challenges for scaffold fabrication are i) to tune an internal structure and ii) to load bio-molecules such as growth factors and control their local concentration and distribution. Here, a new approach for the design of hollow polymeric scaffolds using porous CaCO3 particles (cores) as templates is presented. The cores packed into a microfluidic channel are coated with polymers employing the layer-by-layer (LbL) technique. Subsequent core elimination at mild conditions results in formation of the scaffold composed of interconnected hollow polymer microspheres. The size of the cores determines the feature dimensions and, as a consequence, governs cellular adhesion: for 3T3 fibroblasts an optimal microsphere size is 12 μm. By making use of the carrier properties of the porous CaCO3 cores, the microspheres are loaded with BSA as a model protein. The scaffolds developed here may also be well suited for the localized release of bio-molecules using external triggers such as IR-light. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. A functional monomer is not enough: principal component analysis of the influence of template complexation in pre-polymerization mixtures on imprinted polymer recognition and morphology.

    Science.gov (United States)

    Golker, Kerstin; Karlsson, Björn C G; Rosengren, Annika M; Nicholls, Ian A

    2014-11-10

    In this report, principal component analysis (PCA) has been used to explore the influence of template complexation in the pre-polymerization phase on template molecularly imprinted polymer (MIP) recognition and polymer morphology. A series of 16 bupivacaine MIPs were studied. The ethylene glycol dimethacrylate (EGDMA)-crosslinked polymers had either methacrylic acid (MAA) or methyl methacrylate (MMA) as the functional monomer, and the stoichiometry between template, functional monomer and crosslinker was varied. The polymers were characterized using radioligand equilibrium binding experiments, gas sorption measurements, swelling studies and data extracted from molecular dynamics (MD) simulations of all-component pre-polymerization mixtures. The molar fraction of the functional monomer in the MAA-polymers contributed to describing both the binding, surface area and pore volume. Interestingly, weak positive correlations between the swelling behavior and the rebinding characteristics of the MAA-MIPs were exposed. Polymers prepared with MMA as a functional monomer and a polymer prepared with only EGDMA were found to share the same characteristics, such as poor rebinding capacities, as well as similar surface area and pore volume, independent of the molar fraction MMA used in synthesis. The use of PCA for interpreting relationships between MD-derived descriptions of events in the pre-polymerization mixture, recognition properties and morphologies of the corresponding polymers illustrates the potential of PCA as a tool for better understanding these complex materials and for their rational design.

  20. The 3D protein of duck hepatitis A virus type 1 binds to a viral genomic 3' UTR and shows RNA-dependent RNA polymerase activity.

    Science.gov (United States)

    Zhang, Yu; Cao, Qianda; Wang, Mingshu; Jia, Renyong; Chen, Shun; Zhu, Dekang; Liu, Mafeng; Sun, Kunfeng; Yang, Qiao; Wu, Ying; Zhao, Xinxin; Chen, Xiaoyue; Cheng, Anchun

    2017-12-01

    To explore the RNA-dependent RNA polymerase (RdRP) function of the 3D protein of duck hepatitis A virus type 1 (DHAV-1), the gene was cloned into the pET-32a(+) vector for prokaryotic expression. The 3' untranslated region (3' UTR) of DHAV-1 together with a T7 promoter was cloned into the pMD19-T vector for in vitro transcription of 3' UTR RNA, which was further used as a template in RNA-dependent RNA polymerization. In this study, three methods were applied to analyze the RdRP function of the 3D protein: (1) ammonium molybdate spectrophotometry to detect pyrophosphate produced during polymerization; (2) quantitative reverse transcription PCR (RT-qPCR) to investigate the changes in RNA quantity during polymerization; and (3) electrophoresis mobility shift assay to examine the interaction between the 3D protein and 3' UTR. The results showed the 3D protein was successfully expressed in bacteria culture supernatant in a soluble form, which could be purified by affinity chromatography. In 3D enzymatic activity assays, pyrophosphate and RNA were produced, the amounts of which increased based on approximative kinetics, and binding of the 3D protein to the 3' UTR was observed. These results indicate that prokaryotically expressed soluble DHAV-13D protein can bind to a viral genomic 3' UTR and exhibit RdRP activity.

  1. A Functional Monomer Is Not Enough: Principal Component Analysis of the Influence of Template Complexation in Pre-Polymerization Mixtures on Imprinted Polymer Recognition and Morphology

    Directory of Open Access Journals (Sweden)

    Kerstin Golker

    2014-11-01

    Full Text Available In this report, principal component analysis (PCA has been used to explore the influence of template complexation in the pre-polymerization phase on template molecularly imprinted polymer (MIP recognition and polymer morphology. A series of 16 bupivacaine MIPs were studied. The ethylene glycol dimethacrylate (EGDMA-crosslinked polymers had either methacrylic acid (MAA or methyl methacrylate (MMA as the functional monomer, and the stoichiometry between template, functional monomer and crosslinker was varied. The polymers were characterized using radioligand equilibrium binding experiments, gas sorption measurements, swelling studies and data extracted from molecular dynamics (MD simulations of all-component pre-polymerization mixtures. The molar fraction of the functional monomer in the MAA-polymers contributed to describing both the binding, surface area and pore volume. Interestingly, weak positive correlations between the swelling behavior and the rebinding characteristics of the MAA-MIPs were exposed. Polymers prepared with MMA as a functional monomer and a polymer prepared with only EGDMA were found to share the same characteristics, such as poor rebinding capacities, as well as similar surface area and pore volume, independent of the molar fraction MMA used in synthesis. The use of PCA for interpreting relationships between MD-derived descriptions of events in the pre-polymerization mixture, recognition properties and morphologies of the corresponding polymers illustrates the potential of PCA as a tool for better understanding these complex materials and for their rational design.

  2. Binding of transcription termination protein nun to nascent RNA and template DNA.

    Science.gov (United States)

    Watnick, R S; Gottesman, M E

    1999-12-17

    The amino-terminal arginine-rich motif of coliphage HK022 Nun binds phage lambda nascent transcript, whereas the carboxyl-terminal domain interacts with RNA polymerase (RNAP) and blocks transcription elongation. RNA binding is inhibited by zinc (Zn2+) and stimulated by Escherichia coli NusA. To study these interactions, the Nun carboxyl terminus was extended by a cysteine residue conjugated to a photochemical cross-linker. The carboxyl terminus contacted NusA and made Zn2+-dependent intramolecular contacts. When Nun was added to a paused transcription elongation complex, it cross-linked to the DNA template. Nun may arrest transcription by anchoring RNAP to DNA.

  3. Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination

    Science.gov (United States)

    Chao, Mei; Wang, Tzu-Chi; Lin, Chia-Chi; Yung-Liang Wang, Robert; Lin, Wen-Bin; Lee, Shang-En; Cheng, Ying-Yu; Yeh, Chau-Ting; Iang, Shan-Bei

    2017-01-01

    The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription. PMID:28977829

  4. Ionic Liquid Microemullsions, Templates for Directing Morphology of Cellulose Biopolymer Nanoparticles (Briefing Charts)

    Science.gov (United States)

    2015-08-19

    Charts 3. DATES COVERED (From - To) July 2015-August 2015 4. TITLE AND SUBTITLE Ionic Liquid Microemullsions, Templates for Directing Morphology of...unlimited AFRL Public Affairs Clearance No. TBD Ionic Liquid Microemullsions, Templates for Directing Morphology of Cellulose Biopolymer...AFRL Public Affairs Clearance No. 15438 Outline • Background on Cellulose and Ionic Liquids • Materials and Methods • Results: Designing an IL

  5. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon

    2017-08-24

    The CRISPR/Cas9 system has been applied in diverse eukaryotic organisms for targeted mutagenesis. However, targeted gene editing is inefficient and requires the simultaneous delivery of a DNA template for homology-directed repair (HDR). Here, we used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate the double-strand breaks) and repair template sequences (to direct HDR), flanked by regions of homology to the target. Gene editing was more efficient in rice protoplasts using repair templates complementary to the non-target DNA strand, rather than the target strand. We applied this cgRNA repair method to generate herbicide resistance in rice, which showed that this cgRNA repair method can be used for targeted gene editing in plants. Our findings will facilitate applications in functional genomics and targeted improvement of crop traits.

  6. The putative Leishmania telomerase RNA (LeishTER undergoes trans-splicing and contains a conserved template sequence.

    Directory of Open Access Journals (Sweden)

    Elton J R Vasconcelos

    Full Text Available Telomerase RNAs (TERs are highly divergent between species, varying in size and sequence composition. Here, we identify a candidate for the telomerase RNA component of Leishmania genus, which includes species that cause leishmaniasis, a neglected tropical disease. Merging a thorough computational screening combined with RNA-seq evidence, we mapped a non-coding RNA gene localized in a syntenic locus on chromosome 25 of five Leishmania species that shares partial synteny with both Trypanosoma brucei TER locus and a putative TER candidate-containing locus of Crithidia fasciculata. Using target-driven molecular biology approaches, we detected a ∼2,100 nt transcript (LeishTER that contains a 5' spliced leader (SL cap, a putative 3' polyA tail and a predicted C/D box snoRNA domain. LeishTER is expressed at similar levels in the logarithmic and stationary growth phases of promastigote forms. A 5'SL capped LeishTER co-immunoprecipitated and co-localized with the telomerase protein component (TERT in a cell cycle-dependent manner. Prediction of its secondary structure strongly suggests the existence of a bona fide single-stranded template sequence and a conserved C[U/C]GUCA motif-containing helix II, representing the template boundary element. This study paves the way for further investigations on the biogenesis of parasite TERT ribonucleoproteins (RNPs and its role in parasite telomere biology.

  7. Viral RNA polymerase scanning and the gymnastics of Sendai virus RNA synthesis

    International Nuclear Information System (INIS)

    Kolakofsky, Daniel; Le Mercier, Philippe; Iseni, Frederic; Garcin, Dominique

    2004-01-01

    mRNA synthesis from nonsegmented negative-strand RNA virus (NNV) genomes is unique in that the genome RNA is embedded in an N protein assembly (the nucleocapsid) and the viral RNA polymerase does not dissociate from the template after release of each mRNA, but rather scans the genome RNA for the next gene-start site. A revised model for NNV RNA synthesis is presented, in which RNA polymerase scanning plays a prominent role. Polymerase scanning of the template is known to occur as the viral transcriptase negotiates gene junctions without falling off the template

  8. Template polymerization of N-vinylimidazole along poly(methacrylic acid) in water

    NARCIS (Netherlands)

    Grampel, Hendrik Theodorus van de

    1990-01-01

    Template polymerisaties zijn polymerisaties waarbij radicalen gedurende het grootste gedeelte van hun bestaan langs het template polymeer groeien. In het algemeen kan de template invloed hebben op de polymerisatiesnelheid, als ook op het molecuulgewicht en de tacticiteit van het bijgevormde

  9. Characterization behavior of some polymeric composite ion exchangers

    International Nuclear Information System (INIS)

    El-Zahhar, A.A; Ahdel-Aziz, H.M.; Siyam, T.

    2005-01-01

    Polymeric composite resins were prepared by template polymerization process in aqueous solution. Thermogravimetric analysis (TGA), differential thermal analysis (DTA) and The X-ray diffraction patterns (XRD) were performed to evaluate the physico chemical properties of the different polymeric composite resins. The TGA and DTA clarify high thermal stability of prepared polymeric composite resins. XRD of prepared polymeric composite shows that there is crystalline structure of some resins while other are amorphous one

  10. Direct surface PEGylation of nanodiamond via RAFT polymerization

    International Nuclear Information System (INIS)

    Shi, Yingge; Liu, Meiying; Wang, Ke; Huang, Hongye; Wan, Qing; Tao, Lei; Fu, Lihua; Zhang, Xiaoyong; Wei, Yen

    2015-01-01

    Graphical abstract: In this paper, we describe an efficient, practical and novel method to modify ND via direct immobilization of chain transfer agent for RAFT polymerization. - Highlights: • Surface PEGylation of ND via RAFT polymerization. • ND with high water dispersibility and excellent biocompatibility. • Controlled living polymerization. - Abstract: Nanodiamond (ND) is a novel class of carbon nanomaterials, which has been extensively investigated for biomedical applications because of its small size, high surface area and excellent biocompatibility. However, the biomedical applications of unmodified ND are still largely restricted because of their poor dispersibility in both aqueous and organic medium. In this work, we reported a novel strategy for the surface modification of ND via reversible addition fragmentation chain transfer (RAFT) polymerization. For preparation of the PEGylated ND (pPEGMA-ND), chain transfer agent (CTA) was immobilized onto ND through reaction between the hydroxyl group of ND and the carboxyl group of CTA, which was used as the initiator for surface-initiated RAFT polymerization. The successful preparation of pPEGMA-ND was characterized by nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectra and thermal gravimetric analysis in detail. Results demonstrated that pPEGMA-ND exhibited enhanced water dispersibility and desirable biocompatibility, making it promising for biomedical applications.

  11. Direct surface PEGylation of nanodiamond via RAFT polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Shi, Yingge [Department of Chemistry and Jiangxi Provincial Key Laboratory of New Energy Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031 (China); School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Liu, Meiying [Department of Chemistry and Jiangxi Provincial Key Laboratory of New Energy Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031 (China); Wang, Ke [Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing 100084 (China); Huang, Hongye; Wan, Qing [Department of Chemistry and Jiangxi Provincial Key Laboratory of New Energy Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031 (China); Tao, Lei [Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing 100084 (China); Fu, Lihua [School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004 (China); Zhang, Xiaoyong, E-mail: xiaoyongzhang1980@gmail.com [Department of Chemistry and Jiangxi Provincial Key Laboratory of New Energy Chemistry, Nanchang University, 999 Xuefu Avenue, Nanchang 330031 (China); Wei, Yen, E-mail: weiyen@tsinghua.edu.cn [Department of Chemistry and the Tsinghua Center for Frontier Polymer Research, Tsinghua University, Beijing 100084 (China)

    2015-12-01

    Graphical abstract: In this paper, we describe an efficient, practical and novel method to modify ND via direct immobilization of chain transfer agent for RAFT polymerization. - Highlights: • Surface PEGylation of ND via RAFT polymerization. • ND with high water dispersibility and excellent biocompatibility. • Controlled living polymerization. - Abstract: Nanodiamond (ND) is a novel class of carbon nanomaterials, which has been extensively investigated for biomedical applications because of its small size, high surface area and excellent biocompatibility. However, the biomedical applications of unmodified ND are still largely restricted because of their poor dispersibility in both aqueous and organic medium. In this work, we reported a novel strategy for the surface modification of ND via reversible addition fragmentation chain transfer (RAFT) polymerization. For preparation of the PEGylated ND (pPEGMA-ND), chain transfer agent (CTA) was immobilized onto ND through reaction between the hydroxyl group of ND and the carboxyl group of CTA, which was used as the initiator for surface-initiated RAFT polymerization. The successful preparation of pPEGMA-ND was characterized by nuclear magnetic resonance spectroscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectra and thermal gravimetric analysis in detail. Results demonstrated that pPEGMA-ND exhibited enhanced water dispersibility and desirable biocompatibility, making it promising for biomedical applications.

  12. Herpesvirus telomerase RNA (vTR with a mutated template sequence abrogates herpesvirus-induced lymphomagenesis.

    Directory of Open Access Journals (Sweden)

    Benedikt B Kaufer

    2011-10-01

    Full Text Available Telomerase reverse transcriptase (TERT and telomerase RNA (TR represent the enzymatically active components of telomerase. In the complex, TR provides the template for the addition of telomeric repeats to telomeres, a protective structure at the end of linear chromosomes. Human TR with a mutation in the template region has been previously shown to inhibit proliferation of cancer cells in vitro. In this report, we examined the effects of a mutation in the template of a virus encoded TR (vTR on herpesvirus-induced tumorigenesis in vivo. For this purpose, we used the oncogenic avian herpesvirus Marek's disease virus (MDV as a natural virus-host model for lymphomagenesis. We generated recombinant MDV in which the vTR template sequence was mutated from AATCCCAATC to ATATATATAT (vAU5 by two-step Red-mediated mutagenesis. Recombinant viruses harboring the template mutation replicated with kinetics comparable to parental and revertant viruses in vitro. However, mutation of the vTR template sequence completely abrogated virus-induced tumor formation in vivo, although the virus was able to undergo low-level lytic replication. To confirm that the absence of tumors was dependent on the presence of mutant vTR in the telomerase complex, a second mutation was introduced in vAU5 that targeted the P6.1 stem loop, a conserved region essential for vTR-TERT interaction. Absence of vTR-AU5 from the telomerase complex restored virus-induced lymphoma formation. To test if the attenuated vAU5 could be used as an effective vaccine against MDV, we performed vaccination-challenge studies and determined that vaccination with vAU5 completely protected chickens from lethal challenge with highly virulent MDV. Taken together, our results demonstrate 1 that mutation of the vTR template sequence can completely abrogate virus-induced tumorigenesis, likely by the inhibition of cancer cell proliferation, and 2 that this strategy could be used to generate novel vaccine candidates

  13. Physical controls on directed virus assembly at nanoscale chemical templates

    International Nuclear Information System (INIS)

    Cheung, C L; Chung, S; Chatterji, A; Lin, T; Johnson, J E; Hok, S; Perkins, J; De Yoreo, J

    2006-01-01

    Viruses are attractive building blocks for nanoscale heterostructures, but little is understood about the physical principles governing their directed assembly. In-situ force microscopy was used to investigate organization of Cowpea Mosaic Virus engineered to bind specifically and reversibly at nanoscale chemical templates with sub-30nm features. Morphological evolution and assembly kinetics were measured as virus flux and inter-viral potential were varied. The resulting morphologies were similar to those of atomic-scale epitaxial systems, but the underlying thermodynamics was analogous to that of colloidal systems in confined geometries. The 1D templates biased the location of initial cluster formation, introduced asymmetric sticking probabilities, and drove 1D and 2D condensation at subcritical volume fractions. The growth kinetics followed a t 1/2 law controlled by the slow diffusion of viruses. The lateral expansion of virus clusters that initially form on the 1D templates following introduction of polyethylene glycol (PEG) into the solution suggests a significant role for weak interaction

  14. Preparation of polymeric superhydrophobic surfaces and analysis of their wettability

    Science.gov (United States)

    Zhuang, Jian; Huang, Manling; Zhang, Yajun; Wu, Daming; Kuang, Tairong; Xu, Hong; Zhang, Xiaoxu

    2015-10-01

    In this paper, we presented three simple, facile and low-cost manufacturing methods—template method, nanoparticle filling method and extrusion stamping forming method—to fabricate the polymeric superhydrophobic surfaces. The stainless steel wire mesh as the template and glass beads was investigated in this study for the first time and low-cost hollow glass beads were rarely used as particles for fabricating the superhydrophobic surface. The water contact angle measurement of polymeric surfaces was used to investigate the effect of mesh count, glass beads and PTFE on fabricating polymeric superhydrophobic surface. It was found that the mesh count significantly affected the hydrophobicity of polymer surface in template method. The addition of glass beads improved the hydrophobicity by nanoparticle filling method. The addition of PTFE was of importance to fabricate the superhydrophobic surface by extrusion stamping forming method. The surface microstructure was also observed by scanning electron microscope.

  15. Carboxyl-Functionalized Polymeric Microspheres Prepared by One-Stage Photoinitiated RAFT Dispersion Polymerization

    Directory of Open Access Journals (Sweden)

    Jianbo Tan

    2017-12-01

    Full Text Available Herein, we report a photoinitiated reversible addition-fragmentation chain transfer (RAFT dispersion copolymerization of methyl methacrylate (MMA and methyl methacrylic (MAA for the preparation of highly monodisperse carboxyl-functionalized polymeric microspheres. High rates of polymerization were observed, with more than 90% particle yields being achieved within 3 h of UV irradiation. Effects of reaction parameters (e.g., MAA concentration, RAFT agent concentration, photoinitiator concentration, and solvent composition were studied in detail, and highly monodisperse polymeric microspheres were obtained in most cases. Finally, silver (Ag composite microspheres were prepared by in situ reduction of AgNO3 using the carboxyl-functionalized polymeric microspheres as the template. The obtained Ag composite microspheres were able to catalyze the reduction of methylene blue (MB with NaBH4 as a reductant.

  16. Diatom-inspired templates for 3D replication: natural diatoms versus laser written artificial diatoms

    International Nuclear Information System (INIS)

    Belegratis, M R; Schmidt, V; Nees, D; Stadlober, B; Hartmann, P

    2014-01-01

    The diatoms are ubiquitous, exist in large numbers and show a great diversity of features on their porous silica structures. Therefore, they inspire the fabrication of nanostructured templates for nanoimprint processes (NIL), where large structured areas with nanometer precision are required. In this study, two approaches regarding the respective challenges and potential exploitations are followed and discussed: the first one takes advantage of a template that is directly made of natural occurring diatoms. Here, two replication steps via soft lithography are needed to obtain a template which is subsequently used for NIL. The second approach exploits the technical capabilities of the precise 3D laser lithography (3DLL) based on two-photon polymerization of organic materials. This method enables the fabrication of arbitrary artificial diatom-inspired micro- and nanostructures and the design of an inverse structure. Therefore, only one replication step is needed to obtain a template for NIL. In both approaches, a replication technique for true 3D structures is shown. (paper)

  17. Biochemical characterization of a recombinant Japanese encephalitis virus RNA-dependent RNA polymerase

    Directory of Open Access Journals (Sweden)

    Kim Chan-Mi

    2007-07-01

    Full Text Available Abstract Background Japanese encephalitis virus (JEV NS5 is a viral nonstructural protein that carries both methyltransferase and RNA-dependent RNA polymerase (RdRp domains. It is a key component of the viral RNA replicase complex that presumably includes other viral nonstructural and cellular proteins. The biochemical properties of JEV NS5 have not been characterized due to the lack of a robust in vitro RdRp assay system, and the molecular mechanisms for the initiation of RNA synthesis by JEV NS5 remain to be elucidated. Results To characterize the biochemical properties of JEV RdRp, we expressed in Escherichia coli and purified an enzymatically active full-length recombinant JEV NS5 protein with a hexahistidine tag at the N-terminus. The purified NS5 protein, but not the mutant NS5 protein with an Ala substitution at the first Asp of the RdRp-conserved GDD motif, exhibited template- and primer-dependent RNA synthesis activity using a poly(A RNA template. The NS5 protein was able to use both plus- and minus-strand 3'-untranslated regions of the JEV genome as templates in the absence of a primer, with the latter RNA being a better template. Analysis of the RNA synthesis initiation site using the 3'-end 83 nucleotides of the JEV genome as a minimal RNA template revealed that the NS5 protein specifically initiates RNA synthesis from an internal site, U81, at the two nucleotides upstream of the 3'-end of the template. Conclusion As a first step toward the understanding of the molecular mechanisms for JEV RNA replication and ultimately for the in vitro reconstitution of viral RNA replicase complex, we for the first time established an in vitro JEV RdRp assay system with a functional full-length recombinant JEV NS5 protein and characterized the mechanisms of RNA synthesis from nonviral and viral RNA templates. The full-length recombinant JEV NS5 will be useful for the elucidation of the structure-function relationship of this enzyme and for the

  18. Oligonucleotides as probes for studying polymerization reactions in dilute aqueous solution

    Science.gov (United States)

    Kolb, V.; Orgel, L. E.; Miller, S. L. (Principal Investigator)

    1994-01-01

    We have prepared a [32P]-labled oligonucleotide probe carrying a free primary amine at its 3'-terminus. This probe is used to initiate polymerization of aziridine (ethyleneimine) in aqueous solution. The nature of the oligomeric products and the kinetics of their formation are then monitored by gel electrophoresis. Our results are generally consistent with those obtained using conventional techniques. We have also investigated the effect of polyanionic templates on the rate of oligomerization of aziridine. We find that water-soluble polyanions generally accelerate the polymerization. The sodium salt of polymethacrylic acid is the most effective of the templates that we studied. The methods introduced in this paper should be applicable to a variety of polymerization reactions in aqueous solution. They should greatly simplify the screening of potentially prebiotic polymerization reactions.

  19. Functionalized ormosil scaffolds processed by direct laser polymerization for application in tissue engineering

    DEFF Research Database (Denmark)

    Matei, A.; Schou, Jørgen; Canulescu, Stela

    2013-01-01

    Synthesized N,N′-(methacryloyloxyethyl triehtoxy silyl propyl carbamoyl-oxyhexyl)-urea hybrid methacrylate was polymerized by direct laser polymerization using femtosecond laser pulses with the aim of using it for subsequent applications in tissue engineering. The as-obtained scaffolds were...

  20. A ribonuclease coordinates siRNA amplification and mRNA cleavage during RNAi.

    Science.gov (United States)

    Tsai, Hsin-Yue; Chen, Chun-Chieh G; Conte, Darryl; Moresco, James J; Chaves, Daniel A; Mitani, Shohei; Yates, John R; Tsai, Ming-Daw; Mello, Craig C

    2015-01-29

    Effective silencing by RNA-interference (RNAi) depends on mechanisms that amplify and propagate the silencing signal. In some organisms, small-interfering RNAs (siRNAs) are amplified from target mRNAs by RNA-dependent RNA polymerase (RdRP). Both RdRP recruitment and mRNA silencing require Argonaute proteins, which are generally thought to degrade RNAi targets by directly cleaving them. However, in C. elegans, the enzymatic activity of the primary Argonaute, RDE-1, is not required for silencing activity. We show that RDE-1 can instead recruit an endoribonuclease, RDE-8, to target RNA. RDE-8 can cleave RNA in vitro and is needed for the production of 3' uridylated fragments of target mRNA in vivo. We also find that RDE-8 promotes RdRP activity, thereby ensuring amplification of siRNAs. Together, our findings suggest a model in which RDE-8 cleaves target mRNAs to mediate silencing, while generating 3' uridylated mRNA fragments to serve as templates for the RdRP-directed amplification of the silencing signal. Copyright © 2015 Elsevier Inc. All rights reserved.

  1. In vitro synthesis of minus-strand RNA by an isolated cereal yellow dwarf virus RNA-dependent RNA polymerase requires VPg and a stem-loop structure at the 3' end of the virus RNA.

    Science.gov (United States)

    Osman, Toba A M; Coutts, Robert H A; Buck, Kenneth W

    2006-11-01

    Cereal yellow dwarf virus (CYDV) RNA has a 5'-terminal genome-linked protein (VPg). We have expressed the VPg region of the CYDV genome in bacteria and used the purified protein (bVPg) to raise an antiserum which was able to detect free VPg in extracts of CYDV-infected oat plants. A template-dependent RNA-dependent RNA polymerase (RdRp) has been produced from a CYDV membrane-bound RNA polymerase by treatment with BAL 31 nuclease. The RdRp was template specific, being able to utilize templates from CYDV plus- and minus-strand RNAs but not those of three unrelated viruses, Red clover necrotic mosaic virus, Cucumber mosaic virus, and Tobacco mosaic virus. RNA synthesis catalyzed by the RdRp required a 3'-terminal GU sequence and the presence of bVPg. Additionally, synthesis of minus-strand RNA on a plus-strand RNA template required the presence of a putative stem-loop structure near the 3' terminus of CYDV RNA. The base-paired stem, a single-nucleotide (A) bulge in the stem, and the sequence of a tetraloop were all required for the template activity. Evidence was produced showing that minus-strand synthesis in vitro was initiated by priming by bVPg at the 3' end of the template. The data are consistent with a model in which the RdRp binds to the stem-loop structure which positions the active site to recognize the 3'-terminal GU sequence for initiation of RNA synthesis by the addition of an A residue to VPg.

  2. Direct, rapid RNA sequence analysis

    International Nuclear Information System (INIS)

    Peattie, D.A.

    1987-01-01

    The original methods of RNA sequence analysis were based on enzymatic production and chromatographic separation of overlapping oligonucleotide fragments from within an RNA molecule followed by identification of the mononucleotides comprising the oligomer. Over the past decade the field of nucleic acid sequencing has changed dramatically, however, and RNA molecules now can be sequenced in a variety of more streamlined fashions. Most of the more recent advances in RNA sequencing have involved one-dimensional electrophoretic separation of 32 P-end-labeled oligoribonucleotides on polyacrylamide gels. In this chapter the author discusses two of these methods for determining the nucleotide sequences of RNA molecules rapidly: the chemical method and the enzymatic method. Both methods are direct and degradative, i.e., they rely on fragmatic and chemical approaches should be utilized. The single-strand-specific ribonucleases (A, T 1 , T 2 , and S 1 ) provide an efficient means to locate double-helical regions rapidly, and the chemical reactions provide a means to determine the RNA sequence within these regions. In addition, the chemical reactions allow one to assign interactions to specific atoms and to distinguish secondary interactions from tertiary ones. If the RNA molecule is small enough to be sequenced directly by the enzymatic or chemical method, the probing reactions can be done easily at the same time as sequencing reactions

  3. Direct RNA detection without nucleic acid purification and PCR: Combining sandwich hybridization with signal amplification based on branched hybridization chain reaction.

    Science.gov (United States)

    Xu, Yao; Zheng, Zhi

    2016-05-15

    We have developed a convenient, robust and low-cost RNA detection system suitable for high-throughput applications. This system uses a highly specific sandwich hybridization to capture target RNA directly onto solid support, followed by on-site signal amplification via 2-dimensional, branched hybridizing chain polymerization through toehold-mediated strand displacement reaction. The assay uses SYBR Green to detect targets at concentrations as low as 1 pM, without involving nucleic acid purification or any enzymatic reaction, using ordinary oligonucleotides without modification or labeling. The system was demonstrated in the detection of malaria RNA in blood and GAPDH gene expression in cell lysate. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. Mesoporous silicon oxide films and their uses as templates in obtaining nanostructured conductive polymers

    Science.gov (United States)

    Salgado, R.; Arteaga, G. C.; Arias, J. M.

    2018-04-01

    Obtaining conductive polymers (CPs) for the manufacture of OLEDs, solar cells, electrochromic devices, sensors, etc., has been possible through the use of electrochemical techniques that allow obtaining films of controlled thickness with positive results in different applications. Current trends point towards the manufacture of nanomaterials, and therefore it is necessary to develop methods that allow obtaining CPs with nanostructured morphology. This is possible by using a porous template to allow the growth of the polymeric materials. However, prior and subsequent treatments are required to separate the material from the template so that it can be evaluated in the applications mentioned above. This is why mesoporous silicon oxide films (template) are essential for the synthesis of nanostructured polymers since both the template and the polymer are obtained on the electrode surface, and therefore it is not necessary to separate the material from the template. Thus, the material can be evaluated directly in the applications mentioned above. The dimensions of the resulting nanostructures will depend on the power, time and technique used for electropolymerization as well as the monomer and the surfactant of the mesoporous film.

  5. Mutations in the RNA-binding domains of tombusvirus replicase proteins affect RNA recombination in vivo

    International Nuclear Information System (INIS)

    Panaviene, Zivile; Nagy, Peter D.

    2003-01-01

    RNA recombination, which is thought to occur due to replicase errors during viral replication, is one of the major driving forces of virus evolution. In this article, we show evidence that the replicase proteins of Cucumber necrosis virus, a tombusvirus, are directly involved in RNA recombination in vivo. Mutations within the RNA-binding domains of the replicase proteins affected the frequency of recombination observed with a prototypical defective-interfering (DI) RNA, a model template for recombination studies. Five of the 17 replicase mutants tested showed delay in the formation of recombinants when compared to the wild-type helper virus. Interestingly, two replicase mutants accelerated recombinant formation and, in addition, these mutants also increased the level of subgenomic RNA synthesis (Virology 308 (2003), 191-205). A trans-complementation system was used to demonstrate that mutation in the p33 replicase protein resulted in altered recombination rate. Isolated recombinants were mostly imprecise (nonhomologous), with the recombination sites clustered around a replication enhancer region and a putative cis-acting element, respectively. These RNA elements might facilitate the proposed template switching events by the tombusvirus replicase. Together with data in the article cited above, results presented here firmly establish that the conserved RNA-binding motif of the replicase proteins is involved in RNA replication, subgenomic RNA synthesis, and RNA recombination

  6. Cystoviral polymerase complex protein P7 uses its acidic C-terminal tail to regulate the RNA-directed RNA polymerase P2.

    Science.gov (United States)

    Alphonse, Sébastien; Arnold, Jamie J; Bhattacharya, Shibani; Wang, Hsin; Kloss, Brian; Cameron, Craig E; Ghose, Ranajeet

    2014-07-15

    In bacteriophages of the cystovirus family, the polymerase complex (PX) encodes a 75-kDa RNA-directed RNA polymerase (P2) that transcribes the double-stranded RNA genome. Also a constituent of the PX is the essential protein P7 that, in addition to accelerating PX assembly and facilitating genome packaging, plays a regulatory role in transcription. Deletion of P7 from the PX leads to aberrant plus-strand synthesis suggesting its influence on the transcriptase activity of P2. Here, using solution NMR techniques and the P2 and P7 proteins from cystovirus ϕ12, we demonstrate their largely electrostatic interaction in vitro. Chemical shift perturbations on P7 in the presence of P2 suggest that this interaction involves the dynamic C-terminal tail of P7, more specifically an acidic cluster therein. Patterns of chemical shift changes induced on P2 by the P7 C-terminus resemble those seen in the presence of single-stranded RNA suggesting similarities in binding. This association between P2 and P7 reduces the affinity of the former toward template RNA and results in its decreased activity both in de novo RNA synthesis and in extending a short primer. Given the presence of C-terminal acidic tracts on all cystoviral P7 proteins, the electrostatic nature of the P2/P7 interaction is likely conserved within the family and could constitute a mechanism through which P7 regulates transcription in cystoviruses. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Preparation of interconnected highly porous polymeric structures by a replication and freeze-drying process

    NARCIS (Netherlands)

    Hou, Q.; Grijpma, Dirk W.; Feijen, Jan

    2003-01-01

    Three-dimensional degradable porous polymeric structures with high porosities (93-98%) and well-interconnected pore networks have been prepared by freeze-drying polymer solutions in the presence of a leachable template followed by leaching of the template. Templates of the pore network were prepared

  8. Structure and morphology of magnetron sputter deposited ultrathin ZnO films on confined polymeric template

    Science.gov (United States)

    Singh, Ajaib; Schipmann, Susanne; Mathur, Aakash; Pal, Dipayan; Sengupta, Amartya; Klemradt, Uwe; Chattopadhyay, Sudeshna

    2017-08-01

    The structure and morphology of ultra-thin zinc oxide (ZnO) films with different film thicknesses on confined polymer template were studied through X-ray reflectivity (XRR) and grazing incidence small angle X-ray scattering (GISAXS). Using magnetron sputter deposition technique ZnO thin films with different film thicknesses (weight of polystyrene). The detailed internal structure, along the surface/interfaces and the growth direction of the system were explored in this study, which provides insight into the growth procedure of ZnO on confined polymer and reveals that a thin layer of ZnO, with very low surface and interface roughness, can be grown by DC magnetron sputtering technique, with approximately full coverage (with bulk like electron density) even in nm order of thickness, in 2-7 nm range on confined polymer template, without disturbing the structure of the underneath template. The resulting ZnO-polystyrene hybrid systems show strong ZnO near band edge (NBE) and deep-level (DLE) emissions in their room temperature photoluminescence spectra, where the contribution of DLE gets relatively stronger with decreasing ZnO film thickness, indicating a significant enhancement of surface defects because of the greater surface to volume ratio in thinner films.

  9. Nucleolin Mediates MicroRNA-directed CSF-1 mRNA Deadenylation but Increases Translation of CSF-1 mRNA*

    Science.gov (United States)

    Woo, Ho-Hyung; Baker, Terri; Laszlo, Csaba; Chambers, Setsuko K.

    2013-01-01

    CSF-1 mRNA 3′UTR contains multiple unique motifs, including a common microRNA (miRNA) target in close proximity to a noncanonical G-quadruplex and AU-rich elements (AREs). Using a luciferase reporter system fused to CSF-1 mRNA 3′UTR, disruption of the miRNA target region, G-quadruplex, and AREs together dramatically increased reporter RNA levels, suggesting important roles for these cis-acting regulatory elements in the down-regulation of CSF-1 mRNA. We find that nucleolin, which binds both G-quadruplex and AREs, enhances deadenylation of CSF-1 mRNA, promoting CSF-1 mRNA decay, while having the capacity to increase translation of CSF-1 mRNA. Through interaction with the CSF-1 3′UTR miRNA common target, we find that miR-130a and miR-301a inhibit CSF-1 expression by enhancing mRNA decay. Silencing of nucleolin prevents the miRNA-directed mRNA decay, indicating a requirement for nucleolin in miRNA activity on CSF-1 mRNA. Downstream effects followed by miR-130a and miR-301a inhibition of directed cellular motility of ovarian cancer cells were found to be dependent on nucleolin. The paradoxical effects of nucleolin on miRNA-directed CSF-1 mRNA deadenylation and on translational activation were explored further. The nucleolin protein contains four acidic stretches, four RNA recognition motifs (RRMs), and nine RGG repeats. All three domains in nucleolin regulate CSF-1 mRNA and protein levels. RRMs increase CSF-1 mRNA, whereas the acidic and RGG domains decrease CSF-1 protein levels. This suggests that nucleolin has the capacity to differentially regulate both CSF-1 RNA and protein levels. Our finding that nucleolin interacts with Ago2 indirectly via RNA and with poly(A)-binding protein C (PABPC) directly suggests a nucleolin-Ago2-PABPC complex formation on mRNA. This complex is in keeping with our suggestion that nucleolin may work with PABPC as a double-edged sword on both mRNA deadenylation and translational activation. Our findings underscore the complexity of

  10. Surface engineering: molecularly imprinted affinity membranes by photograft polymerization

    Science.gov (United States)

    Matuschewski, Heike; Sergeyeva, Tatiana A.; Bendig, Juergen; Piletsky, Sergey A.; Ulbricht, Matthies; Schedler, Uwe

    2001-02-01

    Commercial polymer microfiltration membranes were surface-modified with a graft copolymer of a functional monomer and a crosslinker in the presence of a template (triazine-herbicide). As result, membranes covered with a thin layer of imprinted polymer (MIP) selective to the template were obtained. The influence of the polymerization conditions on membrane recognition properties was studied by membranes

  11. DNA template dependent accuracy variation of nucleotide selection in transcription.

    Directory of Open Access Journals (Sweden)

    Harriet Mellenius

    Full Text Available It has been commonly assumed that the effect of erroneous transcription of DNA genes into messenger RNAs on peptide sequence errors are masked by much more frequent errors of mRNA translation to protein. We present a theoretical model of transcriptional accuracy. It uses experimentally estimated standard free energies of double-stranded DNA and RNA/DNA hybrids and predicts a DNA template dependent transcriptional accuracy variation spanning several orders of magnitude. The model also identifies high-error as well a high-accuracy transcription motifs. The source of the large accuracy span is the context dependent variation of the stacking free energy of pairs of correct and incorrect base pairs in the ever moving transcription bubble. Our model predictions have direct experimental support from recent single molecule based identifications of transcriptional errors in the C. elegans transcriptome. Our conclusions challenge the general view that amino acid substitution errors in proteins are mainly caused by translational errors. It suggests instead that transcriptional error hotspots are the dominating source of peptide sequence errors in some DNA template contexts, while mRNA translation is the major cause of protein errors in other contexts.

  12. Investigation of magnetic nanoparticles in acrylonitrile-methyl methacrylate-divinylbenzene mesoporous template

    Energy Technology Data Exchange (ETDEWEB)

    Rabelo, D. E-mail: denilson@quimica.ufg.br; Lima, E.C.D.; Barbosa, D.P.; Silva, V.J.; Silva, O.; Azevedo, R.B.; Silva, L.P.; Lemos, A.P.C.; Morais, P.C

    2002-11-01

    Preparation and characterization of nanosized magnetic particles using alkaline oxidation of ferrous ion retained in acrylonitrile-methyl methacrylate-divinylbenzene (AN-MMA-DVB) spherical micron-sized polymer template is described. Atomic absorption, transmission electron microscopy and magnetic resonance were used to investigate chemically cycled nanoparticle-based composites. The resonance field shifts towards higher values as the nanoparticle concentration reduces in the polymeric template, following two very distinct regimes.

  13. RNA-Catalyzed Polymerization and Replication of RNA

    Science.gov (United States)

    Horning, D. P.; Samantha, B.; Tjhung, K. F.; Joyce, G. F.

    2017-07-01

    In an effort to reconstruct RNA-based life, in vitro evolution was used to obtain an RNA polymerase ribozyme that can synthesize a variety of complex functional RNAs and can catalyze the exponential amplification of short RNAs.

  14. Fabrication of periodic arrays of metallic nanoparticles by block copolymer templates on HfO_2 substrates

    International Nuclear Information System (INIS)

    Frascaroli, Jacopo; Seguini, Gabriele; Spiga, Sabina; Perego, Michele; Boarino, Luca

    2015-01-01

    Block copolymer-based templates can be exploited for the fabrication of ordered arrays of metal nanoparticles (NPs) with a diameter down to a few nanometers. In order to develop this technique on metal oxide substrates, we studied the self-assembly of polymeric templates directly on the HfO_2 surface. Using a random copolymer neutralization layer, we obtained an effective HfO_2 surface neutralization, while the effects of surface cleaning and annealing temperature were carefully examined. Varying the block copolymer molecular weight, we produced regular nanoporous templates with feature size variable between 10 and 30 nm and a density up to 1.5 × 10"1"1 cm"−"2. With the adoption of a pattern transfer process, we produced ordered arrays of Pt and Pt/Ti NPs with diameters of 12, 21 and 29 nm and a constant size dispersion (σ) of 2.5 nm. For the smallest template adopted, the NP diameter is significantly lower than the original template dimension. In this specific configuration, the granularity of the deposited film probably influences the pattern transfer process and very small NPs of 12 nm were achieved without a significant broadening of the size distribution. (paper)

  15. Polymeric hydrogels for burn wound care: Advanced skin wound dressings and regenerative templates.

    Science.gov (United States)

    Madaghiele, Marta; Demitri, Christian; Sannino, Alessandro; Ambrosio, Luigi

    2014-01-01

    Wound closure represents a primary goal in the treatment of very deep and/or large wounds, for which the mortality rate is particularly high. However, the spontaneous healing of adult skin eventually results in the formation of epithelialized scar and scar contracture (repair), which might distort the tissues and cause lifelong deformities and disabilities. This clinical evidence suggests that wound closure attained by means of skin regeneration, instead of repair, should be the true goal of burn wound management. The traditional concept of temporary wound dressings, able to stimulate skin healing by repair, is thus being increasingly replaced by the idea of temporary scaffolds, or regenerative templates, able to promote healing by regeneration. As wound dressings, polymeric hydrogels provide an ideal moisture environment for healing while protecting the wound, with the additional advantage of being comfortable to the patient, due to their cooling effect and non-adhesiveness to the wound tissue. More importantly, recent advances in regenerative medicine demonstrate that bioactive hydrogels can be properly designed to induce at least partial skin regeneration in vivo. The aim of this review is to provide a concise insight on the key properties of hydrogels for skin healing and regeneration, particularly highlighting the emerging role of hydrogels as next generation skin substitutes for the treatment of full-thickness burns.

  16. Polymeric hydrogels for burn wound care: Advanced skin wound dressings and regenerative templates

    Directory of Open Access Journals (Sweden)

    Marta Madaghiele

    2014-10-01

    Full Text Available Wound closure represents a primary goal in the treatment of very deep and/or large wounds, for which the mortality rate is particularly high. However, the spontaneous healing of adult skin eventually results in the formation of epithelialized scar and scar contracture (repair, which might distort the tissues and cause lifelong deformities and disabilities. This clinical evidence suggests that wound closure attained by means of skin regeneration, instead of repair, should be the true goal of burn wound management. The traditional concept of temporary wound dressings, able to stimulate skin healing by repair, is thus being increasingly replaced by the idea of temporary scaffolds, or regenerative templates, able to promote healing by regeneration. As wound dressings, polymeric hydrogels provide an ideal moisture environment for healing while protecting the wound, with the additional advantage of being comfortable to the patient, due to their cooling effect and non-adhesiveness to the wound tissue. More importantly, recent advances in regenerative medicine demonstrate that bioactive hydrogels can be properly designed to induce at least partial skin regeneration in vivo. The aim of this review is to provide a concise insight on the key properties of hydrogels for skin healing and regeneration, particularly highlighting the emerging role of hydrogels as next generation skin substitutes for the treatment of full-thickness burns.

  17. Enzymatic activities of the GB virus-B RNA-dependent RNA polymerase

    International Nuclear Information System (INIS)

    Ranjith-Kumar, C.T.; Santos, Jan Lee; Gutshall, Lester L.; Johnston, Victor K.; Juili, L.-G.; Kim, M.-J.; Porter, David J.; Maley, Derrick; Greenwood, Cathy; Earnshaw, David L.; Baker, Audrey; Gu Baohua; Silverman, Carol; Sarisky, Robert T.; Kao Cheng

    2003-01-01

    The GB virus-B (GBV-B) nonstructural protein 5B (NS5B) encodes an RNA-dependent RNA polymerase (RdRp) with greater than 50% sequence similarity to the hepatitis C virus (HCV) NS5B. Recombinant GBV-B NS5B was reported to possess RdRp activity (W. Zhong et al., 2000, J. Viral Hepat. 7, 335-342). In this study, the GBV-B RdRp was examined more thoroughly for different RNA synthesis activities, including primer-extension, de novo initiation, template switch, terminal nucleotide addition, and template specificity. The results can be compared with previous characterizations of the HCV RdRp. The two RdRps share similarities in terms of metal ion and template preference, the abilities to add nontemplated nucleotides, perform both de novo initiation and extension from a primer, and switch templates. However, several differences in RNA synthesis between the GBV-B and HCV RdRps were observed, including (i) optimal temperatures for activity, (ii) ranges of Mn 2+ concentration tolerated for activity, and (iii) cation requirements for de novo RNA synthesis and terminal transferase activity. To assess whether the recombinant GBV-B RdRp may represent a relevant surrogate system for testing HCV antiviral agents, two compounds demonstrated to be active at nanomolar concentrations against HCV NS5B were tested on the GBV RdRp. A chain terminating nucleotide analog could prevent RNA synthesis, while a nonnucleoside HCV inhibitor was unable to affect RNA synthesis by the GBV RdRp

  18. Synthesis of functional polypyrrole/prussian blue and polypyrrole/Ag composite microtubes by using a reactive template

    Energy Technology Data Exchange (ETDEWEB)

    Feng Xiaomiao; Sun Zhengzong; Hou Wenhua; Zhu Junjie [Key Laboratory of Mesoscopic Chemistry, Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093 (China)

    2007-05-16

    Polypyrrole (PPy)/PB and PPy/Ag composite microtubes were synthesized in one pot by using methyl orange (MO) as a reactive self-degraded template. In contrast to reported conventional template approaches, the MO template did not need to be removed after polymerization. The formation mechanism, structural characteristics, conductivity, and electrochemical properties of the obtained PPy/PB and PPy/Ag microtubes are reported.

  19. Synthesis of functional polypyrrole/prussian blue and polypyrrole/Ag composite microtubes by using a reactive template

    International Nuclear Information System (INIS)

    Feng Xiaomiao; Sun Zhengzong; Hou Wenhua; Zhu Junjie

    2007-01-01

    Polypyrrole (PPy)/PB and PPy/Ag composite microtubes were synthesized in one pot by using methyl orange (MO) as a reactive self-degraded template. In contrast to reported conventional template approaches, the MO template did not need to be removed after polymerization. The formation mechanism, structural characteristics, conductivity, and electrochemical properties of the obtained PPy/PB and PPy/Ag microtubes are reported

  20. Facile Fabrication of Uniform Polyaniline Nanotubes with Tubular Aluminosilicates as Templates

    OpenAIRE

    Zhang, Long; Liu, Peng

    2008-01-01

    AbstractThe uniform polyaniline (PANI) nanotubes, with inner diameter, outer diameter, and tubular thickness of 40, 60, and 10 nm, respectively, were prepared successfully by using natural tubular aluminosilicates as templates. The halloysite nanotubes were coated with PANI via the in situ chemical oxidation polymerization. Then the templates were etched with HCl/HF solution. The PANI nanotubes were characterized using FTIR, X-ray diffraction, and transmission electron microscopy. The conduct...

  1. pEVL: A Linear Plasmid for Generating mRNA IVT Templates With Extended Encoded Poly(A Sequences

    Directory of Open Access Journals (Sweden)

    Alexandra E Grier

    2016-01-01

    Full Text Available Increasing demand for large-scale synthesis of in vitro transcribed (IVT mRNA is being driven by the increasing use of mRNA for transient gene expression in cell engineering and therapeutic applications. An important determinant of IVT mRNA potency is the 3′ polyadenosine (poly(A tail, the length of which correlates with translational efficiency. However, present methods for generation of IVT mRNA rely on templates derived from circular plasmids or PCR products, in which homopolymeric tracts are unstable, thus limiting encoded poly(A tail lengths to ≃120 base pairs (bp. Here, we have developed a novel method for generation of extended poly(A tracts using a previously described linear plasmid system, pJazz. We find that linear plasmids can successfully propagate poly(A tracts up to ≃500 bp in length for IVT mRNA production. We then modified pJazz by removing extraneous restriction sites, adding a T7 promoter sequence upstream from an extended multiple cloning site, and adding a unique type-IIS restriction site downstream from the encoded poly(A tract to facilitate generation of IVT mRNA with precisely defined encoded poly(A tracts and 3′ termini. The resulting plasmid, designated pEVL, can be used to generate IVT mRNA with consistent defined lengths and terminal residue(s.

  2. Polymeric flat focal field arrayed waveguide grating using electron-beam direct writing

    Science.gov (United States)

    Lu, Si; Yan, Yingbai; Jin, Guofan; Wong, W. H.; Pun, E. Y. B.

    2004-06-01

    A four-channel 400-GHz spacing flat focal field arrayed waveguide grating (AWG) demultiplexer is designed based on polymeric optical waveguide. The waveguide core-layer material is a newly developed negative tone epoxy Novolak resin (ENR) polymer with ultravoilet (UV) cured resin Norland optical adhesive 61 (NOA61) as the cladding layer. The device is fabricated using electron-beam direct writing, which has less processing steps than the reported polymeric AWGs. The experimental result is presented.

  3. Preparation of poly (alkylcyanoacrylate) nanoparticles by polymerization of water-free microemulsions

    DEFF Research Database (Denmark)

    Krauel, Karen; Graf, Anja; Hook, Sarah M

    2006-01-01

    designated as droplet, bicontinuous or solution type microemulsions using conductivity, viscosity and self-diffusion NMR. Nanoparticles were prepared by polymerization of selected microemulsions with ethyl-2-cyanoacrylate and the morphology of the particles was investigated. Addition of monomer to all types...... that polymerization is expected to occur at a water-oil interface by base-catalysed polymerization. It would appear that propylene glycol is sufficiently nucleophilic to initiate the polymerization. The use of water-free microemulsions as templates for the preparation of poly (alkylcyanoacrylate) nanoparticles opens...

  4. RNA Interference - Towards RNA becoming a Medicine -42 ...

    Indian Academy of Sciences (India)

    research. A brief history of the development ofRNAi is shown in. Box 2. Mechanism of ... new RNA strand using target RNA as the template and thereby converting it ... thought to excise precursor stRNA from their -70 nt stem loop precursor to ...

  5. Directed Self-assembly of Block Copolymer with Sub-15 nm Domain Spacing Using Nanoimprinted Photoresist Templates

    Science.gov (United States)

    Sun, Zhiwei; Chen, Zhenbin; Zhang, Wenxu; Coughlin, E. Bryan; Xiao, Shuaigang; Russell, Thomas

    There has been increasing interest in preparing block copolymer thin films with ultra-small domain spacings for use as etching masks for ultra-high resolution nanolithography. One method to prepare block copolymer materials with small feature sizes is salt doping, increasing the Flory-Huggins interaction and allowing microphase separation to be maintained at lower molecular weights. Lamellae-forming P2VP- b-PS- b-P2VP block copolymer with various molecular weight was synthesized using RAFT polymerization with a dual functional chain transfer agent. Copper (II) Chloride or Gold (III) chloride was found to be selectively associated with P2VP block and increase the unfavorable interactions between PS and P2VP blocks, driving the disordered block copolymer into the ordered state. A 14 nm lamellar spacing of P2VP- b-PS- b-P2VP thin film was prepared using copper (II) Chloride doping after acetone vapor annealing on neutral brushes. Metallic nano-wire arrays were prepared after selective infiltration of platinum salt into the P2VP domain and oxygen plasma treatment. The directed self-assembly of salt doped P2VP- b-PS- b-P2VP triblock copolymer having long-rang lateral order on nanoimprinted photoresist templates with shallow trenches was also studied.

  6. Template-Directed Ligation of Peptides to Oligonucleotides

    Science.gov (United States)

    Bruick, Richard K.; Dawson, Philip E.; Kent, Stephen BH; Usman, Nassim; Joyce, Gerald F.

    1996-01-01

    Synthetic oligonucleotides and peptides have enjoyed a wide range of applications in both biology and chemistry. As a consequence, oligonucleotide-peptide conjugates have received considerable attention, most notably in the development of antisense constructs with improved pharmacological properties. In addition, oligonucleotide-peptide conjugates have been used as molecular tags, in the assembly of supramolecular arrays and in the construction of encoded combinatorial libraries. To make these chimeric molecules more accessible for a broad range of investigations, we sought to develop a facile method for joining fully deprotected oligonucleotides and peptides through a stable amide bond linkage. Furthermore, we wished to make this ligation reaction addressable, enabling one to direct the ligation of specific oligonucleotide and peptide components.To confer specificity and accelerate the rate of the reaction, the ligation process was designed to be dependent on the presence of a complementary oligonucleotide template.

  7. Laser-ignited frontal polymerization of shape-controllable poly(VI-co-AM) hydrogels based on 3D templates toward adsorption of heavy metal ions

    Science.gov (United States)

    Fan, Suzhen; Liu, Sisi; Wang, Xiao-Qiao; Wang, Cai-Feng; Chen, Su

    2016-06-01

    Given the increasing heavy metal pollution issue, fast preparation of polymeric hydrogels with excellent adsorption property toward heavy metal ions is very attractive. In this work, a series of poly( N-vinylimidazole-co-acrylamide) (poly(VI-co-AM)) hydrogels were synthesized via laser-ignited frontal polymerization (LIFP) for the first time. The dependence of frontal velocity and temperature on two factors monomer ratios and initiator concentrations was systematically investigated. Poly(VI-co-AM) hydrogels with any self-supporting shapes can be synthesized by a one-step LIFP in seconds through the application of 3D templates. These shape-persistent hydrogels are pH-responsive and exhibit excellent adsorption/desorption characteristics toward Mn(II), Zn(II), Cd(II), Ni(II), Cu(II) and Co(II) ions, and the adsorption conformed to the pseudo-second-order kinetic model. The reusability of the hydrogels toward mental ions adsorption was further researched, which suggested that the hydrogels can be reused without serious decrease in adsorption capacity. This work might open a promising strategy to facilely prepare shape-controllable hydrogels and expand the application of LIFP.

  8. MicroRNA-directed siRNA biogenesis in Caenorhabditis elegans.

    Science.gov (United States)

    Corrêa, Régis L; Steiner, Florian A; Berezikov, Eugene; Ketting, René F

    2010-04-08

    RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi-related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer.

  9. Plasma-assisted quartz-to-quartz direct bonding for the fabrication of a multilayered quartz template for nanoimprint lithography

    International Nuclear Information System (INIS)

    Lee, Jihye; Ali, Altun; Kim, Ki-don; Choi, Dae-guen; Choi, Jun-Hyuk; Jeong, Jun-ho; Kim, Jae-Hyun

    2010-01-01

    In this paper, a low-temperature plasma-assisted process is developed to realize a uniform, ultraviolet (UV) transparent and chemically inert quartz-to-quartz direct bonding. Two sets of pretests are performed in order to understand how the bond surface energy changes with the plasma exposure time and the wet etching of quartz, respectively. The developed technique is used to fabricate a multilayered quartz template for UV nanoimprint lithography (UV-NIL). The multilayered quartz template is fabricated by bonding a square piece of a standard quartz wafer, which is about 625 µm in thickness, to a wet-etched 6.35 mm thick quartz photomask plate. A fabricated multilayered template is loaded to the commercial UV-NIL tool Imprio(TM) 100, and NIL was performed successfully. The developed direct bonding technique makes it possible for standard quartz wafers, which are compatible with high-resolution semiconductor fabrication processes, to be utilized as the templates in commercial UV-NIL machines with enhanced mechanical stability.

  10. Molecularly Imprinted Microrods via Mesophase Polymerization.

    Science.gov (United States)

    Parisi, Ortensia Ilaria; Scrivano, Luca; Candamano, Sebastiano; Ruffo, Mariarosa; Vattimo, Anna Francesca; Spanedda, Maria Vittoria; Puoci, Francesco

    2017-12-28

    The aim of the present research work was the synthesis of molecularly imprinted polymers (MIPs) with a rod-like geometry via "mesophase polymerization". The ternary lyotropic system consisting of sodium dodecyl sulfate (SDS), water, and decanol was chosen to prepare a hexagonal mesophase to direct the morphology of the synthesized imprinted polymers using theophylline, methacrylic acid, and ethylene glycol dimethacrylate as a drug model template, a functional monomer, and a crosslinker, respectively. The obtained molecularly imprinted microrods (MIMs) were assessed by performing binding experiments and in vitro release studies, and the obtained results highlighted good selective recognition abilities and sustained release properties. In conclusion, the adopted synthetic strategy involving a lyotropic mesophase system allows for the preparation of effective MIPs characterized by a rod-like morphology.

  11. Dual soft-template system based on colloidal chemistry for the synthesis of hollow mesoporous silica nanoparticles.

    Science.gov (United States)

    Li, Yunqi; Bastakoti, Bishnu Prasad; Imura, Masataka; Tang, Jing; Aldalbahi, Ali; Torad, Nagy L; Yamauchi, Yusuke

    2015-04-20

    A new dual soft-template system comprising the asymmetric triblock copolymer poly(styrene-b-2-vinyl pyridine-b-ethylene oxide) (PS-b-P2VP-b-PEO) and the cationic surfactant cetyltrimethylammonium bromide (CTAB) is used to synthesize hollow mesoporous silica (HMS) nanoparticles with a center void of around 17 nm. The stable PS-b-P2VP-b-PEO polymeric micelle serves as a template to form the hollow interior, while the CTAB surfactant serves as a template to form mesopores in the shells. The P2VP blocks on the polymeric micelles can interact with positively charged CTA(+) ions via negatively charged hydrolyzed silica species. Thus, dual soft-templates clearly have different roles for the preparation of the HMS nanoparticles. Interestingly, the thicknesses of the mesoporous shell are tunable by varying the amounts of TEOS and CTAB. This study provides new insight on the preparation of mesoporous materials based on colloidal chemistry. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  12. Ribosomal synthesis of polylysine from individual lysyl-tRNA/sup Lys/ in the absence of a template

    International Nuclear Information System (INIS)

    Yusupova, G.Z.; Remme, Y.L.; Belitsina, N.B.; Spirin, A.S.

    1987-01-01

    Earlier studies showed that ribosomes of Escherichia coli, in the absence of a template, can synthesize oligolysine, using lysyl-tRNA as a substrate. The authors present results on the use of preparations of individual lysyl-tRNA/sup Lys/ and phenylalanyl-tRNA/sup Phe/ in a system of templateless peptide synthesis. For these studies, the authors used ribosomes of E. coli MRE 600, washed four times with 1 M NH 4 Cl with 10 MM MgCl 2 . The purified ribosomes were stored at -70 0 C in standard buffer, containing 20 mM Tris-HCl, 100 mM NH 4 Cl, 10 mM MgCl 2 , 0.1 mM ethylenediamine tetraacetate (EDTA), and 10% glycerin, pH/sub 37 0 C/7.6. A preparation of [ 14 C]lysyl-tRNA/sup Lys/ was produced by affinity chromatography on immobilized factor EF-T/sub u/ from Thermus thermophilus HB8. The elongation factor EF-T/sub u/ from T. thermophilus and immobilized on BrCN-activated Sepharose 4B. The initial preparation of total tRNA of E. coli, enzymatically acylated by [ 14 C]lysine (348 Ci/mole, Amersham), was produced as described earlier. The degree of aminoacylation was 52-59 pmoles [ 14 C]lysine per unit of A 260 of tRNA

  13. The Surface Imprinted Polystyrene Beads Prepared via Emulsion Templates

    Institute of Scientific and Technical Information of China (English)

    Guo Xiang CHENG; Guang Ling PEI; Ling Gang ZENG; Li Yong ZHANG; Chao LIU

    2004-01-01

    In this paper, the surface imprinted cross-linked polystyrene beads were prepared via suspension polymerization with styrene (St), divinylbezene (DVB), polyvinyl alcohol (PVA1788), the mixture of Span 85 and xylene or the mixture of Span 85 and paraffin as monomer, cross-linking agent, dispersion stabilizer and templates, respectively. The results indicate that there are dense cavities on the surface of beads, and the diameter and density of cavity are related with the composition and amount of emulsion template. The forming mechanism of cavity from thermodynamics and dynamics was proposed.

  14. Fabrication and manipulation of polymeric magnetic particles with magnetorheological fluid

    International Nuclear Information System (INIS)

    Rodríguez-López, Jaime; Shum, Ho Cheung; Elvira, Luis; Montero de Espinosa, Francisco; Weitz, David A.

    2013-01-01

    Polymeric magnetic microparticles have been created using a microfluidic device via ultraviolet (UV) polymerization of double emulsions, resulting in cores of magnetorheological (MR) fluids surrounded by polymeric shells. We demonstrate that the resultant particles can be manipulated magnetically to achieve triggered rupture of the capsules. This illustrates the great potential of our capsules for triggered release of active ingredients encapsulated in the polymeric magnetic microparticles. - Highlights: ► Polymeric microparticles encapsulating MR fluids have been fabricated. ► A double-emulsion-templated approach using microfluidic techniques has been used. ► The monodisperse microparticles obtained are easily manipulated under magnetic field. ► These microparticles have great potential for encapsulation-and-release applications.

  15. Template-directed ligation of tethered mononucleotides by t4 DNA ligase for kinase ribozyme selection.

    Directory of Open Access Journals (Sweden)

    David G Nickens

    Full Text Available BACKGROUND: In vitro selection of kinase ribozymes for small molecule metabolites, such as free nucleosides, will require partition systems that discriminate active from inactive RNA species. While nucleic acid catalysis of phosphoryl transfer is well established for phosphorylation of 5' or 2' OH of oligonucleotide substrates, phosphorylation of diffusible small molecules has not been demonstrated. METHODOLOGY/PRINCIPAL FINDINGS: This study demonstrates the ability of T4 DNA ligase to capture RNA strands in which a tethered monodeoxynucleoside has acquired a 5' phosphate. The ligation reaction therefore mimics the partition step of a selection for nucleoside kinase (deoxyribozymes. Ligation with tethered substrates was considerably slower than with nicked, fully duplex DNA, even though the deoxynucleotides at the ligation junction were Watson-Crick base paired in the tethered substrate. Ligation increased markedly when the bridging template strand contained unpaired spacer nucleotides across from the flexible tether, according to the trends: A(2>A(1>A(3>A(4>A(0>A(6>A(8>A(10 and T(2>T(3>T(4>T(6 approximately T(1>T(8>T(10. Bridging T's generally gave higher yield of ligated product than bridging A's. ATP concentrations above 33 microM accumulated adenylated intermediate and decreased yields of the gap-sealed product, likely due to re-adenylation of dissociated enzyme. Under optimized conditions, T4 DNA ligase efficiently (>90% joined a correctly paired, or TratioG wobble-paired, substrate on the 3' side of the ligation junction while discriminating approximately 100-fold against most mispaired substrates. Tethered dC and dG gave the highest ligation rates and yields, followed by tethered deoxyinosine (dI and dT, with the slowest reactions for tethered dA. The same kinetic trends were observed in ligase-mediated capture in complex reaction mixtures with multiple substrates. The "universal" analog 5-nitroindole (dNI did not support ligation when

  16. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.

    Science.gov (United States)

    Schneider, Dominik; Wemheuer, Franziska; Pfeiffer, Birgit; Wemheuer, Bernd

    2017-01-01

    Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.

  17. RNA-Based Vaccines in Cancer Immunotherapy

    Directory of Open Access Journals (Sweden)

    Megan A. McNamara

    2015-01-01

    Full Text Available RNA vaccines traditionally consist of messenger RNA synthesized by in vitro transcription using a bacteriophage RNA polymerase and template DNA that encodes the antigen(s of interest. Once administered and internalized by host cells, the mRNA transcripts are translated directly in the cytoplasm and then the resulting antigens are presented to antigen presenting cells to stimulate an immune response. Alternatively, dendritic cells can be loaded with either tumor associated antigen mRNA or total tumor RNA and delivered to the host to elicit a specific immune response. In this review, we will explain why RNA vaccines represent an attractive platform for cancer immunotherapy, discuss modifications to RNA structure that have been developed to optimize mRNA vaccine stability and translational efficiency, and describe strategies for nonviral delivery of mRNA vaccines, highlighting key preclinical and clinical data related to cancer immunotherapy.

  18. Template-directed synthesis of oligoguanylic acids - Metal ion catalysis

    Science.gov (United States)

    Bridson, P. K.; Fakhrai, H.; Lohrmann, R.; Orgel, L. E.; Van Roode, M.

    1981-01-01

    The effects of Zn(2+), Pb(2+) and other metal ions on the efficiency and stereo-selectivity of the template-directed oligomerization of guanosine 5'-phosphorimidazolide are investigated. Reactions were run in the presence of a polyC template in a 2,6-lutidine buffer, and products analyzed by high-performance liquid chromatography on an RPC-5 column. The presence of the Pb(2+) ion is found to lead to the formation of 2'-5' linked oligomers up to the 40-mer, while Zn(2+) favors the formation of predominantly 3'-5' linked oligomers up to the 35-mer. When amounts of uracil, cytidine or adenosine 5'-phosphorimidazole equal to those of the guanosine derivative are included in the reaction mixture, the incorrect base is incorporated into the oligomer about 10% of the time with a Pb(2+) catalyst, but less than 0.5% of the time with Zn(2+). The Sn(2+), Sb(3+) and Bi(3+) ions are also found to promote the formation of 2'-5' oligomers, although not as effectively as Pb(2+), while no metal ions other than Zn(2+) promote the formation of the 3'-5' oligomers. The results may be important for the understanding of the evolution of nucleic acid replication in the absence of enzymes.

  19. RNA-directed DNA methylation: Mechanisms and functions

    KAUST Repository

    Mahfouz, Magdy M.

    2010-01-01

    Epigenetic RNA based gene silencing mechanisms play a major role in genome stability and control of gene expression. Transcriptional gene silencing via RNA-directed DNA methylation (RdDM) guides the epigenetic regulation of the genome in response

  20. Creating Metamaterial Building Blocks with Directed Photochemical Metallization of Silver onto DNA Origami Templates.

    Science.gov (United States)

    Hossen, Md Mir; Bendickson, Lee; Palo, Pierre; Yao, Zhiqi; Nilsen-Hamilton, Marit; Hillier, Andrew C

    2018-06-07

    DNA origami can be used to create a variety of complex and geometrically unique nanostructures that can be further modified to produce building blocks for applications such as in optical metamaterials. We describe a method for creating metal-coated nanostructures using DNA origami templates and a photochemical metallization technique. Triangular DNA origami were fabricated and coated with a thin metal layer by photochemical silver reduction while either in solution or supported on a surface. The DNA origami template serves as a localized photosensitizer to facilitate reduction of silver ions directly from solution onto the DNA surface. The metallizing process is shown to result in a conformal metal coating, which grows in height to a self-limiting value with increasing photoreduction steps. Although this coating process results in a slight decrease in the triangle dimensions, the overall template shape is retained. Notably, this coating method exhibits characteristics of self-limiting and defect-filling growth, which results in a metal nanostructure that maps the shape of the original origami template with a continuous and uniform metal layer and stops growing once all available DNA sites are exhausted. © 2018 IOP Publishing Ltd.

  1. Advance care planning in 21st century Australia: a systematic review and appraisal of online advance care directive templates against national framework criteria.

    Science.gov (United States)

    Luckett, Tim; Bhattarai, Priyanka; Phillips, Jane; Agar, Meera; Currow, David; Krastev, Yordanka; Davidson, Patricia M

    2015-11-01

    A drive to promote advance care planning at a population level has led to a proliferation of online advance care directive (ACD) templates but little information to guide consumer choice. The current study aimed to appraise the quality of online ACD templates promoted for use in Australia. A systematic review of online Australian ACD templates was conducted in February 2014. ACD templates were identified via Google searches, and quality was independently appraised by two reviewers against criteria from the 2011 report A National Frameworkfor Advance Care Directives. Bias either towards or against future medical treatment was assessed using criteria designed to limit subjectivity. Fourteen online ACD templates were included, all of which were available only in English. Templates developed by Southern Cross University best met the framework criteria. One ACD template was found to be biased against medical treatment--the Dying with Dignity Victoria Advance Healthcare Directive. More research is needed to understand how online resources can optimally elicit and record consumers' individual preferences for future care. Future iterations of the framework should address online availability and provide a simple rating system to inform choice and drive quality improvement.

  2. Characterization of purified Sindbis virus nsP4 RNA-dependent RNA polymerase activity in vitro

    International Nuclear Information System (INIS)

    Rubach, Jon K.; Wasik, Brian R.; Rupp, Jonathan C.; Kuhn, Richard J.; Hardy, Richard W.; Smith, Janet L.

    2009-01-01

    The Sindbis virus RNA-dependent RNA polymerase (nsP4) is responsible for the replication of the viral RNA genome. In infected cells, nsP4 is localized in a replication complex along with the other viral non-structural proteins. nsP4 has been difficult to homogenously purify from infected cells due to its interactions with the other replication proteins and the fact that its N-terminal residue, a tyrosine, causes the protein to be rapidly turned over in cells. We report the successful expression and purification of Sindbis nsP4 in a bacterial system, in which nsP4 is expressed as an N-terminal SUMO fusion protein. After purification the SUMO tag is removed, resulting in the isolation of full-length nsP4 possessing the authentic N-terminal tyrosine. This purified enzyme is able to produce minus-strand RNA de novo from plus-strand templates, as well as terminally add adenosine residues to the 3' end of an RNA substrate. In the presence of the partially processed viral replicase polyprotein, P123, purified nsP4 is able to synthesize discrete template length minus-strand RNA products. Mutations in the 3' CSE or poly(A) tail of viral template RNA prevent RNA synthesis by the replicase complex containing purified nsP4, consistent with previously reported template requirements for minus-strand RNA synthesis. Optimal reaction conditions were determined by investigating the effects of time, pH, and the concentrations of nsP4, P123 and magnesium on the synthesis of RNA

  3. Carbazole-based copolymers via direct arylation polymerization (DArP) for Suzuki-convergent polymer solar cell performance

    DEFF Research Database (Denmark)

    Gobalasingham, Nemal S.; Ekiz, Seyma; Pankow, Robert M.

    2017-01-01

    Although direct arylation polymerization (DArP) has recently emerged as an alternative to traditional cross-coupling methods like Suzuki polymerization, the evaluation of DArP polymers in practical applications like polymer solar cells (PSCs) is limited. Because even the presence of minute...

  4. Cellulose acetate-based molecularly imprinted polymeric membrane for separation of vanillin and o-vanillin

    OpenAIRE

    Zhang,Chunjing; Zhong,Shian; Yang,Zhengpeng

    2008-01-01

    Cellulose acetate-based molecularly imprinted polymeric membranes were prepared using vanillin as template molecule. The microscopic structure of the resultant polymeric membranes was characterized by SEM and FTIR spectroscopy, and the selective binding properties and separation capacity of the membranes for vanillin and o-vanillin were tested with binding experiments and separate experiments, respectively. The results showed that the vanillin-imprinted polymeric membranes displayed higher bi...

  5. Sol-gel auto-combustion synthesis of hydroxyapatite nanotubes array in porous alumina template

    International Nuclear Information System (INIS)

    Yuan Yuan; Liu Changsheng; Zhang Yuan; Shan Xiaoqian

    2008-01-01

    In this paper, an array of highly ordered hydroxyapatite (HAP) nanotubes was synthesized by sol-gel auto-combustion method with porous anodic aluminum oxide (AAO) template for the first time. Based on thermogravimetry (DTA/TG), Fourier transform infrared (FTIR) and X-ray diffraction (XRD), the dried gel, derived from the sol solution with Ca(NO 3 ) 2 .4H 2 O and PO(CH 3 O) 3 as precursors and ethylene glycol as the polymeric matrix, exhibited a typical self-propagating combustion behavior at low temperature, directly resulting in hexagonal crystalline HAP materials. The resultant HAP arrays fabricated from the above sol-gel in the AAO template were uniformly distributed, highly ordered nanotubes with uniform length and diameter according to the observations of scanning electron microscopy (SEM) and transmission electron microscope (TEM). The electron diffraction (ED), XRD and X-ray photoelectron spectroscopy (XPS) survey proved the formation of HAP phase with polycrystalline structure in the AAO template. Based on these results, a potential mechanism of 'an auto-combustion from dried gel to nanoparticles and a subsequent in situ reaction from nanoparticles to nanotubes' was proposed

  6. Functionalized Ormosil Scaffolds Processed by Direct Laser Polymerization for Application in Tissue Engineering

    DEFF Research Database (Denmark)

    Matei, A.; Schou, Jørgen; Canulescu, Stela

    The N,N’-(methacryloyloxyethyl triehtoxy silyl propyl carbamoyl-oxyhexyl)-urea hybrid methacrylate for applications in tissue engineering was synthesized and afterwards polymerized by direct laser polymerization using femtosecond laser pulses with the aim of using it for further applications...... in tissue engineering. The as-obtained scaffolds were modified either by low pressure argon plasma treatment or by using two different proteins (lysozyme, fibrinogen). For improved adhesion, the proteins were deposited by matrix assisted pulsed laser evaporation. The functionalized structures were tested...

  7. In vitro transcription of a torsionally constrained template

    DEFF Research Database (Denmark)

    Bentin, Thomas; Nielsen, Peter E

    2002-01-01

    RNA polymerase (RNAP) and the DNA template must rotate relative to each other during transcription elongation. In the cell, however, the components of the transcription apparatus may be subject to rotary constraints. For instance, the DNA is divided into topological domains that are delineated...... of torsionally constrained DNA by free RNAP. We asked whether or not a newly synthesized RNA chain would limit transcription elongation. For this purpose we developed a method to immobilize covalently closed circular DNA to streptavidin-coated beads via a peptide nucleic acid (PNA)-biotin conjugate in principle...... constrained. We conclude that transcription of a natural bacterial gene may proceed with high efficiency despite the fact that newly synthesized RNA is entangled around the template in the narrow confines of torsionally constrained supercoiled DNA....

  8. Polymer grafting surface as templates for the site-selective metallization

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Fang [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Li, Peiyuan, E-mail: lipearpear@yahoo.cn [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Li, Xiangcheng [School of computer, electronics and information, Guangxi University, Nanning 530001 (China); Huo, Lini [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Chen, Jinhao [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Chen, Rui [College of Pharmacy, Guangxi University of Chinese Medicine, Nanning 530001 (China); Na, Wei; Tang, Wanning; Liang, Lifang [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China); Su, Wei, E-mail: aaasuwei@yahoo.com.cn [College of Chemistry and Life Science, Guangxi Teachers Education University, Nanning 530001 (China)

    2013-06-01

    We report a simple, low-cost and universal method for the fabrication of copper circuit patterns on a wide range of flexible polymeric substrates. This method relies on procedures to modify the polymeric substrates with grafted polymer template to form surface-bound N-containing groups, which can bind palladium catalysts that subsequently initiate the site-selective deposition of copper granular layer patterns. The fabrications of patterned copper films were demonstrated on three kinds of flexible polymeric films including poly(imide) (PI), poly(ethylene naphthalate) (PEN) and poly(ethylene terephthalate) (PET) with minimum feature sizes of 200 μm. The films were characterized by ATR FT-IR, contact angle, XPS, XRD, TEM, SEM. Furthermore, the copper layered structure shows good adhesion with polymeric film. This method, which provides a promising strategy for the fabrication of copper circuit patterns on flexible polymeric substrates, has the potential in manufacturing conductive features adopted in various fields including modern electronics, opto-electronics and photovoltaic applications.

  9. Polymer grafting surface as templates for the site-selective metallization

    International Nuclear Information System (INIS)

    Yang, Fang; Li, Peiyuan; Li, Xiangcheng; Huo, Lini; Chen, Jinhao; Chen, Rui; Na, Wei; Tang, Wanning; Liang, Lifang; Su, Wei

    2013-01-01

    We report a simple, low-cost and universal method for the fabrication of copper circuit patterns on a wide range of flexible polymeric substrates. This method relies on procedures to modify the polymeric substrates with grafted polymer template to form surface-bound N-containing groups, which can bind palladium catalysts that subsequently initiate the site-selective deposition of copper granular layer patterns. The fabrications of patterned copper films were demonstrated on three kinds of flexible polymeric films including poly(imide) (PI), poly(ethylene naphthalate) (PEN) and poly(ethylene terephthalate) (PET) with minimum feature sizes of 200 μm. The films were characterized by ATR FT-IR, contact angle, XPS, XRD, TEM, SEM. Furthermore, the copper layered structure shows good adhesion with polymeric film. This method, which provides a promising strategy for the fabrication of copper circuit patterns on flexible polymeric substrates, has the potential in manufacturing conductive features adopted in various fields including modern electronics, opto-electronics and photovoltaic applications.

  10. An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions

    Directory of Open Access Journals (Sweden)

    Daisy W. Leung

    2015-04-01

    Full Text Available During viral RNA synthesis, Ebola virus (EBOV nucleoprotein (NP alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20–48 that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development.

  11. An Intrinsically Disordered Peptide from Ebola Virus VP35 Controls Viral RNA Synthesis by Modulating Nucleoprotein-RNA Interactions.

    Science.gov (United States)

    Leung, Daisy W; Borek, Dominika; Luthra, Priya; Binning, Jennifer M; Anantpadma, Manu; Liu, Gai; Harvey, Ian B; Su, Zhaoming; Endlich-Frazier, Ariel; Pan, Juanli; Shabman, Reed S; Chiu, Wah; Davey, Robert A; Otwinowski, Zbyszek; Basler, Christopher F; Amarasinghe, Gaya K

    2015-04-21

    During viral RNA synthesis, Ebola virus (EBOV) nucleoprotein (NP) alternates between an RNA-template-bound form and a template-free form to provide the viral polymerase access to the RNA template. In addition, newly synthesized NP must be prevented from indiscriminately binding to noncognate RNAs. Here, we investigate the molecular bases for these critical processes. We identify an intrinsically disordered peptide derived from EBOV VP35 (NPBP, residues 20-48) that binds NP with high affinity and specificity, inhibits NP oligomerization, and releases RNA from NP-RNA complexes in vitro. The structure of the NPBP/ΔNPNTD complex, solved to 3.7 Å resolution, reveals how NPBP peptide occludes a large surface area that is important for NP-NP and NP-RNA interactions and for viral RNA synthesis. Together, our results identify a highly conserved viral interface that is important for EBOV replication and can be targeted for therapeutic development. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  12. Hierarchically templated beads with tailored pore structure for phosphopeptide capture and phosphoproteomics

    DEFF Research Database (Denmark)

    Wierzbicka, Celina; Torsetnes, Silje B.; Jensen, Ole N.

    2017-01-01

    Two templating approaches to produce imprinted phosphotyrosine capture beads with a controllable pore structure are reported and compared with respect to their ability to enrich phosphopeptides from a tryptic peptide mixture. The beads were prepared by the polymerization of urea-based host monomers...... and crosslinkers inside the pores of macroporous silica beads with both free and immobilized template. In the final step the silica was removed by fluoride etching resulting in mesoporous polymer replicas with narrow pore size distributions, pore diameters ≈ 10 nm and surface area > 260 m2 g-1. The beads displayed...... pronounced phosphotyrosine affinity and selectivity in binding tests using model peptides in acetonitrile rich solutions with a performance surpassing solution polymerized bulk imprinted materials. Tests of the beads for the enrichment of phosphopeptides from tryptic digests of twelve proteins revealed both...

  13. Identification of a premature termination of DNA polymerization in ...

    Indian Academy of Sciences (India)

    2013-04-25

    Apr 25, 2013 ... strands to the 5′ end of the template strands, forming double- stranded DNA with ... duplex stem is important for high processive polymerization. HIV-1 reverse ... KF has been used as a model to study DNA polymerase.

  14. The cis-acting replication signal at the 3' end of Flock House virus RNA2 is RNA3-dependent

    International Nuclear Information System (INIS)

    Albarino, Cesar G.; Eckerle, Lance D.; Ball, L. Andrew

    2003-01-01

    The nodavirus Flock House virus has a bipartite positive-sense RNA genome consisting of RNAs 1 and 2, which encode the viral RNA-dependent RNA polymerase (RdRp) and capsid protein precursor, respectively. The RdRp catalyzes replication of both genome segments and produces from RNA1 a subgenomic RNA (RNA3) that transactivates RNA2 replication. Here, we replaced internal sequences of RNAs 1 and 2 with a common heterologous core and were thereby able to test the RNA termini for compatibility in supporting the replication of chimeric RNAs. The results showed that the 3' 50 nt of RNA2 contained an RNA3-dependent cis-acting replication signal. Since covalent RNA dimers can direct the synthesis of monomeric replication products, the RdRp can evidently respond to cis-acting replication signals located internally. Accordingly, RNA templates containing the 3' termini of both RNAs 1 and 2 in tandem generated different replication products depending on the presence or absence of RNA3

  15. Direct deposition of inorganic–organic hybrid semiconductors and their template-assisted microstructures

    International Nuclear Information System (INIS)

    Dwivedi, V.K.; Baumberg, J.J.; Prakash, G. Vijaya

    2013-01-01

    A straight-forward method is developed to deposit a new class of self-organized inorganic–organic (IO) hybrid, (C 12 H 25 NH 3 ) 2 PbI 4 . These IO hybrid structures are stacked-up as natural multiple quantum well structures and exhibit strong room-temperature exciton emission and other multifunctional features. Here it is successfully demonstrated that these materials can be directly carved into 2D photonic structures from the inexpensive template-assisted electrochemical deposition followed by solution processing. The applicability of this method for many such varieties of IO-hybrids is also explored. By appropriately controlling the deposition conditions and the self-assembly templates, target structures are developed for new-generation low-cost photonic devices. -- Highlights: ► New fabrication methodology for self-organized inorganic–organic hybrids. ► Strongly confined exciton emission and photoconductive properties. ► Simple bottom-up fabrication for device applications.

  16. Facile Fabrication of Uniform Polyaniline Nanotubes with Tubular Aluminosilicates as Templates

    Science.gov (United States)

    Zhang, Long; Liu, Peng

    2008-08-01

    The uniform polyaniline (PANI) nanotubes, with inner diameter, outer diameter, and tubular thickness of 40, 60, and 10 nm, respectively, were prepared successfully by using natural tubular aluminosilicates as templates. The halloysite nanotubes were coated with PANI via the in situ chemical oxidation polymerization. Then the templates were etched with HCl/HF solution. The PANI nanotubes were characterized using FTIR, X-ray diffraction, and transmission electron microscopy. The conductivity of the PANI nanotubes was found to be 1.752 × 10-5 (Ω·cm)-1.

  17. Cloning nanocrystal morphology with soft templates

    Science.gov (United States)

    Thapa, Dev Kumar; Pandey, Anshu

    2016-08-01

    In most template directed preparative methods, while the template decides the nanostructure morphology, the structure of the template itself is a non-general outcome of its peculiar chemistry. Here we demonstrate a template mediated synthesis that overcomes this deficiency. This synthesis involves overgrowth of silica template onto a sacrificial nanocrystal. Such templates are used to copy the morphologies of gold nanorods. After template overgrowth, gold is removed and silver is regrown in the template cavity to produce a single crystal silver nanorod. This technique allows for duplicating existing nanocrystals, while also providing a quantifiable breakdown of the structure - shape interdependence.

  18. Colloidal micro- and nano-particles as templates for polyelectrolyte multilayer capsules.

    Science.gov (United States)

    Parakhonskiy, Bogdan V; Yashchenok, Alexey M; Konrad, Manfred; Skirtach, Andre G

    2014-05-01

    Colloidal particles play an important role in various areas of material and pharmaceutical sciences, biotechnology, and biomedicine. In this overview we describe micro- and nano-particles used for the preparation of polyelectrolyte multilayer capsules and as drug delivery vehicles. An essential feature of polyelectrolyte multilayer capsule preparations is the ability to adsorb polymeric layers onto colloidal particles or templates followed by dissolution of these templates. The choice of the template is determined by various physico-chemical conditions: solvent needed for dissolution, porosity, aggregation tendency, as well as release of materials from capsules. Historically, the first templates were based on melamine formaldehyde, later evolving towards more elaborate materials such as silica and calcium carbonate. Their advantages and disadvantages are discussed here in comparison to non-particulate templates such as red blood cells. Further steps in this area include development of anisotropic particles, which themselves can serve as delivery carriers. We provide insights into application of particles as drug delivery carriers in comparison to microcapsules templated on them. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Isothermal circular-strand-displacement polymerization of DNA and microRNA in digital microfluidic devices.

    Science.gov (United States)

    Giuffrida, Maria Chiara; Zanoli, Laura Maria; D'Agata, Roberta; Finotti, Alessia; Gambari, Roberto; Spoto, Giuseppe

    2015-02-01

    Nucleic-acid amplification is a crucial step in nucleic-acid-sequence-detection assays. The use of digital microfluidic devices to miniaturize amplification techniques reduces the required sample volume and the analysis time and offers new possibilities for process automation and integration in a single device. The recently introduced droplet polymerase-chain-reaction (PCR) amplification methods require repeated cycles of two or three temperature-dependent steps during the amplification of the nucleic-acid target sequence. In contrast, low-temperature isothermal-amplification methods have no need for thermal cycling, thus requiring simplified microfluidic-device features. Here, the combined use of digital microfluidics and molecular-beacon (MB)-assisted isothermal circular-strand-displacement polymerization (ICSDP) to detect microRNA-210 sequences is described. MicroRNA-210 has been described as the most consistently and predominantly upregulated hypoxia-inducible factor. The nmol L(-1)-pmol L(-1) detection capabilities of the method were first tested by targeting single-stranded DNA sequences from the genetically modified Roundup Ready soybean. The ability of the droplet-ICSDP method to discriminate between full-matched, single-mismatched, and unrelated sequences was also investigated. The detection of a range of nmol L(-1)-pmol L(-1) microRNA-210 solutions compartmentalized in nanoliter-sized droplets was performed, establishing the ability of the method to detect as little as 10(-18) mol of microRNA target sequences compartmentalized in 20 nL droplets. The suitability of the method for biological samples was tested by detecting microRNA-210 from transfected K562 cells.

  20. Facile Fabrication of Uniform Polyaniline Nanotubes with Tubular Aluminosilicates as Templates

    Directory of Open Access Journals (Sweden)

    Zhang Long

    2008-01-01

    Full Text Available AbstractThe uniform polyaniline (PANI nanotubes, with inner diameter, outer diameter, and tubular thickness of 40, 60, and 10 nm, respectively, were prepared successfully by using natural tubular aluminosilicates as templates. The halloysite nanotubes were coated with PANI via the in situ chemical oxidation polymerization. Then the templates were etched with HCl/HF solution. The PANI nanotubes were characterized using FTIR, X-ray diffraction, and transmission electron microscopy. The conductivity of the PANI nanotubes was found to be 1.752 × 10−5(Ω·cm−1.

  1. Gamma Radiation -Induced Preparation of Polymeric Composite Resins and their Structure Assignments

    International Nuclear Information System (INIS)

    El-Zahhar, A.A.; Abdel-Aziz, H.M.; Siyam, T.

    2005-01-01

    Poly(acrylamide-acrylic acid). ethylenediamine tetra acetic acid disodium salt P(AM-AA). EDTANa2, Poly(acrylamide-acrylic acid)montmorillonite P(AM-AA). montmorillonite, and Poly(acrylamide acrylic acid)-potassium nickel hexacyanoferrate P(AM-AA)-KNiHCF were prepared by gamma radiation- induced template polymerization of (AA) on P(AM) as a template polymer in the presence of EDTANa2, Clay(montmorillonite), KNiHCF and KZnHCF, respectively. The capacity of the prepared P (AM-AA)-EDTANa2 and P (AM-AA)-montmorillonite composites increases with increasing of EDTANa2 and montmorillonite concentration then decreases. While the capacity of P(AM- AA). KNiHCF composites increases with increasing of KNiHCF content. The characteristic properties of prepared polymeric composites resins were studied by using FTIR spectroscopy

  2. Kinetic Analysis for Macrocyclizations Involving Anionic Template at the Transition State

    Directory of Open Access Journals (Sweden)

    Vicente Martí-Centelles

    2012-01-01

    competitive oligomerization/polymerization processes yielding undesired oligomeric/polymeric byproducts. The effect of anions has also been included in the kinetic models, as they can act as catalytic templates in the transition state reducing and stabilizing the transition state. The corresponding differential equation systems for each kinetic model can be solved numerically. Through a comprehensive analysis of these results, it is possible to obtain a better understanding of the different parameters that are involved in the macrocyclization reaction mechanism and to develop strategies for the optimization of the desired processes.

  3. Catalytic silica particles via template-directed molecular imprinting

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, M.A.; Kust, P.R.; Deng, G.; Schoen, P.E.; Dordick, J.S.; Clark, D.S.; Gaber, B.P.

    2000-02-22

    The surfaces of silica particle were molecularly imprinted with an {alpha}-chymotrypsin transition-state analogue (TSA) by utilizing the technique of template-directed synthesis of mineralized materials. The resulting catalytic particles hydrolyzed amides in an enantioselective manner. A mixture of a nonionic surfactant and the acylated chymotrysin TSA, with the TSA acting as the headgroup at the surfactant-water interface, was used to form a microemulsion for silica particle formation. Incorporation of amine-, dihydroimidazole-, and carboxylate-terminated trialkoxysilanes into the particles during imprinting resulted in enhancement of the rates of amide hydrolysis. Acylated imprint molecules formed more effective imprints in the presence of the functionalized silanes than nonacylated imprint molecules. Particles surface-imprinted with the chymotrypsin TSA were selective for the trypsin substrate, and particles surface-imprinted with the L-isomer of the enzyme TSA were enantioselective for the D-isomer of the substrate.

  4. Morphology evolution of PS-b-PDMS block copolymer and its hierarchical directed self-assembly on block copolymer templates

    DEFF Research Database (Denmark)

    Rasappa, Sozaraj; Schulte, Lars; Borah, Dipu

    2018-01-01

    Cylinder-forming polystyrene-block-polydimethylsiloxane (PS-b-PDMS, 27.2k-b-11.7k, SD39) block copolymer having a total molecular weight of 39 kg mol−1 was exploited to achieve in-plane morphologies of lines, dots and antidots. Brush-free self-assembly of the SD39 on silicon substrates was invest...... substrates provides a simplified method for surface nanopatterning, templated growth of nanomaterials and nanofabrication....... the pattern into the underlying substrate. Directed self-assembly and hierarchical directed self-assembly on block copolymer templates for confinement of dots was successfully demonstrated. The strategy for achieving multiple morphologies using one BCP by mere choice of the annealing solvents on unmodified...

  5. Hairpin DNA-Templated Silver Nanoclusters as Novel Beacons in Strand Displacement Amplification for MicroRNA Detection.

    Science.gov (United States)

    Zhang, Jingpu; Li, Chao; Zhi, Xiao; Ramón, Gabriel Alfranca; Liu, Yanlei; Zhang, Chunlei; Pan, Fei; Cui, Daxiang

    2016-01-19

    MicroRNA (miRNA) biomarkers display great potential for cancer diagnosis and prognosis. The development of rapid and specific methods for miRNA detection has become a hotspot. Herein, hairpin DNA-templated silver nanoclusters (AgNCs/HpDNA) were prepared and integrated into strand-displacement amplification (SDA) as a novel beacon for miRNA detection. The light-up platform was established based on guanine (G)-rich fluorescence enhancement that essentially converted the excitation/emission pair of AgNCs/HpDNAs from a shorter wavelength to a longer wavelength, and then achieved fluorescent enhancement at longer wavelength. On the basis of the validation of the method, the single and duplex detection were conducted in two plasma biomarkers (miR-16-5p and miR-19b-3p) for the diagnosis of gastric cancer. The probe (AgNCs/RED 16(7s)C) utilized for miR-16-5p detection adopted a better conformation with high specificity to recognize single-base mismatches by producing dramatically opposite signals (increase or decrease at 580 nm ex/640 nm em) while the probe (AgNCs/GRE 19b(5s)C) for miR-19b-3p generated dual signals (increase at 490 nm ex/570 nm em and decrease at 430 nm ex/530 nm em) with bright fluorescence in one reaction during the amplification, but unexpectedly was partially digested. This is for the first time to allow the generation of enhanced fluorescent AgNCs and the target recognition integrated into a single process, which offers great opportunity for specific miRNA detection in an easy and rapid way.

  6. Singular anti-RNA virus-directed proteins.

    Directory of Open Access Journals (Sweden)

    Rayanade R

    2000-07-01

    Full Text Available AIMS: To additionally purify and characterise the anti-RNA virus-directed protein termed p14. MATERIALS AND METHODS: Antiviral assays of p14 against RNA and DNA viruses were carried out and its antigenic similarities with chicken interferon (CIFN were studied. HPLC-Reverse Phase of p14 was performed to further purify p14. RESULTS: p14 showed antiviral activity against RNA viruses only and not against DNA viruses. It was antigenically distinct from CIFN. Purification of p14 yielded three proteins with antiviral activity, which had different physico-chemical properties than those described for interferons. CONCLUSIONS: The data presented on the antiviral, immunological and physico-chemical properties, establish the unique nature of p14 vis-á-vis those of interferons.

  7. Carprofen-imprinted monolith prepared by reversible addition-fragmentation chain transfer polymerization in room temperature ionic liquids.

    Science.gov (United States)

    Ban, Lu; Han, Xu; Wang, Xian-Hua; Huang, Yan-Ping; Liu, Zhao-Sheng

    2013-10-01

    To obtain fast separation, ionic liquids were used as porogens first in combination with reversible addition-fragmentation chain transfer (RAFT) polymerization to prepare a new type of molecularly imprinted polymer (MIP) monolith. The imprinted monolithic column was synthesized using a mixture of carprofen (template), 4-vinylpyridine, ethylene glycol dimethacrylate, [BMIM]BF4, and chain transfer agent (CTA). Some polymerization factors, such as template-monomer molar ratio, the degree of crosslinking, the composition of the porogen, and the content of CTA, on the column efficiency and imprinting effect of the resulting MIP monolith were systematically investigated. Affinity screening of structurally similar compounds with the template can be achieved in 200 s on the MIP monolith due to high column efficiency (up to 12,070 plates/m) and good column permeability. Recognition mechanism of the imprinted monolith was also investigated.

  8. UV-initiated template copolymerization of AM and MAPTAC: Microblock structure, copolymerization mechanism, and flocculation performance.

    Science.gov (United States)

    Li, Xiang; Zheng, Huaili; Gao, Baoyu; Sun, Yongjun; Liu, Bingzhi; Zhao, Chuanliang

    2017-01-01

    Flocculation as the core technology of sludge pretreatment can improve the dewatering performance of sludge that enables to reduce the cost of sludge transportation and the subsequent disposal costs. Therefore, synthesis of high-efficiency and economic flocculant is remarkably desired in this field. This study presents a cationic polyacrylamide (CPAM) flocculant with microblock structure synthesized through ultraviolet (UV)-initiated template copolymerization by using acrylamide (AM) and methacrylamido propyl trimethyl ammonium chloride (MAPTAC) as monomers, sodium polyacrylate (PAAS) as template, and 2,2'-azobis [2-(2-imidazolin-2-yl) propane] dihydrochloride (VA-044) as photoinitiator. The microblock structure of the CPAM was observed through nuclear magnetic resonance ( 1 H NMR and 13 C NMR) spectroscopy, Fourier transform infrared (FTIR) spectroscopy, and scanning electron microscopy (SEM) analyses. Furthermore, thermogravimetric/differential scanning calorimetry (TG/DSC) analysis was used to evaluate its thermal decomposition property. The copolymerization mechanism was investigated through the determination of the binding constant M K and study on polymerization kinetics. Results showed that the copolymerization was conducted in accordance with the I (ZIP) template polymerization mechanism, and revealed the coexistence of bimolecular termination free-radical reaction and mono-radical termination in the polymerization process. Results of sludge dewatering tests indicated the superior flocculation performance of microblock flocculant than random distributed CPAM. The residual turbidity, filter cake moisture content, and specific resistance to filtration reached 9.37 NTU, 68.01%, and 6.24 (10 12  m kg -1 ), respectively, at 40 mg L -1 of template poly(AM-MAPTAC) and pH 6.0. Furthermore, all flocculant except commercial CPAM showed a wide scope of pH application. Copyright © 2016 Elsevier Ltd. All rights reserved.

  9. Direct-Dispense Polymeric Waveguides Platform for Optical Chemical Sensors

    Directory of Open Access Journals (Sweden)

    Mohamad Hajj-Hassan

    2008-12-01

    Full Text Available We describe an automated robotic technique called direct-dispense to fabricate a polymeric platform that supports optical sensor arrays. Direct-dispense, which is a type of the emerging direct-write microfabrication techniques, uses fugitive organic inks in combination with cross-linkable polymers to create microfluidic channels and other microstructures. Specifically, we describe an application of direct-dispensing to develop optical biochemical sensors by fabricating planar ridge waveguides that support sol-gelderived xerogel-based thin films. The xerogel-based sensor materials act as host media to house luminophore biochemical recognition elements. As a prototype implementation, we demonstrate gaseous oxygen (O2 responsive optical sensors that operate on the basis of monitoring luminescence intensity signals. The optical sensor employs a Light Emitting Diode (LED excitation source and a standard silicon photodiode as the detector. The sensor operates over the full scale (0%-100% of O2 concentrations with a response time of less than 1 second. This work has implications for the development of miniaturized multisensor platforms that can be cost-effectively and reliably mass-produced.

  10. 'Gate effect' in templated polyacrylamide membranes influences the electrotransport of proteins and finds applications in proteome analysis.

    Science.gov (United States)

    Bossi, Alessandra; Andreoli, Matteo; Bonini, Francesca; Piletsky, Sergey

    2007-09-01

    Templating is an effective way for the structural modifications of a material and hence for altering its functional properties. Here protein imprinting was exploited to alter polymeric polyacrylamide (PAA) membranes. The sieving properties and selection abilities of the material formed were evaluated by studying the electrically driven transport of various proteins across templated PAA membranes. The sieving properties correlated with the templating process and depended on the quantity of template used during the polymerisation. For 1 mg/mL protein-templated membranes a 'gate effect' was shown, which induced a preferential migration of the template and of similar-size proteins. Such template preferential electrotransport was exploited for the selective removal of certain proteins in biological fluids prior to proteome analysis (depletion of albumin from human serum); the efficiency of the removal was demonstrated by analysing the serum proteome by two-dimensional electrophoresis experiments.

  11. Quantitative Three-Dimensional Characterization of Block Copolymer Directed Self-Assembly on Combined Chemical and Topographical Prepatterned Templates.

    Science.gov (United States)

    Segal-Peretz, Tamar; Ren, Jiaxing; Xiong, Shisheng; Khaira, Gurdaman; Bowen, Alec; Ocola, Leonidas E; Divan, Ralu; Doxastakis, Manolis; Ferrier, Nicola J; de Pablo, Juan; Nealey, Paul F

    2017-02-28

    Characterization of the three-dimensional (3D) structure in directed self-assembly (DSA) of block copolymers is crucial for understanding the complex relationships between the guiding template and the resulting polymer structure so DSA could be successfully implemented for advanced lithography applications. Here, we combined scanning transmission electron microscopy (STEM) tomography and coarse-grain simulations to probe the 3D structure of P2VP-b-PS-b-P2VP assembled on prepatterned templates using solvent vapor annealing. The templates consisted of nonpreferential background and raised guiding stripes that had PS-preferential top surfaces and P2VP-preferential sidewalls. The full 3D characterization allowed us to quantify the shape of the polymer domains and the interface between domains as a function of depth in the film and template geometry and offered important insights that were not accessible with 2D metrology. Sidewall guiding was advantageous in promoting the alignment and lowering the roughness of the P2VP domains over the sidewalls, but incommensurate confinement from the increased topography could cause roughness and intermittent dislocations in domains over the background region at the bottom of the film. The 3D characterization of bridge structures between domains over the background and breaks within domains on guiding lines sheds light on possible origins of common DSA defects. The positional fluctuations of the PS/P2VP interface between domains showed a depth-dependent behavior, with high levels of fluctuations near both the free surface of the film and the substrate and lower fluctuation levels in the middle of the film. This research demonstrates how 3D characterization offers a better understanding of DSA processes, leading to better design and fabrication of directing templates.

  12. Lysosomal putative RNA transporter SIDT2 mediates direct uptake of RNA by lysosomes.

    Science.gov (United States)

    Aizawa, Shu; Fujiwara, Yuuki; Contu, Viorica Raluca; Hase, Katsunori; Takahashi, Masayuki; Kikuchi, Hisae; Kabuta, Chihana; Wada, Keiji; Kabuta, Tomohiro

    2016-01-01

    Lysosomes are thought to be the major intracellular compartment for the degradation of macromolecules. We recently identified a novel type of autophagy, RNautophagy, where RNA is directly taken up by lysosomes in an ATP-dependent manner and degraded. However, the mechanism of RNA translocation across the lysosomal membrane and the physiological role of RNautophagy remain unclear. In the present study, we performed gain- and loss-of-function studies with isolated lysosomes, and found that SIDT2 (SID1 transmembrane family, member 2), an ortholog of the Caenorhabditis elegans putative RNA transporter SID-1 (systemic RNA interference deficient-1), mediates RNA translocation during RNautophagy. We also observed that SIDT2 is a transmembrane protein, which predominantly localizes to lysosomes. Strikingly, knockdown of Sidt2 inhibited up to ˜50% of total RNA degradation at the cellular level, independently of macroautophagy. Moreover, we showed that this impairment is mainly due to inhibition of lysosomal RNA degradation, strongly suggesting that RNautophagy plays a significant role in constitutive cellular RNA degradation. Our results provide a novel insight into the mechanisms of RNA metabolism, intracellular RNA transport, and atypical types of autophagy.

  13. Preparation of TiO2 hollow fibers using poly(vinylidene fluoride) hollow fiber microfiltration membrane as a template

    International Nuclear Information System (INIS)

    Lu Haiqiang; Zhang Lixiong; Xing Weihong; Wang Huanting; Xu Nanping

    2005-01-01

    TiO 2 hollow fibers were successfully prepared by using poly(vinylidene fluoride) hollow fiber microfiltration membrane as a template. The preparation procedure includes repeated impregnation of the TiO 2 precursor in the pores of the polymeric membrane, and calcination to burn off the template, producing the TiO 2 hollow fibers. The TiO 2 hollow fibers were characterized by X-ray diffraction (XRD) and scanning electron microscopy (SEM). TiO 2 hollow fibers with other structures, such as honeycomb monolith and spring, were also prepared by preshaping the polymeric membranes into the honeycomb structure and spring, respectively. The phase structure of the TiO 2 hollow fibers could be readily adjusted by changing the calcination temperature

  14. Inhibition of Poliovirus-Induced Cleavage of Cellular Protein PCBP2 Reduces the Levels of Viral RNA Replication

    Science.gov (United States)

    Chase, Amanda J.; Daijogo, Sarah

    2014-01-01

    ABSTRACT Due to their small genome size, picornaviruses must utilize host proteins to mediate cap-independent translation and viral RNA replication. The host RNA-binding protein poly(rC) binding protein 2 (PCBP2) is involved in both processes in poliovirus infected cells. It has been shown that the viral proteinase 3CD cleaves PCBP2 and contributes to viral translation inhibition. However, cleaved PCBP2 remains active in viral RNA replication. This would suggest that both cleaved and intact forms of PCBP2 have a role in the viral RNA replication cycle. The picornavirus genome must act as a template for both translation and RNA replication. However, a template that is actively being translated cannot function as a template for RNA replication, suggesting that there is a switch in template usage from translation to RNA replication. We demonstrate that the cleavage of PCBP2 by the poliovirus 3CD proteinase is a necessary step for efficient viral RNA replication and, as such, may be important for mediating a switch in template usage from translation to RNA replication. IMPORTANCE Poliovirus, like all positive-strand RNA viruses that replicate in the cytoplasm of eukaryotic cells, uses its genomic RNA as a template for both viral protein synthesis and RNA replication. Given that these processes cannot occur simultaneously on the same template, poliovirus has evolved a mechanism(s) to facilitate the switch from using templates for translation to using them for RNA synthesis. This study explores one possible scenario for how the virus alters the functions of a host cell RNA binding protein to mediate, in part, this important transition. PMID:24371074

  15. In situ preparation of magnetic nanocomposites of goethite in a styrene-maleimide copolymer template

    International Nuclear Information System (INIS)

    Sepulveda-Guzman, S.; Perez-Camacho, O.; Rodriguez-Fernandez, O.; Garcia-Zamora, M.

    2005-01-01

    Magnetic composites were prepared by in situ precipitation of α-FeOOH (goethite) using a new styrene-co-N-4 carboxybutylmaleimide cross-linked copolymer as template. Thermogravimetric analysis showed iron oxide content in the composites up to 45%. The iron oxide phase was identified as goethite by X-ray diffraction analysis. Transmission electron microscopy revealed that the crosslinking extent of polymeric templates affected both the shape and dimension of the goethite particles, and consequently, the magnetic behavior of the polymer/iron oxide composites

  16. Comparison of molecular imprinted particles prepared using precipitation polymerization in water and chloroform for fluorescent detection of nitroaromatics

    Energy Technology Data Exchange (ETDEWEB)

    Stringer, R. Cody, E-mail: rcsm84@mail.mizzou.edu [Department of Biological Engineering, University of Missouri, Columbia, MO (United States); Gangopadhyay, Shubhra, E-mail: gangopadhyays@missouri.edu [Department of Electrical and Computer Engineering, University of Missouri, Columbia, MO (United States); Grant, Sheila A., E-mail: grantsa@missouri.edu [Department of Biological Engineering, University of Missouri, Columbia, MO (United States)

    2011-10-10

    Highlights: {yields} Imprinted polymers prepared using precipitation polymerization. {yields} Comparison of chloroform and water as polymerization solvent. {yields} Imprinted polymer doped with quantum dots for fluorescent sensor. {yields} Fluorescent imprinted polymer used to detect nitroaromatic explosives. {yields} Chloroform is ideal solvent for molecular imprinting of nitroaromatics. - Abstract: A comparative study was conducted to study the effects that two different polymerization solvents would have on the properties of imprinted polymer microparticles prepared using precipitation polymerization. Microparticles prepared in chloroform, which previous results indicated was the optimal solvent for molecular imprinting of nitroaromatic explosive compounds, were compared to water, which was hypothesized to decrease water swelling of the polymer and allow enhanced rebinding of aqueous template. The microparticles were characterized and were integrated into a fluorescence sensing mechanism for detection of nitroaromatic explosive compounds. The performance of the sensing mechanisms was compared to illustrate which polymerization solvent produced optimal imprinted polymer microparticles for detection of nitroaromatic molecules. Results indicated that the structures of microparticles synthesized in chloroform versus water varied greatly. Sensor performance studies showed that the microparticles prepared in chloroform had greater imprinting efficiency and higher template rebinding than those prepared in water. For detection of 2,4,6-trinitrotoluene, the chloroform-based fluorescent microparticles achieved a lower limit of detection of 0.1 {mu}M, as compared to 100 {mu}M for the water-based fluorescent microparticles. Detection limits for 2,4-dinitrotoluene, as well as time response studies, also demonstrated that the chloroform-based particles are more effective for detection of nitroaromatic compounds than water-based particles. These results illustrate that the

  17. Comparison of molecular imprinted particles prepared using precipitation polymerization in water and chloroform for fluorescent detection of nitroaromatics

    International Nuclear Information System (INIS)

    Stringer, R. Cody; Gangopadhyay, Shubhra; Grant, Sheila A.

    2011-01-01

    Highlights: → Imprinted polymers prepared using precipitation polymerization. → Comparison of chloroform and water as polymerization solvent. → Imprinted polymer doped with quantum dots for fluorescent sensor. → Fluorescent imprinted polymer used to detect nitroaromatic explosives. → Chloroform is ideal solvent for molecular imprinting of nitroaromatics. - Abstract: A comparative study was conducted to study the effects that two different polymerization solvents would have on the properties of imprinted polymer microparticles prepared using precipitation polymerization. Microparticles prepared in chloroform, which previous results indicated was the optimal solvent for molecular imprinting of nitroaromatic explosive compounds, were compared to water, which was hypothesized to decrease water swelling of the polymer and allow enhanced rebinding of aqueous template. The microparticles were characterized and were integrated into a fluorescence sensing mechanism for detection of nitroaromatic explosive compounds. The performance of the sensing mechanisms was compared to illustrate which polymerization solvent produced optimal imprinted polymer microparticles for detection of nitroaromatic molecules. Results indicated that the structures of microparticles synthesized in chloroform versus water varied greatly. Sensor performance studies showed that the microparticles prepared in chloroform had greater imprinting efficiency and higher template rebinding than those prepared in water. For detection of 2,4,6-trinitrotoluene, the chloroform-based fluorescent microparticles achieved a lower limit of detection of 0.1 μM, as compared to 100 μM for the water-based fluorescent microparticles. Detection limits for 2,4-dinitrotoluene, as well as time response studies, also demonstrated that the chloroform-based particles are more effective for detection of nitroaromatic compounds than water-based particles. These results illustrate that the enhanced chemical properties of

  18. Novel polymeric nanocomposites and porous materials prepared using organogels

    International Nuclear Information System (INIS)

    Lai, Wei-Chi; Tseng, Shen-Chen

    2009-01-01

    We propose a new method for preparing polymeric nanocomposites and porous materials using self-assembled templates formed by 1,3:2,4-dibenzylidene sorbitol (DBS) organogels. DBS is capable of self-assembling into a 3D nanofibrillar network at relatively low concentrations in some organic solvents to produce organogels. In this study, we induced the formation of such physical cross-linked networks in styrene. Subsequently, we polymerized the styrene in the presence of chemical cross-linkers, divinyl benzene (DVB), with different amounts of DBS using thermal-initiated polymerization. The resulting materials were transparent, homogeneous polystyrene (PS) nanocomposites with both physical and chemical cross-links. The porous polymeric materials were obtained by solvent extraction of the DBS nanofibrils from the PS. Brunauer-Emmett-Teller (BET) measurements show that the amounts of DBS and DVB influenced the specific surface area after the removal of the DBS fibrils.

  19. Novel polymeric nanocomposites and porous materials prepared using organogels

    Energy Technology Data Exchange (ETDEWEB)

    Lai, Wei-Chi; Tseng, Shen-Chen, E-mail: wclai@mail.tku.edu.t [Department of Chemical and Materials Engineering, Tamkang University, 151 Ying-chuan Road, Tamsui, Taipei 25137, Taiwan (China)

    2009-11-25

    We propose a new method for preparing polymeric nanocomposites and porous materials using self-assembled templates formed by 1,3:2,4-dibenzylidene sorbitol (DBS) organogels. DBS is capable of self-assembling into a 3D nanofibrillar network at relatively low concentrations in some organic solvents to produce organogels. In this study, we induced the formation of such physical cross-linked networks in styrene. Subsequently, we polymerized the styrene in the presence of chemical cross-linkers, divinyl benzene (DVB), with different amounts of DBS using thermal-initiated polymerization. The resulting materials were transparent, homogeneous polystyrene (PS) nanocomposites with both physical and chemical cross-links. The porous polymeric materials were obtained by solvent extraction of the DBS nanofibrils from the PS. Brunauer-Emmett-Teller (BET) measurements show that the amounts of DBS and DVB influenced the specific surface area after the removal of the DBS fibrils.

  20. High-temperature nanoporous ceramic monolith prepared from a polymeric bicontinuous microemulsion template.

    Science.gov (United States)

    Jones, Brad H; Lodge, Timothy P

    2009-02-11

    Nanoporous ceramic with a unique pore structure was derived from an all-hydrocarbon polymeric bicontinuous microemulsion (BmuE). The BmuE was designed to allow facile removal of one phase, resulting in a nanoporous polymer monolith with BmuE-like structure. The pores were filled with a commercially available, polymeric precursor to nonoxide, Si-based ceramics. Pyrolysis resulted in a monolith of nanoporous ceramic, stable to at least 1000 degrees C, with a BmuE-like pore structure. The pore structure is disordered and 3-D continuous. Microscopy and gas sorption measurements suggest a well-defined pore size distribution spanning roughly 60-100 nm, sizes previously unattainable through related techniques.

  1. Grafting of molecularly imprinted polymer to porous polyethylene filtration membranes by plasma polymerization.

    Science.gov (United States)

    Cowieson, D; Piletska, E; Moczko, E; Piletsky, S

    2013-08-01

    An application of plasma-induced grafting of polyethylene membranes with a thin layer of molecularly imprinted polymer (MIP) was presented. High-density polyethylene (HDPE) membranes, "Vyon," were used as a substrate for plasma grafting modification. The herbicide atrazine, one of the most popular targets of the molecular imprinting, was chosen as a template. The parameters of the plasma treatment were optimized in order to achieve a good balance between polymerization and ablation processes. Modified HDPE membranes were characterized, and the presence of the grafted polymeric layer was confirmed based on the observed weight gain, pore size measurements, and infrared spectrometry. Since there was no significant change in the porosity of the modified membranes, it was assumed that only a thin layer of the polymer was introduced on the surface. The experiments on the re-binding of the template atrazine to the membranes modified with MIP and blank polymers were performed. HDPE membranes which were grafted with polymer using continuous plasma polymerization demonstrated the best result which was expressed in an imprinted factor equal to 3, suggesting that molecular imprinting was successfully achieved.

  2. Development of polymeric nanoparticles showing tuneable pH-responsive precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Vakurov, Alexander, E-mail: a.v.vakourov@bmb.leeds.ac.uk; Pchelintsev, Nikolay A., E-mail: n.a.pchelintsev@googlemail.com; Gibson, Tim, E-mail: timdgibson@merchab.fsnet.co.uk; Millner, Paul, E-mail: p.a.millner@leeds.ac.uk [Research Institute of Membrane and Systems Biology, University of Leeds (United Kingdom)

    2012-12-15

    A reverse micellar system comprising dioctyl-sulfosuccinate (AOT)/toluene was used as a template for polymerization of acrylamide/bisacrylamide-based functionalized polymeric nanoparticles. Such nanoparticles were typically sized between 20 and 90 nm and could be synthesized with a wide range of functional groups according to the monomers added to the polymerization mixture. Carboxy nanoparticles with acrylic acid as the functional monomer were synthesized in the reported work. The carboxy nanoparticles were pH sensitive and precipitated at pHs below 4. Modification of carboxy-functionalized polymeric nanoparticles with polyetheleneimine (PEI) resulted in the fabrication of a series of pH-responsive nanoparticles which could precipitate at different pHs and ionic strengths according to the PEI/carboxy ratio in the system. Both non-covalent PEI-nanoparticles conjugates and nanoparticles with covalently linked PEI behaved in this way.

  3. Development of polymeric nanoparticles showing tuneable pH-responsive precipitation

    International Nuclear Information System (INIS)

    Vakurov, Alexander; Pchelintsev, Nikolay A.; Gibson, Tim; Millner, Paul

    2012-01-01

    A reverse micellar system comprising dioctyl-sulfosuccinate (AOT)/toluene was used as a template for polymerization of acrylamide/bisacrylamide-based functionalized polymeric nanoparticles. Such nanoparticles were typically sized between 20 and 90 nm and could be synthesized with a wide range of functional groups according to the monomers added to the polymerization mixture. Carboxy nanoparticles with acrylic acid as the functional monomer were synthesized in the reported work. The carboxy nanoparticles were pH sensitive and precipitated at pHs below 4. Modification of carboxy-functionalized polymeric nanoparticles with polyetheleneimine (PEI) resulted in the fabrication of a series of pH-responsive nanoparticles which could precipitate at different pHs and ionic strengths according to the PEI/carboxy ratio in the system. Both non-covalent PEI-nanoparticles conjugates and nanoparticles with covalently linked PEI behaved in this way.

  4. Histamine-imprinted microspheres: Comparison between conventional and raft-mediated polymerization techniques

    International Nuclear Information System (INIS)

    Romano, Edwin F. Jr.; So, Regina C.; Holdsworth, Clovia I.

    2015-01-01

    Molecularly imprinted microspheres (MIM) were synthesized via conventional free radical polymerization (CTP) and RAFT-mediated controlled radical polymerization (CRP) method using histamine as the template molecule. Optimal polymerization conditions were achieved using 4%(w/w) monomer feed concentration with 80=90% EGDMA as crosslinker, and histamine: MAA ratio of 1:4 in acetonitrile at 60°C for 24 hours. The size of CTP-M90 and CTP-M80 imprinted microspheres are comparable with that of RAFT polymer CRP-M80 at 264.5 ±12 nm in the swollen (DLS-DMSO) and collapsed state (SEM). For the CTP method, the presence of the template allows for a bigger particle size compared to the non-imprinted counterpart (NIM). Further, controlled growth was observed for the CRP technique, where the size of the imprinted microsphere, CRP-M80, is comparable to CRP-N80. The binding studies of CTP and CRP microspheres toward histamine were studied at concentrations well below biding with buffer concentration of 25mM at pH7. Results showed that the binding isotherms were found to conform to the Freundlich model. Moreover, results revealed that the difference in binding capacity (N) between MIM and NIM imparted by the imprinting process is significantly higher in CTP-80 (26 μmol/g) than both CTP-90 and CRP-80 (9 μmol/g). Non-competitive and competitive binding assays with L-histidine, imidazole, and tryptamine using CTP-80 and CRP-80 were also carried out. MIMs were shown to exhibit binding preference towards the template. (author)

  5. Targeting NF-kB signaling with polymeric hybrid micelles that co-deliver siRNA and dexamethasone for arthritis therapy.

    Science.gov (United States)

    Wang, Qin; Jiang, Hao; Li, Yan; Chen, Wenfei; Li, Hanmei; Peng, Ke; Zhang, Zhirong; Sun, Xun

    2017-04-01

    The transcription factor NF-kB plays a pivotal role in the pathogenesis of rheumatoid arthritis. Here we attempt to slow arthritis progression by co-delivering the glucocorticoid dexamethasone (Dex) and small-interfering RNA targeting NF-kB p65 using our previously developed polymeric hybrid micelle system. These micelles contain two similar amphiphilic copolymers: polycaprolactone-polyethylenimine (PCL-PEI) and polycaprolactone-polyethyleneglycol (PCL-PEG). The hybrid micelles loaded with Dex and siRNA effectively inhibited NF-kB signaling in murine macrophages more efficiently than micelles containing either Dex or siRNA on their own. In addition, the co-delivery system was able to switch macrophages from the M1 to M2 state. Injecting hybrid micelles containing Dex and siRNA into mice with collagen-induced arthritis led the therapeutic agents to accumulate in inflamed joints and reduce inflammation, without damaging renal or liver function. Thus, blocking NF-kB activation in inflammatory tissue using micelle-based co-delivery may provide a new approach for treating inflammatory disease. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. Self-folding micropatterned polymeric containers.

    Science.gov (United States)

    Azam, Anum; Laflin, Kate E; Jamal, Mustapha; Fernandes, Rohan; Gracias, David H

    2011-02-01

    We demonstrate self-folding of precisely patterned, optically transparent, all-polymeric containers and describe their utility in mammalian cell and microorganism encapsulation and culture. The polyhedral containers, with SU-8 faces and biodegradable polycaprolactone (PCL) hinges, spontaneously assembled on heating. Self-folding was driven by a minimization of surface area of the liquefying PCL hinges within lithographically patterned two-dimensional (2D) templates. The strategy allowed for the fabrication of containers with variable polyhedral shapes, sizes and precisely defined porosities in all three dimensions. We provide proof-of-concept for the use of these polymeric containers as encapsulants for beads, chemicals, mammalian cells and bacteria. We also compare accelerated hinge degradation rates in alkaline solutions of varying pH. These optically transparent containers resemble three-dimensional (3D) micro-Petri dishes and can be utilized to sustain, monitor and deliver living biological components.

  7. Direct Synthesis of Telechelic Polyethylene by Selective Insertion Polymerization

    KAUST Repository

    Jian, Zhongbao

    2016-10-14

    A single-step route to telechelic polyethylene (PE) is enabled by selective insertion polymerization. PdII-catalyzed copolymerization of ethylene and 2-vinylfuran (VF) generates α,ω-di-furan telechelic polyethylene. Orthogonally reactive exclusively in-chain anhydride groups are formed by terpolymerization with carbic anhydride. Combined experimental and theoretical DFT studies reveal the key for this direct approach to telechelics to be a match of the comonomers’ different electronics and bulk. Identified essential features of the comonomer are that it is an electron-rich olefin that forms an insertion product stabilized by an additional interaction, namely a π–η3 interaction for the case of VF.

  8. Optimal Hydrophobicity in Ring-Opening Metathesis Polymerization-Based Protein Mimics Required for siRNA Internalization.

    Science.gov (United States)

    deRonde, Brittany M; Posey, Nicholas D; Otter, Ronja; Caffrey, Leah M; Minter, Lisa M; Tew, Gregory N

    2016-06-13

    Exploring the role of polymer structure for the internalization of biologically relevant cargo, specifically siRNA, is of critical importance to the development of improved delivery reagents. Herein, we report guanidinium-rich protein transduction domain mimics (PTDMs) based on a ring-opening metathesis polymerization scaffold containing tunable hydrophobic moieties that promote siRNA internalization. Structure-activity relationships using Jurkat T cells and HeLa cells were explored to determine how the length of the hydrophobic block and the hydrophobic side chain compositions of these PTDMs impacted siRNA internalization. To explore the hydrophobic block length, two different series of diblock copolymers were synthesized: one series with symmetric block lengths and one with asymmetric block lengths. At similar cationic block lengths, asymmetric and symmetric PTDMs promoted siRNA internalization in the same percentages of the cell population regardless of the hydrophobic block length; however, with 20 repeat units of cationic charge, the asymmetric block length had greater siRNA internalization, highlighting the nontrivial relationships between hydrophobicity and overall cationic charge. To further probe how the hydrophobic side chains impacted siRNA internalization, an additional series of asymmetric PTDMs was synthesized that featured a fixed hydrophobic block length of five repeat units that contained either dimethyl (dMe), methyl phenyl (MePh), or diphenyl (dPh) side chains and varied cationic block lengths. This series was further expanded to incorporate hydrophobic blocks consisting of diethyl (dEt), diisobutyl (diBu), and dicyclohexyl (dCy) based repeat units to better define the hydrophobic window for which our PTDMs had optimal activity. High-performance liquid chromatography retention times quantified the relative hydrophobicities of the noncationic building blocks. PTDMs containing the MePh, diBu, and dPh hydrophobic blocks were shown to have superior

  9. The RNA binding protein HuR does not interact directly with HIV-1 reverse transcriptase and does not affect reverse transcription in vitro

    Directory of Open Access Journals (Sweden)

    Gronenborn Angela M

    2010-05-01

    Full Text Available Abstract Background Lemay et al recently reported that the RNA binding protein HuR directly interacts with the ribonuclease H (RNase H domain of HIV-1 reverse transcriptase (RT and influences the efficiency of viral reverse transcription (Lemay et al., 2008, Retrovirology 5:47. HuR is a member of the embryonic lethal abnormal vision protein family and contains 3 RNA recognition motifs (RRMs that bind AU-rich elements (AREs. To define the structural determinants of the HuR-RT interaction and to elucidate the mechanism(s by which HuR influences HIV-1 reverse transcription activity in vitro, we cloned and purified full-length HuR as well as three additional protein constructs that contained the N-terminal and internal RRMs, the internal and C-terminal RRMs, or the C-terminal RRM only. Results All four HuR proteins were purified and characterized by biophysical methods. They are well structured and exist as monomers in solution. No direct protein-protein interaction between HuR and HIV-1 RT was detected using NMR titrations with 15N labeled HuR variants or the 15N labeled RNase H domain of HIV-1 RT. Furthermore, HuR did not significantly affect the kinetics of HIV-1 reverse transcription in vitro, even on RNA templates that contain AREs. Conclusions Our results suggest that HuR does not impact HIV-1 replication through a direct protein-protein interaction with the viral RT.

  10. Hierarchical meso/macro-porous carbon fabricated from dual MgO templates for direct electron transfer enzymatic electrodes

    Science.gov (United States)

    Funabashi, Hiroto; Takeuchi, Satoshi; Tsujimura, Seiya

    2017-03-01

    We designed a three-dimensional (3D) hierarchical pore structure to improve the current production efficiency and stability of direct electron transfer-type biocathodes. The 3D hierarchical electrode structure was fabricated using a MgO-templated porous carbon framework produced from two MgO templates with sizes of 40 and 150 nm. The results revealed that the optimal pore composition for a bilirubin oxidase-catalysed oxygen reduction cathode was a mixture of 33% macropores and 67% mesopores (MgOC33). The macropores improve mass transfer inside the carbon material, and the mesopores improve the electron transfer efficiency of the enzyme by surrounding the enzyme with carbon.

  11. Functional Programming with C++ Template Metaprograms

    Science.gov (United States)

    Porkoláb, Zoltán

    Template metaprogramming is an emerging new direction of generative programming. With the clever definitions of templates we can force the C++ compiler to execute algorithms at compilation time. Among the application areas of template metaprograms are the expression templates, static interface checking, code optimization with adaption, language embedding and active libraries. However, as template metaprogramming was not an original design goal, the C++ language is not capable of elegant expression of metaprograms. The complicated syntax leads to the creation of code that is hard to write, understand and maintain. Although template metaprogramming has a strong relationship with functional programming, this is not reflected in the language syntax and existing libraries. In this paper we give a short and incomplete introduction to C++ templates and the basics of template metaprogramming. We will enlight the role of template metaprograms, and some important and widely used idioms. We give an overview of the possible application areas as well as debugging and profiling techniques. We suggest a pure functional style programming interface for C++ template metaprograms in the form of embedded Haskell code which is transformed to standard compliant C++ source.

  12. Direct Regulation of tRNA and 5S rRNA Gene Transcription by Polo-like Kinase 1

    NARCIS (Netherlands)

    Fairley, Jennifer A.; Mitchell, Louise E.; Berg, Tracy; Kenneth, Niall S.; von Schubert, Conrad; Sillje, Herman H. W.; Medema, Rene H.; Nigg, Erich A.; White, Robert J.

    2012-01-01

    Polo-like kinase Plk1 controls numerous aspects of cell-cycle progression. We show that it associates with tRNA and 5S rRNA genes and regulates their transcription by RNA polymerase Ill (pol Ill) through direct binding and phosphorylation of transcription factor Brit During interphase, Plk1 promotes

  13. Influence of Functionality on Direct Arylation of Model Systems as a Route Toward Fluorinated Copolymers via Direct Arylation Polymerization (DArP)

    DEFF Research Database (Denmark)

    Livi, Francesco; Gobalasingham, Nemal S.; Bundgaard, Eva

    2015-01-01

    A screening of direct arylation conditions on amodel small molecule system is carried out to develop suitableconditions for the direct arylation polymerization (DArP) of fluorinatedcopolymers, which are incompatible with conditionspreviously utilized successfully for nonfluorinated systems. Themo......,4-phenylene)dithiophene. Polymers arefree of β-defects and significant homocoupling. This work furtherunderscores the attractive simplicity, relevance, and easeof DArP while reconfirming its broad compatibility withincreasingly popular fluorinated copolymers....

  14. Direct Regulation of Mitochondrial RNA Synthesis by Thyroid Hormone

    Science.gov (United States)

    Enríquez, José A.; Fernández-Silva, Patricio; Garrido-Pérez, Nuria; López-Pérez, Manuel J.; Pérez-Martos, Acisclo; Montoya, Julio

    1999-01-01

    We have analyzed the influence of in vivo treatment and in vitro addition of thyroid hormone on in organello mitochondrial DNA (mtDNA) transcription and, in parallel, on the in organello footprinting patterns at the mtDNA regions involved in the regulation of transcription. We found that thyroid hormone modulates mitochondrial RNA levels and the mRNA/rRNA ratio by influencing the transcriptional rate. In addition, we found conspicuous differences between the mtDNA dimethyl sulfate footprinting patterns of mitochondria derived from euthyroid and hypothyroid rats at the transcription initiation sites but not at the mitochondrial transcription termination factor (mTERF) binding region. Furthermore, direct addition of thyroid hormone to the incubation medium of mitochondria isolated from hypothyroid rats restored the mRNA/rRNA ratio found in euthyroid rats as well as the mtDNA footprinting patterns at the transcription initiation area. Therefore, we conclude that the regulatory effect of thyroid hormone on mitochondrial transcription is partially exerted by a direct influence of the hormone on the mitochondrial transcription machinery. Particularly, the influence on the mRNA/rRNA ratio is achieved by selective modulation of the alternative H-strand transcription initiation sites and does not require the previous activation of nuclear genes. These results provide the first functional demonstration that regulatory signals, such as thyroid hormone, that modify the expression of nuclear genes can also act as primary signals for the transcriptional apparatus of mitochondria. PMID:9858589

  15. Template-Directed Instrumentation Reduces Cost and Improves Efficiency for Total Knee Arthroplasty: An Economic Decision Analysis and Pilot Study.

    Science.gov (United States)

    McLawhorn, Alexander S; Carroll, Kaitlin M; Blevins, Jason L; DeNegre, Scott T; Mayman, David J; Jerabek, Seth A

    2015-10-01

    Template-directed instrumentation (TDI) for total knee arthroplasty (TKA) may streamline operating room (OR) workflow and reduce costs by preselecting implants and minimizing instrument tray burden. A decision model simulated the economics of TDI. Sensitivity analyses determined thresholds for model variables to ensure TDI success. A clinical pilot was reviewed. The accuracy of preoperative templates was validated, and 20 consecutive primary TKAs were performed using TDI. The model determined that preoperative component size estimation should be accurate to ±1 implant size for 50% of TKAs to implement TDI. The pilot showed that preoperative template accuracy exceeded 97%. There were statistically significant improvements in OR turnover time and in-room time for TDI compared to an historical cohort of TKAs. TDI reduces costs and improves OR efficiency. Copyright © 2015 Elsevier Inc. All rights reserved.

  16. Optical properties of template synthesized nanowalled ZnS microtubules

    Science.gov (United States)

    Kumar, Rajesh; Chakarvarti, S. K.

    2007-12-01

    Electrodeposition is a versatile technique combining low processing cost with ambient conditions that can be used to prepare metallic, polymeric and semiconducting nano/micro structures. In the present work, track-etch membranes (TEMs) of makrofol (KG) have been used as templates for synthesis of ZnS nanowalled microtubules using electrodeposition technique. The morphology of the microtubules was characterized by scanning electron microscopy. Size effects on the band gap of tubules have also been studied by UV-visible spectrophotometer.

  17. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode

    KAUST Repository

    Jergic, Slobodan; Horan, Nicholas P.; Elshenawy, Mohamed; Mason, Claire E.; Urathamakul, Thitima; Ozawa, Kiyoshi; Robinson, Andrew J.; Goudsmits, Joris M H; Wang, Yao; Pan, Xuefeng; Beck, Jennifer L.; Van Oijen, Antoine M.; Huber, Thomas L.; Hamdan, Samir; Dixon, Nicholas E.

    2013-01-01

    Processive DNA synthesis by the αÉ"θ core of the Escherichia coli Pol III replicase requires it to be bound to the β 2 clamp via a site in the α polymerase subunit. How the É" proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of É". Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in É" that, in conjunction with the site in α, maintains a closed state of the αÉ"θ-β 2 replicase in the polymerization mode of DNA synthesis. The É"-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states. © 2013 European Molecular Biology Organization.

  18. A direct proofreader-clamp interaction stabilizes the Pol III replicase in the polymerization mode

    KAUST Repository

    Jergic, Slobodan

    2013-02-22

    Processive DNA synthesis by the αÉ"θ core of the Escherichia coli Pol III replicase requires it to be bound to the β 2 clamp via a site in the α polymerase subunit. How the É" proofreading exonuclease subunit influences DNA synthesis by α was not previously understood. In this work, bulk assays of DNA replication were used to uncover a non-proofreading activity of É". Combination of mutagenesis with biophysical studies and single-molecule leading-strand replication assays traced this activity to a novel β-binding site in É" that, in conjunction with the site in α, maintains a closed state of the αÉ"θ-β 2 replicase in the polymerization mode of DNA synthesis. The É"-β interaction, selected during evolution to be weak and thus suited for transient disruption to enable access of alternate polymerases and other clamp binding proteins, therefore makes an important contribution to the network of protein-protein interactions that finely tune stability of the replicase on the DNA template in its various conformational states. © 2013 European Molecular Biology Organization.

  19. New 'monolithic' templates and improved protocols for soft lithography and microchip fabrication

    International Nuclear Information System (INIS)

    Pallandre, Antoine; Pal, Debjani; Lambert, Bertrand de; Viovy, Jean-Louis; Fuetterer, Claus

    2006-01-01

    We report a new method for fast prototyping and fabrication of polydimethylsiloxane (PDMS) and plastic microfluidic chips. These methods share in common the preparation of monolithic masters which includes the fabrication of the planar support, the 'negative pattern' of the microchannels and the fluidic connectors. The monolithic templates are extremely robust compared to conventional ones made of silicon and SU-8, and easier to produce and cheaper than all-silicon or electroplated templates. In contrast to the above-mentioned methods, our process allows one to cast both micrometre- (e.g. the microchannel) and millimetre-sized structures (e.g. the fluidic connection to the outer world) in a single fabrication step. The 'monolithic template' strategy can be used to fabricate both elastomeric (e.g. poly(dimethyl siloxane (PDMS)) polyester thermoset masters and glassy polymeric (e.g. cyclic olefin copolymer (COC)) devices. In this study we also report on one step fabrication of elastomer chips and on surface modifications of the above mentioned monolithically fabricated masters in order to improve separation of the chip from the template

  20. Purification and properties of poliovirus RNA polymerase expressed in Escherichia coli

    International Nuclear Information System (INIS)

    Plotch, S.J.; Palant, O.; Gluzman, Y.

    1989-01-01

    A cDNA clone encoding the RNA polymerase of poliovirus has been expressed in Escherichia coli under the transcriptional control of a T7 bacteriophage promoter. This poliovirus enzyme was designed to contain only a single additional amino acid, the N-terminal methionine. The recombinant enzyme has been purified to near homogeneity, and polyclonal antibodies have been prepared against it. The enzyme exhibits poly(A)-dependent oligo(U)-primed ply(U) polymerase activity as well as RNA polymerase activity. In the presence of an oligo(U) primer, the enzyme catalyzes the synthesis of a full-length copy of either poliovirus or globin RNA templates. In the absence of added primer, RNA products up to twice the length of the template are synthesized. When incubated in the presence of a single nucleoside triphosphate, [α- 32 P]UTP, the enzyme catalyzes the incorporation of radioactive label into template RNA. These results are discussed in light of previously proposed models of poliovirus RNA synthesis in vitro

  1. Polyspecific pyrrolysyl-tRNA synthetases from directed evolution.

    Science.gov (United States)

    Guo, Li-Tao; Wang, Yane-Shih; Nakamura, Akiyoshi; Eiler, Daniel; Kavran, Jennifer M; Wong, Margaret; Kiessling, Laura L; Steitz, Thomas A; O'Donoghue, Patrick; Söll, Dieter

    2014-11-25

    Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNA(Pyl) have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate N(ε)-acetyl-Lys (AcK) onto tRNA(Pyl). Here, we examine an N(ε)-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids.

  2. Absolute and direct microRNA quantification using DNA-gold nanoparticle probes.

    Science.gov (United States)

    Degliangeli, Federica; Kshirsagar, Prakash; Brunetti, Virgilio; Pompa, Pier Paolo; Fiammengo, Roberto

    2014-02-12

    DNA-gold nanoparticle probes are implemented in a simple strategy for direct microRNA (miRNA) quantification. Fluorescently labeled DNA-probe strands are immobilized on PEGylated gold nanoparticles (AuNPs). In the presence of target miRNA, DNA-RNA heteroduplexes are formed and become substrate for the endonuclease DSN (duplex-specific nuclease). Enzymatic hydrolysis of the DNA strands yields a fluorescence signal due to diffusion of the fluorophores away from the gold surface. We show that the molecular design of our DNA-AuNP probes, with the DNA strands immobilized on top of the PEG-based passivation layer, results in nearly unaltered enzymatic activity toward immobilized heteroduplexes compared to substrates free in solution. The assay, developed in a real-time format, allows absolute quantification of as little as 0.2 fmol of miR-203. We also show the application of the assay for direct quantification of cancer-related miR-203 and miR-21 in samples of extracted total RNA from cell cultures. The possibility of direct and absolute quantification may significantly advance the use of microRNAs as biomarkers in the clinical praxis.

  3. Separations using biological carriers immobilized in porous polymeric and sol-gel template synthesized nanotubular membranes

    Science.gov (United States)

    Lakshmi, Brinda B.

    1998-12-01

    The overall goal of the dissertation was to use immobilized biological carriers in membranes to separate compounds as challenging as enantiomers. The membranes were prepared by a process called 'template synthesis'. Template synthesis has been used to synthesize semiconductor nanostructures and also membranes which do the enantioseparation by a process called facilitated transport. The immobilized proteins act as carriers facilitating the transport of the substrate molecules through the membrane. The apoenzymes are enzymes devoid of cofactor. Apoenzymes will possess the molecular recognition site for the substrate but will not catalyze the reaction. Apoenzymes immobilized in the pores of porous polycarbonate membrane was used as a carrier. The ends of the pores were closed with porous polypyrrole. Compounds as interesting as enantiomers were separated with these membranes. Template synthesis has been extended to the synthesis of many important semiconductor oxide naostructures like TiO2, SiO2, ZnO, Co3O4 and MnO2. These structures were made by dipping the alumina template membrane in the sol and heating. Ti0 2 tubules and fibers were obtained by this method. The fibers were used to study photocatalysis reaction of organic compounds in sunlight. Proteins were immobilized within the inner surface of the tubules using Sn chemistry. Bovine serum albumn (BSA) immobilized within the different diameter tubules showed varying degree of facilitation with phenylalanine. The membranes also show interesting switching of selectivity from L to D depending on the tube size and feed concentration.

  4. RNA Crystallization

    Science.gov (United States)

    Golden, Barbara L.; Kundrot, Craig E.

    2003-01-01

    RNA molecules may be crystallized using variations of the methods developed for protein crystallography. As the technology has become available to syntheisize and purify RNA molecules in the quantities and with the quality that is required for crystallography, the field of RNA structure has exploded. The first consideration when crystallizing an RNA is the sequence, which may be varied in a rational way to enhance crystallizability or prevent formation of alternate structures. Once a sequence has been designed, the RNA may be synthesized chemically by solid-state synthesis, or it may be produced enzymatically using RNA polymerase and an appropriate DNA template. Purification of milligram quantities of RNA can be accomplished by HPLC or gel electrophoresis. As with proteins, crystallization of RNA is usually accomplished by vapor diffusion techniques. There are several considerations that are either unique to RNA crystallization or more important for RNA crystallization. Techniques for design, synthesis, purification, and crystallization of RNAs will be reviewed here.

  5. RNA Study Using DNA Nanotechnology.

    Science.gov (United States)

    Tadakuma, Hisashi; Masubuchi, Takeya; Ueda, Takuya

    2016-01-01

    Transcription is one of the fundamental steps of gene expression, where RNA polymerases (RNAPs) bind to their template genes and make RNAs. In addition to RNAP and the template gene, many molecules such as transcription factors are involved. The interaction and the effect of these factors depend on the geometry. Molecular layout of these factors, RNAP and gene is thus important. DNA nanotechnology is a promising technology that allows controlling of the molecular layout in the range of nanometer to micrometer scale with nanometer resolution; thus, it is expected to expand the RNA study beyond the current limit. Copyright © 2016 Elsevier Inc. All rights reserved.

  6. MDV-1 variant of Qβ RNA. Final report

    International Nuclear Information System (INIS)

    Gordon, M.P.

    1981-01-01

    MDV-1 is a variant of Qβ RNA which consists of complementary plus (+) and minus (-) strands. The sequences of these strands are well established. MDV-1 is an active template in replication reactions. High-resolution polyacrylamide gel electrophoresis was used to locate sites of replication inhibition in the molecule induced by irradiation of (+) and (-) MDV-1 RNA templates with 254 nanometer (uv) light at a dose of 2500 Jm -2 . Presumably, this inhibition was caused by uridine hydrates and pyrimidine cyclobutane dimers. Each of the ten inhibition sites identified corresponds to regions in the template which contain two or more pyrimidines. Dose-response studies showed that the uv-induced inactivation of the template activity of MDV-1 RNA closely paralleled the formation of uridine hydrates when replication occurred at 12 0 C. At higher temperatures, the template activity of MDV-1 appeared to be less sensitive to uv light. Since pre-incubation of irradiated MDV-1 at 37 0 for 35 min did not affect replication inhibition at 12 0 C, inhibition of replication at 37 0 C does not appear to be due to dehydration of uridine hydrate at the higher temperature. Pauses in nucleic acid synthesis, attributed to kinetic modulators, were observed in a number of systems and were proposed to play a role in the regulation of nucleic acid synthesis. The results reported here suggest that some photolesions might mimic such modulators. The replication of (+) MDV-1 RNA was also inhibited at specific sites by kethoxal, semicarbazide, and methoxyamine. These sites were near some of the sites at which uv-induced replication inhibition occurred. These results suggested that some regions of the (+) MDV-1 molecule are structurally exposed to modification by uv and base-specific chemicals, and were consistent with some features of a computer-generated model of the secondary structure of (+) MDV-1 RNA

  7. Synthesis of thermo-responsive bovine hemoglobin imprinted nanoparticles by combining ionic liquid immobilization with aqueous precipitation polymerization.

    Science.gov (United States)

    Wang, Yongmei; Yang, Chongchong; Sun, Yan; Qiu, Fengtao; Xiang, Yang; Fu, Guoqi

    2018-02-01

    Surface molecular imprinting over functionalized nanoparticles has proved to be an effective approach for construction of artificial nanomaterials for protein recognition. Herein, we report a strategy for synthesis of core-shell protein-imprinted nanoparticles by the functionalization of nano-cores with ionic liquids followed by aqueous precipitation polymerization to build thermo-responsive imprinted polymer nano-shells. The immobilized ionic liquids can form multiple interactions with the protein template. The polymerization process can produce thermo-reversible physical crosslinks, which are advantageous to enhancing imprinting and facilitating template removal. With bovine hemoglobin as a model template, the imprinted nanoparticles showed temperature-sensitivity in both dispersion behaviors and rebinding capacities. Compared with the ionic-liquid-modified core nanoparticles, the imprinted particles exhibited greatly increased selectivity and two orders of magnitude higher binding affinity for the template protein. The imprinted nanoparticles achieved relatively high imprinting factor up to 5.0 and specific rebinding capacity of 67.7 mg/g, respectively. These nanoparticles also demonstrated rapid rebinding kinetics and good reproducibility after five cycles of adsorption-regeneration. Therefore, the presented approach may be viable for the fabrication of high-performance protein-imprinted nanoparticles with temperature sensitivity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. An efficient polymeric micromotor doped with Pt nanoparticle@carbon nanotubes for complex bio-media.

    Science.gov (United States)

    Li, Yana; Wu, Jie; Xie, Yuzhe; Ju, Huangxian

    2015-04-14

    A highly efficient polymeric tubular micromotor doped with Pt nanoparticle@carbon nanotubes is fabricated by template-assisted electrochemical growth. The micromotors preserve good navigation in multi-media and surface modification, along with simple synthesis, easy functionalization and good biocompatibility, displaying great promise in biological applications.

  9. Smart polymeric nanoparticles with pH-responsive and PEG-detachable properties for co-delivering paclitaxel and survivin siRNA to enhance antitumor outcomes.

    Science.gov (United States)

    Jin, Mingji; Jin, Guangming; Kang, Lin; Chen, Liqing; Gao, Zhonggao; Huang, Wei

    2018-01-01

    The co-delivery of chemotherapeutic agents and small interfering RNA (siRNA) within one cargo can enhance the anticancer outcomes through its synergistic therapeutic effects. We prepared smart polymeric nanoparticles (NPs) with pH-responsive and poly(ethylene glycol) (PEG)-detachable properties to systemically co-deliver paclitaxel (PTX) and siRNA against survivin gene for lung cancer therapy. The cationic polyethyleneimine-block-polylactic acid (PEI-PLA) was first synthesized and characterized, with good biocompatibility. PTX was encapsulated into the hydrophobic core of the PEI-PLA polymers by dialysis, and then the survivin siRNA was loaded onto the PTX-loaded NPs (PEI-PLA/PTX) through electrostatic interaction between siRNA and PEI block. Finally, the negatively charged poly(ethylene glycol)-block-poly(L-aspartic acid sodium salt) (PEG-PAsp) was coated onto the surface of NPs by electrostatic interaction to form final smart polymeric NPs with mean particle size of 82.4 nm and zeta potential of 4.1 mV. After uptake of NPs by tumor cells, the PEG-PAsp segments became electrically neutral owing to the lower endosome pH and consequently detached from the smart NPs. This process allowed endosomal escape of the NPs through the proton-sponge effect of the exposed PEI moiety. The resulting NPs achieved drug loading of 6.04 wt% and exhibited good dispersibility within 24 h in 10% fetal bovine serum (FBS). At pH 5.5, the NPs presented better drug release and cellular uptake than at pH 7.4. The NPs with survivin siRNA effectively knocked down the expression of survivin mRNA and protein owing to enhanced cell uptake of NPs. Cell counting kit-8 (CCK-8) assay showed that the NPs presented low systemic toxicity and improved antiproliferation effect of PTX on A549 cells. Moreover, in vivo studies demonstrated that accumulated NPs in the tumor site were capable of inhibiting the tumor growth and extending the survival rate of the mice by silencing the survivin gene and

  10. Synthesis of polymer nanostructures via the use of surfactant surface aggregates as templates

    Science.gov (United States)

    Marquez, Maricel

    The subject of this work is the synthesis of polymer nanostructures via the use of surfactant surface aggregates as templates, also termed Template Assisted Admicellar Polymerization (TAAP). The first chapter reviews some of the most current nanopatterning techniques (including both top-down and bottom-up approaches), with particular emphasis on the fabrication of organic and inorganic patterned nanostructures via particle lithography. In chapter 2, highly ordered hexagonal arrays of latex spheres were prepared on highly ordered pyrolytic graphite (HOPG) from a variation of the Langmuir Blodgett technique, using an anionic surfactant (SDS), and a low molecular weight (ca. 10000) polyacrylamide as spreading agents. When a nonionic polyethoxylated (EO = 9) surfactant was used as the spreading agent, no ordered arrays were observed. Based on the correlation found between the surface tension in the presence of the latex particles and the critical concentration at which hexagonal arrangements of latex spheres occurs; a model was proposed to explain the role of the spreading agent in forming stable monolayers at the air/liquid interface, which in turn are necessary for the formation of well-ordered monolayers on a solid substrate from the LB technique. According to this model, solid-like regions of small numbers of latex spheres form at the liquid-air interface, which are then transferred to the substrate. These ordered regions then act as nuclei for the formation of 2D arrays of latex spheres on the surface upon water evaporation. The role of other factors such as relative humidity, substrate and solvent choice, and pulling vs. compression speed were also found to affect the quality of the monolayers formed. Finally, a simple, easy to automate, yet effective surface tension method was proposed to predict the optimal conditions for the formation of ordered monolayers using a variation of the LB deposition method from any monodisperse set of spheres. In chapter 3, a novel

  11. Direct laser writing of synthetic poly(amino acid) hydrogels and poly(ethylene glycol) diacrylates by two-photon polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Käpylä, Elli, E-mail: elli.kapyla@tut.fi [Department of Electronics and Communications Engineering, Tampere University of Technology, P.O. Box 692, 33101 Tampere (Finland); BioMediTech, Biokatu 10, 33520 Tampere (Finland); Sedlačík, Tomáš [Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 162 06 Praha 6, Břevnov, Prague (Czech Republic); Aydogan, Dogu Baran [Department of Electronics and Communications Engineering, Tampere University of Technology, P.O. Box 692, 33101 Tampere (Finland); BioMediTech, Biokatu 10, 33520 Tampere (Finland); Viitanen, Jouko [VTT Technical Research Centre of Finland, P.O. Box 1300, 33101 Tampere (Finland); Rypáček, František [Institute of Macromolecular Chemistry of the Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 162 06 Praha 6, Břevnov, Prague (Czech Republic); Kellomäki, Minna [Department of Electronics and Communications Engineering, Tampere University of Technology, P.O. Box 692, 33101 Tampere (Finland); BioMediTech, Biokatu 10, 33520 Tampere (Finland)

    2014-10-01

    The additive manufacturing technique of direct laser writing by two-photon polymerization (2PP-DLW) enables the fabrication of three-dimensional microstructures with superior accuracy and flexibility. When combined with biomimetic hydrogel materials, 2PP-DLW can be used to recreate the microarchitectures of the extracellular matrix. However, there are currently only a limited number of hydrogels applicable for 2PP-DLW. In order to widen the selection of synthetic biodegradable hydrogels, in this work we studied the 2PP-DLW of methacryloylated and acryloylated poly(α-amino acid)s (poly(AA)s). The performance of these materials was compared to widely used poly(ethylene glycol) diacrylates (PEGdas) in terms of polymerization and damage thresholds, voxel size, line width, post-polymerization swelling and deformation. We found that both methacryloylated and acryloylated poly(AA) hydrogels are suitable to 2PP-DLW with a wider processing window than PEGdas. The poly(AA) with the highest degree of acryloylation showed the greatest potential for 3D microfabrication. - Highlights: • Methacryloylated and acryloylated poly(α-amino acid)s (poly(AA)s) were synthesized. • Direct laser writing by two-photon polymerization (2PP-DLW) of poly(AA)s is shown. • Poly(AA)s have wider processing windows than poly(ethylene glycol) diacrylates. • 3D poly(AA) structures with 80% water content were fabricated.

  12. Direct laser writing of synthetic poly(amino acid) hydrogels and poly(ethylene glycol) diacrylates by two-photon polymerization

    International Nuclear Information System (INIS)

    Käpylä, Elli; Sedlačík, Tomáš; Aydogan, Dogu Baran; Viitanen, Jouko; Rypáček, František; Kellomäki, Minna

    2014-01-01

    The additive manufacturing technique of direct laser writing by two-photon polymerization (2PP-DLW) enables the fabrication of three-dimensional microstructures with superior accuracy and flexibility. When combined with biomimetic hydrogel materials, 2PP-DLW can be used to recreate the microarchitectures of the extracellular matrix. However, there are currently only a limited number of hydrogels applicable for 2PP-DLW. In order to widen the selection of synthetic biodegradable hydrogels, in this work we studied the 2PP-DLW of methacryloylated and acryloylated poly(α-amino acid)s (poly(AA)s). The performance of these materials was compared to widely used poly(ethylene glycol) diacrylates (PEGdas) in terms of polymerization and damage thresholds, voxel size, line width, post-polymerization swelling and deformation. We found that both methacryloylated and acryloylated poly(AA) hydrogels are suitable to 2PP-DLW with a wider processing window than PEGdas. The poly(AA) with the highest degree of acryloylation showed the greatest potential for 3D microfabrication. - Highlights: • Methacryloylated and acryloylated poly(α-amino acid)s (poly(AA)s) were synthesized. • Direct laser writing by two-photon polymerization (2PP-DLW) of poly(AA)s is shown. • Poly(AA)s have wider processing windows than poly(ethylene glycol) diacrylates. • 3D poly(AA) structures with 80% water content were fabricated

  13. Banks of templates for directed searches of gravitational waves from spinning neutron stars

    International Nuclear Information System (INIS)

    Pisarski, Andrzej; Jaranowski, Piotr; Pietka, Maciej

    2011-01-01

    We construct efficient banks of templates suitable for directed searches of almost monochromatic gravitational waves originating from spinning neutron stars in our Galaxy in data being collected by currently operating interferometric detectors. We thus assume that the position of the gravitational-wave source in the sky is known, but we do not assume that the wave's frequency and its derivatives are a priori known. In the construction we employ a simplified model of the signal with constant amplitude and phase which is a polynomial function of time. All our template banks enable usage of the fast Fourier transform algorithm in the computation of the maximum-likelihood F-statistic for nodes of the grids defining the bank. We study and employ the dependence of the grid's construction on the choice of the position of the observational interval with respect to the origin of time axis. We also study the usage of the fast Fourier transform algorithms with nonstandard frequency resolutions achieved by zero padding or folding the data. In the case of the gravitational-wave signal with one spin-down parameter included we have found grids with covering thicknesses which are only 0.1-16% larger than the thickness of the optimal 2-dimensional hexagonal covering.

  14. RNA interference and Register Machines (extended abstract

    Directory of Open Access Journals (Sweden)

    Masahiro Hamano

    2012-11-01

    Full Text Available RNA interference (RNAi is a mechanism whereby small RNAs (siRNAs directly control gene expression without assistance from proteins. This mechanism consists of interactions between RNAs and small RNAs both of which may be single or double stranded. The target of the mechanism is mRNA to be degraded or aberrated, while the initiator is double stranded RNA (dsRNA to be cleaved into siRNAs. Observing the digital nature of RNAi, we represent RNAi as a Minsky register machine such that (i The two registers hold single and double stranded RNAs respectively, and (ii Machine's instructions are interpreted by interactions of enzyme (Dicer, siRNA (with RISC com- plex and polymerization (RdRp to the appropriate registers. Interpreting RNAi as a computational structure, we can investigate the computational meaning of RNAi, especially its complexity. Initially, the machine is configured as a Chemical Ground Form (CGF, which generates incorrect jumps. To remedy this problem, the system is remodeled as recursive RNAi, in which siRNA targets not only mRNA but also the machine instructional analogues of Dicer and RISC. Finally, probabilistic termination is investigated in the recursive RNAi system.

  15. The RNA Exosome Channeling and Direct Access Conformations Have Distinct In Vivo Functions

    Directory of Open Access Journals (Sweden)

    Jaeil Han

    2016-09-01

    Full Text Available The RNA exosome is a 3′–5′ ribonuclease complex that is composed of nine core subunits and an essential catalytic subunit, Rrp44. Two distinct conformations of Rrp44 were revealed in previous structural studies, suggesting that Rrp44 may change its conformation to exert its function. In the channeling conformation, (Rrp44ch, RNA accesses the active site after traversing the central channel of the RNA exosome, whereas in the other conformation, (Rrp44da, RNA gains direct access to the active site. Here, we show that the Rrp44da exosome is important for nuclear function of the RNA exosome. Defects caused by disrupting the direct access conformation are distinct from those caused by channel-occluding mutations, indicating specific functions for each conformation. Our genetic analyses provide in vivo evidence that the RNA exosome employs a direct-access route to recruit specific substrates, indicating that the RNA exosome uses alternative conformations to act on different RNA substrates.

  16. Tailoring Lipid and Polymeric Nanoparticles as siRNA Carriers towards the Blood-Brain Barrier – from Targeting to Safe Administration

    DEFF Research Database (Denmark)

    Gomes, Maria João; Fernandes, Carlos; Martins, Susana

    2017-01-01

    . The interaction of modified nanoparticles with brain endothelial cells increased 3-fold compared to non-modified lipid nanoparticles, and 4-fold compared to non-modified PLGA nanoparticles, respectively. These nanosystems, which were also demonstrated to be safe for human brain endothelial cells, without...... and efficient delivery to its target, two different nanoparticles platforms, solid lipid (SLN) and poly-lactic-co-glycolic (PLGA) nanoparticles were used in this study. Polymeric PLGA nanoparticles were around 115 nm in size and had 50 % of siRNA association efficiency, while SLN presented 150 nm...

  17. FACT facilitates chromatin transcription by RNA polymerases I and III

    DEFF Research Database (Denmark)

    Birch, Joanna L; Tan, Bertrand C-M; Panov, Kostya I

    2009-01-01

    Efficient transcription elongation from a chromatin template requires RNA polymerases (Pols) to negotiate nucleosomes. Our biochemical analyses demonstrate that RNA Pol I can transcribe through nucleosome templates and that this requires structural rearrangement of the nucleosomal core particle....... The subunits of the histone chaperone FACT (facilitates chromatin transcription), SSRP1 and Spt16, co-purify and co-immunoprecipitate with mammalian Pol I complexes. In cells, SSRP1 is detectable at the rRNA gene repeats. Crucially, siRNA-mediated repression of FACT subunit expression in cells results...... in a significant reduction in 47S pre-rRNA levels, whereas synthesis of the first 40 nt of the rRNA is not affected, implying that FACT is important for Pol I transcription elongation through chromatin. FACT also associates with RNA Pol III complexes, is present at the chromatin of genes transcribed by Pol III...

  18. Polymeric molecular sieve membranes via in situ cross-linking of non-porous polymer membrane templates.

    Science.gov (United States)

    Qiao, Zhen-An; Chai, Song-Hai; Nelson, Kimberly; Bi, Zhonghe; Chen, Jihua; Mahurin, Shannon M; Zhu, Xiang; Dai, Sheng

    2014-04-16

    High-performance polymeric membranes for gas separation are attractive for molecular-level separations in industrial-scale chemical, energy and environmental processes. Molecular sieving materials are widely regarded as the next-generation membranes to simultaneously achieve high permeability and selectivity. However, most polymeric molecular sieve membranes are based on a few solution-processable polymers such as polymers of intrinsic microporosity. Here we report an in situ cross-linking strategy for the preparation of polymeric molecular sieve membranes with hierarchical and tailorable porosity. These membranes demonstrate exceptional performance as molecular sieves with high gas permeabilities and selectivities for smaller gas molecules, such as carbon dioxide and oxygen, over larger molecules such as nitrogen. Hence, these membranes have potential for large-scale gas separations of commercial and environmental relevance. Moreover, this strategy could provide a possible alternative to 'classical' methods for the preparation of porous membranes and, in some cases, the only viable synthetic route towards certain membranes.

  19. MicroRNA–Directed siRNA Biogenesis in Caenorhabditis elegans

    Science.gov (United States)

    Corrêa, Régis L.; Steiner, Florian A.; Berezikov, Eugene; Ketting, René F.

    2010-01-01

    RNA interference (RNAi) is a post-transcriptional silencing process, triggered by double-stranded RNA (dsRNA), leading to the destabilization of homologous mRNAs. A distinction has been made between endogenous RNAi–related pathways and the exogenous RNAi pathway, the latter being essential for the experimental use of RNAi. Previous studies have shown that, in Caenorhabditis elegans, a complex containing the enzymes Dicer and the Argonaute RDE-1 process dsRNA. Dicer is responsible for cleaving dsRNA into short interfering RNAs (siRNAs) while RDE-1 acts as the siRNA acceptor. RDE-1 then guides a multi-protein complex to homologous targets to trigger mRNA destabilization. However, endogenous role(s) for RDE-1, if any, have remained unexplored. We here show that RDE-1 functions as a scavenger protein, taking up small RNA molecules from many different sources, including the microRNA (miRNA) pathway. This is in striking contrast to Argonaute proteins functioning directly in the miRNA pathway, ALG-1 and ALG-2: these proteins exclusively bind miRNAs. While playing no significant role in the biogenesis of the main pool of miRNAs, RDE-1 binds endogenous miRNAs and triggers RdRP activity on at least one perfectly matching, endogenous miRNA target. The resulting secondary siRNAs are taken up by a set of Argonaute proteins known to act as siRNA acceptors in exogenous RNAi, resulting in strong mRNA destabilization. Our results show that RDE-1 in an endogenous setting is actively screening the transcriptome using many different small RNAs, including miRNAs, as a guide, with implications for the evolution of transcripts with a potential to be recognized by Dicer. PMID:20386745

  20. Role of the Pepino mosaic virus 3'-untranslated region elements in negative-strand RNA synthesis in vitro.

    Science.gov (United States)

    Osman, Toba A M; Olsthoorn, René C L; Livieratos, Ioannis C

    2014-09-22

    Pepino mosaic virus (PepMV) is a mechanically-transmitted positive-strand RNA potexvirus, with a 6410 nt long single-stranded (ss) RNA genome flanked by a 5'-methylguanosine cap and a 3' poly-A tail. Computer-assisted folding of the 64 nt long PepMV 3'-untranslated region (UTR) resulted in the prediction of three stem-loop structures (hp1, hp2, and hp3 in the 3'-5' direction). The importance of these structures and/or sequences for promotion of negative-strand RNA synthesis and binding to the RNA dependent RNA polymerase (RdRp) was tested in vitro using a specific RdRp assay. Hp1, which is highly variable among different PepMV isolates, appeared dispensable for negative-strand synthesis. Hp2, which is characterized by a large U-rich loop, tolerated base-pair changes in its stem as long as they maintained the stem integrity but was very sensitive to changes in the U-rich loop. Hp3, which harbours the conserved potexvirus ACUUAA hexamer motif, was essential for template activity. Template-RNA polymerase binding competition experiments showed that the ACUUAA sequence represents a high-affinity RdRp binding element. Copyright © 2014 Elsevier B.V. All rights reserved.

  1. An RNA polymerase II-and AGO4-associated protein acts in RNA-directed DNA methylation

    KAUST Repository

    Gao, Zhihuan

    2010-04-21

    DNA methylation is an important epigenetic mark in many eukaryotes. In plants, 24-nucleotide small interfering RNAs (siRNAs) bound to the effector protein, Argonaute 4 (AGO4), can direct de novo DNA methylation by the methyltransferase DRM2 (refs 2, 4-6). Here we report a new regulator of RNA-directed DNA methylation (RdDM) in Arabidopsis: RDM1. Loss-of-function mutations in the RDM1 gene impair the accumulation of 24-nucleotide siRNAs, reduce DNA methylation, and release transcriptional gene silencing at RdDM target loci. RDM1 encodes a small protein that seems to bind single-stranded methyl DNA, and associates and co-localizes with RNA polymerase II (Pol II, also known as NRPB), AGO4 and DRM2 in the nucleus. Our results indicate that RDM1 is a component of the RdDM effector complex and may have a role in linking siRNA production with pre-existing or de novo cytosine methylation. Our results also indicate that, although RDM1 and Pol V (also known as NRPE) may function together at some RdDM target sites in the peri-nucleolar siRNA processing centre, Pol II rather than Pol V is associated with the RdDM effector complex at target sites in the nucleoplasm. © 2010 Macmillan Publishers Limited. All rights reserved.

  2. Self-folding polymeric containers for encapsulation and delivery of drugs.

    Science.gov (United States)

    Fernandes, Rohan; Gracias, David H

    2012-11-01

    Self-folding broadly refers to self-assembly processes wherein thin films or interconnected planar templates curve, roll-up or fold into three dimensional (3D) structures such as cylindrical tubes, spirals, corrugated sheets or polyhedra. The process has been demonstrated with metallic, semiconducting and polymeric films and has been used to curve tubes with diameters as small as 2nm and fold polyhedra as small as 100nm, with a surface patterning resolution of 15nm. Self-folding methods are important for drug delivery applications since they provide a means to realize 3D, biocompatible, all-polymeric containers with well-tailored composition, size, shape, wall thickness, porosity, surface patterns and chemistry. Self-folding is also a highly parallel process, and it is possible to encapsulate or self-load therapeutic cargo during assembly. A variety of therapeutic cargos such as small molecules, peptides, proteins, bacteria, fungi and mammalian cells have been encapsulated in self-folded polymeric containers. In this review, we focus on self-folding of all-polymeric containers. We discuss the mechanistic aspects of self-folding of polymeric containers driven by differential stresses or surface tension forces, the applications of self-folding polymers in drug delivery and we outline future challenges. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. Formation of novel morphologies of aragonite induced by inorganic template

    International Nuclear Information System (INIS)

    Wang, Xiaoming; Nan, Zhaodong

    2011-01-01

    Graphical abstract: Glass-slices were used as a template to induce formation and assembly of aragonite. Different morphologies, such as hemisphere, twinborn hemisphere and flower-shaped particles, were produced by direction of the glass-slices. Highlights: → Glass-slices were used as a template to induce formation and assembly of aragonite. → Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. → Planes were always appeared in these as-synthesized samples. → Thermodynamic theory was applied to explain the production of the aragonite. -- Abstract: A glass-slice was used as a template to induce formation and assembly of aragonite. Thermodynamic theory was applied to explain the production of the aragonite. Transformation of three-dimensional nucleation to template-based two-dimensional surface nucleation caused the production of aragonite. Hemisphere, twinborn hemisphere and flower-shaped particles were produced by direction of the glass-slices. Planes were always appeared in these as-synthesized samples because the nucleation and the growth of these samples were adsorbed at the surfaces of the glass-slices. The formation mechanism of the as-formed sample was proposed. Compared with organic template, the present study provides a facile method to apply inorganic template to prepare functional materials.

  4. The histone chaperone TAF-I/SET/INHAT is required for transcription in vitro of chromatin templates.

    Science.gov (United States)

    Gamble, Matthew J; Erdjument-Bromage, Hediye; Tempst, Paul; Freedman, Leonard P; Fisher, Robert P

    2005-01-01

    To uncover factors required for transcription by RNA polymerase II on chromatin, we fractionated a mammalian cell nuclear extract. We identified the histone chaperone TAF-I (also known as INHAT [inhibitor of histone acetyltransferase]), which was previously proposed to repress transcription, as a potent activator of chromatin transcription responsive to the vitamin D3 receptor or to Gal4-VP16. TAF-I associates with chromatin in vitro and can substitute for the related protein NAP-1 in assembling chromatin onto cloned DNA templates in cooperation with the remodeling enzyme ATP-dependent chromatin assembly factor (ACF). The chromatin assembly and transcriptional activation functions are distinct, however, and can be dissociated temporally. Efficient transcription of chromatin assembled with TAF-I still requires the presence of TAF-I during the polymerization reaction. Conversely, TAF-I cannot stimulate transcript elongation when added after the other factors necessary for assembly of a preinitiation complex on naked DNA. Thus, TAF-I is required to facilitate transcription at a step after chromatin assembly but before transcript elongation.

  5. The origin of polynucleotide-directed protein synthesis

    Science.gov (United States)

    Orgel, Leslie E.

    1989-01-01

    If protein synthesis evolved in an RNA world it was probably preceded by simpler processes by means of which interaction with amino acids conferred selective advantage on replicating RNA molecules. It is suggested that at first the simple attachment of amino acids to the 2'(3') termini of RNA templates favored initiation of replication at the end of the template rather than at internal positions. The second stage in the evolution of protein synthesis would probably have been the association of pairs of charged RNA adaptors in such a way as to favor noncoded formation of peptides. Only after this process had become efficient could coded synthesis have begun.

  6. Durable diamond-like carbon templates for UV nanoimprint lithography

    International Nuclear Information System (INIS)

    Tao, L; Ramachandran, S; Nelson, C T; Overzet, L J; Goeckner, M; Lee, G; Hu, W; Lin, M; Willson, C G; Wu, W

    2008-01-01

    The interaction between resist and template during the separation process after nanoimprint lithography (NIL) can cause the formation of defects and damage to the templates and resist patterns. To alleviate these problems, fluorinated self-assembled monolayers (F-SAMs, i.e. tridecafluoro-1,1,2,2,tetrahydrooctyl trichlorosilane or FDTS) have been employed as template release coatings. However, we find that the FDTS coating undergoes irreversible degradation after only 10 cycles of UV nanoimprint processes with SU-8 resist. The degradation includes a 28% reduction in surface F atoms and significant increases in the surface roughness. In this paper, diamond-like carbon (DLC) films were investigated as an alternative material not only for coating but also for direct fabrication of nanoimprint templates. DLC films deposited on quartz templates in a plasma enhanced chemical vapor deposition system are shown to have better chemical and physical stability than FDTS. After the same 10 cycles of UV nanoimprints, the surface composition as well as the roughness of DLC films were found to be unchanged. The adhesion energy between the DLC surface and SU-8 is found to be smaller than that of FDTS despite the slightly higher total surface energy of DLC. DLC templates with 40 nm features were fabricated using e-beam lithography followed by Cr lift-off and reactive ion etching. UV nanoimprinting using the directly patterned DLC templates in SU-8 resist demonstrates good pattern transfer fidelity and easy template-resist separation. These results indicate that DLC is a promising material for fabricating durable templates for UV nanoimprint lithography

  7. Photocatalytic and microwave absorbing properties of polypyrrole/Fe-doped TiO2 composite by in situ polymerization method

    International Nuclear Information System (INIS)

    Li Qiaoling; Zhang Cunrui; Li Jianqiang

    2011-01-01

    Research highlights: → Polypyrrole/Fe-doped TiO 2 composite is prepared by in situ polymerization of pyrrole on the Fe-doped TiO 2 template. → The Fe-doped TiO 2 microbelts are prepared by sol-gel method using the absorbent cotton template for the first time. → Then the Fe-doped TiO 2 microbelts are used as template for the preparation of polypyrrole/Fe-doped TiO 2 composites. → The structure, morphology and properties of the composites are characterized with scanning electron microscope (SEM), IR, Net-work Analyzer. → A possible formation mechanism of Fe-doped TiO 2 microbelts and polypyrrole/Fe-doped TiO 2 composites has been proposed. → The effect of the mol ratio of pyrrole/Fe-doped TiO 2 on the photocatalysis properties and microwave loss properties of the composites is investigated. - Abstract: The Fe-doped TiO 2 microbelts were prepared by sol-gel method using the absorbent cotton template for the first time. Then the Fe-doped TiO 2 microbelts were used as templates for the preparation of polypyrrole/Fe-doped TiO 2 composites. Polypyrrole/Fe-doped TiO 2 composites were prepared by in situ polymerization of pyrrole on the Fe-doped TiO 2 template. The structure, morphology and properties of the composites were characterized with scanning electron microscope (SEM), FTIR, Net-work Analyzer. The possible formation mechanisms of Fe-doped TiO 2 microbelts and polypyrrole/Fe-doped TiO 2 composites have been proposed. The effect of the molar ratio of pyrrole/Fe-doped TiO 2 on the photocatalytic properties and microwave loss properties of the composites was investigated.

  8. Peptide catalysed prebiotic polymerization of RNA

    DEFF Research Database (Denmark)

    Wieczorek, Rafal; Luisi, Pier Luigi; Monnard, Pierre-Alain

    A short peptide composed of only two amino acid residues, serine and histidine, is here reported to enable oligomerization of RNA monomers. SerHis dipeptide was previously reported to catalyse formation of peptide bonds (Gorlero et al. 2009) as well as possessing broad hydrolytic activities...... – in such environment hydrolysis is thermodynamically favoured over condensation. However, the thermodynamic equilibrium towards condensation can be shifted even in this environment. In this poster we describe a prebiotically plausible system in which the SerHis dipeptide acts as catalyst for the formation of RNA...... oligomers from imidazole derivatives of mononucleotides. The thermodynamic shift towards condensation was achieved using water/ice eutectic phase environment (Monnard and Ziock 2008). To obtain such an environment, a reaction solution is cooled below its freezing point, but above the eutectic point. Under...

  9. Crystalline mesoporous tungsten oxide nanoplate monoliths synthesized by directed soft template method for highly sensitive NO2 gas sensor applications

    International Nuclear Information System (INIS)

    Hoa, Nguyen Duc; Duy, Nguyen Van; Hieu, Nguyen Van

    2013-01-01

    Graphical abstract: Display Omitted Highlights: ► Mesoporous WO 3 nanoplate monoliths were obtained by direct templating synthesis. ► Enable effective accession of the analytic molecules for the sensor applications. ► The WO 3 sensor exhibited a high performance to NO 2 gas at low temperature. -- Abstract: Controllable synthesis of nanostructured metal oxide semiconductors with nanocrystalline size, porous structure, and large specific surface area is one of the key issues for effective gas sensor applications. In this study, crystalline mesoporous tungsten oxide nanoplate-like monoliths with high specific surface areas were obtained through instant direct-templating synthesis for highly sensitive nitrogen dioxide (NO 2 ) sensor applications. The copolymer soft template was converted into a solid carbon framework by heat treatment in an inert gas prior to calcinations in air to sustain the mesoporous structure of tungsten oxide. The multidirectional mesoporous structures of tungsten oxide with small crystalline size, large specific surface area, and superior physical characteristics enabled the rapid and effective accession of analytic gas molecules. As a result, the sensor response was enhanced and the response and recovery times were reduced, in which the mesoporous tungsten oxide based gas sensor exhibited a superior response of 21,155% to 5 ppm NO 2 . In addition, the developed sensor exhibited selective detection of low NO 2 concentration in ammonia and ethanol at a low temperature of approximately 150 °C.

  10. Polyspecific pyrrolysyl-tRNA synthetases from directed evolution

    Science.gov (United States)

    Guo, Li-Tao; Wang, Yane-Shih; Nakamura, Akiyoshi; Eiler, Daniel; Kavran, Jennifer M.; Wong, Margaret; Kiessling, Laura L.; Steitz, Thomas A.; O’Donoghue, Patrick; Söll, Dieter

    2014-01-01

    Pyrrolysyl-tRNA synthetase (PylRS) and its cognate tRNAPyl have emerged as ideal translation components for genetic code innovation. Variants of the enzyme facilitate the incorporation >100 noncanonical amino acids (ncAAs) into proteins. PylRS variants were previously selected to acylate Nε-acetyl-Lys (AcK) onto tRNAPyl. Here, we examine an Nε-acetyl-lysyl-tRNA synthetase (AcKRS), which is polyspecific (i.e., active with a broad range of ncAAs) and 30-fold more efficient with Phe derivatives than it is with AcK. Structural and biochemical data reveal the molecular basis of polyspecificity in AcKRS and in a PylRS variant [iodo-phenylalanyl-tRNA synthetase (IFRS)] that displays both enhanced activity and substrate promiscuity over a chemical library of 313 ncAAs. IFRS, a product of directed evolution, has distinct binding modes for different ncAAs. These data indicate that in vivo selections do not produce optimally specific tRNA synthetases and suggest that translation fidelity will become an increasingly dominant factor in expanding the genetic code far beyond 20 amino acids. PMID:25385624

  11. RNA binding and replication by the poliovirus RNA polymerase

    International Nuclear Information System (INIS)

    Oberste, M.S.

    1988-01-01

    RNA binding and RNA synthesis by the poliovirus RNA-dependent RNA polymerase were studied in vitro using purified polymerase. Templates for binding and RNA synthesis studies were natural RNAs, homopolymeric RNAs, or subgenomic poliovirus-specific RNAs synthesized in vitro from cDNA clones using SP6 or T7 RNA polymerases. The binding of the purified polymerase to poliovirion and other RNAs was studied using a protein-RNA nitrocellulose filter binding assay. A cellular poly(A)-binding protein was found in the viral polymerase preparations, but was easily separated from the polymerase by chromatography on poly(A) Sepharose. The binding of purified polymerase to 32 P-labeled ribohomopolymeric RNAs was examined, and the order of binding observed was poly(G) >>> poly(U) > poly(C) > poly(A). The K a for polymerase binding to poliovirion RNA and to a full-length negative strand transcript was about 1 x 10 9 M -1 . The polymerase binds to a subgenomic RNAs which contain the 3' end of the genome with a K a similar to that for virion RNA, but binds less well to 18S rRNA, globin mRNA, and subgenomic RNAs which lack portions of the 3' noncoding region

  12. Synthesis of Mesoporous ?-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

    OpenAIRE

    Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

    2016-01-01

    This paper reports the synthetic route of 3-D network shape ?-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of ?-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constitue...

  13. Dipeptide catalysed prebiotic polymerization of RNA

    DEFF Research Database (Denmark)

    Wieczorek, Rafal; Luisi, Pier Luigi; Monnard, Pierre-Alain

    2011-01-01

    toward more peptide synthesis. In the present work we describe a prebiotically plausible system in which the SerHis dipeptide acts as catalyst for the formation of RNA oligomers from imidazole derivatives of mononucleotides. The thermodynamic shift towards condensation was achieved using water...... be an important factor from an origin-of-life point of view. Short peptides are plausible products of prebiotic chemistry2. Consequently, they could have influenced chemical evolution on an early stage. An enzyme catalysing hydrolytic reactions can in principle be used as catalyst for condensation: the reverse......-concentrated in the remaining liquid microinclusions, thus creating an environment with low water activity in which condensation reactions can occur. Successful oligomerization of RNA monomers catalysed by the SerHis dipeptide was observed in a broad range of pH, and with all four natural nucleobases. The isomeric dipeptide...

  14. IMP3 RNP safe houses prevent miRNA-directed HMGA2 mRNA decay in cancer and development

    DEFF Research Database (Denmark)

    Jønson, Lars; Christiansen, Jan; Hansen, Thomas van Overeem

    2014-01-01

    by let-7, and let-7 antagomiRs make HMGA2 refractory to IMP3. Removal of let-7 target sites eliminates IMP3-dependent stabilization, and IMP3-containing bodies are depleted of Ago1-4 and miRNAs. The relationship between Hmga2 mRNA and IMPs also exists in the developing limb bud, where IMP1-deficient...... that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression....

  15. Electrochemical synthesis of polydiphenylamine nanofibrils through AAO template

    International Nuclear Information System (INIS)

    Zhao Yanchun; Chen Miao; Liu Xiang; Xu Tao; Liu Weimin

    2005-01-01

    Highly ordered polydiphenylamine (PDPA) nanofibrils arrays have been fabricated within the pores of porous anodic aluminum oxide (AAO) template membrane by electrochemical polymerization. The morphology of PDPA nanofibrils array was observed using transmission electron microscopy (TEM) and its electrochemical behavior and structure were examined by cyclic voltammetry, UV-vis spectroscopy and Fourier transmission infrared spectrum. The result of TEM revealed that the obtained PDPA nanofibrils had uniform and well-aligned array. The UV-vis spectroscopy and electrochemical experimental result indicated that the spatial restraint in the pores of AAO membrane is sufficient to induce the formation of more ordered PDPA chains in the AAO membrane

  16. Electrochemical synthesis of polydiphenylamine nanofibrils through AAO template

    Energy Technology Data Exchange (ETDEWEB)

    Yanchun, Zhao [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Miao, Chen [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Xiang, Liu [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Tao, Xu [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Weimin, Liu [State Key Laboratory of Solid Lubrication, Lanzhou Institute of Chemical Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2005-06-15

    Highly ordered polydiphenylamine (PDPA) nanofibrils arrays have been fabricated within the pores of porous anodic aluminum oxide (AAO) template membrane by electrochemical polymerization. The morphology of PDPA nanofibrils array was observed using transmission electron microscopy (TEM) and its electrochemical behavior and structure were examined by cyclic voltammetry, UV-vis spectroscopy and Fourier transmission infrared spectrum. The result of TEM revealed that the obtained PDPA nanofibrils had uniform and well-aligned array. The UV-vis spectroscopy and electrochemical experimental result indicated that the spatial restraint in the pores of AAO membrane is sufficient to induce the formation of more ordered PDPA chains in the AAO membrane.

  17. Pressure-Induced Polymerization of Acetylene: Structure-Directed Stereoselectivity and a Possible Route to Graphane.

    Science.gov (United States)

    Sun, Jiangman; Dong, Xiao; Wang, Yajie; Li, Kuo; Zheng, Haiyan; Wang, Lijuan; Cody, George D; Tulk, Christopher A; Molaison, Jamie J; Lin, Xiaohuan; Meng, Yufei; Jin, Changqing; Mao, Ho-Kwang

    2017-06-01

    Geometric isomerism in polyacetylene is a basic concept in chemistry textbooks. Polymerization to cis-isomer is kinetically preferred at low temperature, not only in the classic catalytic reaction in solution but also, unexpectedly, in the crystalline phase when it is driven by external pressure without a catalyst. Until now, no perfect reaction route has been proposed for this pressure-induced polymerization. Using in situ neutron diffraction and meta-dynamic simulation, we discovered that under high pressure, acetylene molecules react along a specific crystallographic direction that is perpendicular to those previously proposed. Following this route produces a pure cis-isomer and more surprisingly, predicts that graphane is the final product. Experimentally, polycyclic polymers with a layered structure were identified in the recovered product by solid-state nuclear magnetic resonance and neutron pair distribution functions, which indicates the possibility of synthesizing graphane under high pressure. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Direct Synthesis of Polymer Nanotubes by Aqueous Dispersion Polymerization of a Cyclodextrin/Styrene Complex.

    Science.gov (United States)

    Chen, Xi; Liu, Lei; Huo, Meng; Zeng, Min; Peng, Liao; Feng, Anchao; Wang, Xiaosong; Yuan, Jinying

    2017-12-22

    A one-step synthesis of nanotubes by RAFT dispersion polymerization of cyclodextrin/styrene (CD/St) complexes directly in water is presented. The resulted amphiphilic PEG-b-PS diblock copolymers self-assemble in situ into nanoparticles with various morphologies. Spheres, worms, lamellae, and nanotubes were controllably obtained. Because of the complexation, the swelling degree of polystyrene (PS) blocks by free St is limited, resulting in limited mobility of PS chains. Consequently, kinetically trapped lamellae and nanotubes were obtained instead of spherical vesicles. During the formation of nanotubes, small vesicles first formed at the ends of the tape-like lamellae, then grew and fused into nanotubes with a limited chain rearrangement. The introduction of a host-guest interaction based on CDs enables the aqueous dispersion polymerization of water-immiscible monomers, and produces kinetically trapped nanostructures, which could be a powerful technique for nanomaterials synthesis. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Photoinduced polymerization from direct and sensitized excitation of maleimides

    International Nuclear Information System (INIS)

    Jonsson, S.; Lindgren, K.; Yang, D.; Viswanathan, K.; Nguyen, C.K.; Hoyle, C.

    2000-01-01

    Full text: The efficient photoinitiated polymerization by excited state acceptor monomers, such as maleimides (MI), has been shown in numerous acceptor/donor pair combinations. The strong hydrogen abstractability of excited triplet state MIs have also been evaluated for the initiation of acrylate polymerization and were found to be comparable in efficiency to 'the state of the art' α-cleavage type of photoinitiators. Furthermore, the importance of available abstractable hydrogens as well as the relative abstractabilities has been determined. The unique feature of MIs in general is its dual effect of simultaneously acting as a photoinitiator and as a polymerizable monomer. Once the initiation by photolysis of the acceptor / H-donors has generated a sufficient number of radicals, the unphotolyzed ground state acceptor will copolymerize with the selected monomers chosen. Although the influence of structural variations of the maleimide N-substituent, average functionality, temperature, light intensity, donor structure and acceptor / donor ratio have been carefully investigated, very little information regarding the initiating mechanism has been reported. In this paper, laser flash photolysis has been used in order to clarify and experimentally provide evidence for the mechanism of initiation. The acceptor transient intermediate generated by flash photolysis is readily quenched by typical triplet quenchers. Furthermore, selfquenching and reduction of transient lifetimes as a function of increasing concentrations of typical hydrogen donors have been determined. Stern-Volmer quenching rate constants for direct versus electron transfer induced hydrogen abstractions are calculated and compared to typical H-abstracting photoinitiators such as benzophenone (BP) and thioxanthone derivatives (ITX). From these comparisons it is clear that some triplet state MIs are more efficient in H-abstraction than the corresponding triplet states of BP and ITX. A strong and expected

  20. Simple methods for the 3' biotinylation of RNA.

    Science.gov (United States)

    Moritz, Bodo; Wahle, Elmar

    2014-03-01

    Biotinylation of RNA allows its tight coupling to streptavidin and is thus useful for many types of experiments, e.g., pull-downs. Here we describe three simple techniques for biotinylating the 3' ends of RNA molecules generated by chemical or enzymatic synthesis. First, extension with either the Schizosaccharomyces pombe noncanonical poly(A) polymerase Cid1 or Escherichia coli poly(A) polymerase and N6-biotin-ATP is simple, efficient, and generally applicable independently of the 3'-end sequences of the RNA molecule to be labeled. However, depending on the enzyme and the reaction conditions, several or many biotinylated nucleotides are incorporated. Second, conditions are reported under which splint-dependent ligation by T4 DNA ligase can be used to join biotinylated and, presumably, other chemically modified DNA oligonucleotides to RNA 3' ends even if these are heterogeneous as is typical for products of enzymatic synthesis. Third, we describe the use of 29 DNA polymerase for a template-directed fill-in reaction that uses biotin-dUTP and, thanks to the enzyme's proofreading activity, can cope with more extended 3' heterogeneities.

  1. Poliovirus RNA polymerase: in vitro enzymatic activities, fidelity of replication, and characterization of a temperature-sensitive RNA-negative mutant

    International Nuclear Information System (INIS)

    Stokes, M.A.M.

    1985-01-01

    The in vitro activities of the purified poliovirus RNA polymerase were investigated in this study. The polymerase was shown to be a strict RNA dependent RNA polymerase. It only copied RNA templates but used either a DNA or RNA primer to initiate RNA synthesis. Partially purified polymerase has some DNA polymerase activities. Additional purification of the enzyme and studies with a mutant poliovirus RNA polymerase indicated that the DNA polymerase activities were due to a cellular polymerase. The fidelity of RNA replication in vitro by the purified poliovirus RNA polymerase was studied by measuring the rate of misincorporation of noncomplementary ribonucleotide monophosphates on synthetic homopolymeric RNA templates. The results showed that the ratio of noncomplementary to complementary ribonucleotides incorporated was 1-5 x 10 -3 . The viral polymerase of a poliovirus temperature sensitive RNA-negative mutant, Ts 10, was isolated. This study confirmed that the mutant was viable 33 0 , but was RNA negative at 39 0 . Characterization of the Ts 10 polymerase showed it was significantly more sensitive to heat inactivation than was the old-type polymerase. Highly purified poliovirions were found to contain several noncapsid proteins. At least two of these proteins were labeled by [ 35 S]methionine infected cells and appeared to be virally encoded proteins. One of these proteins was immunoprecipitated by anti-3B/sup vpg/ antiserum. This protein had the approximate Mr = 50,000 and appeared to be one of the previously identified 3B/sup vpg/ precursor proteins

  2. Active RNA polymerases: mobile or immobile molecular machines?

    Directory of Open Access Journals (Sweden)

    Argyris Papantonis

    2010-07-01

    Full Text Available It is widely assumed that active RNA polymerases track along their templates to produce a transcript. We test this using chromosome conformation capture and human genes switched on rapidly and synchronously by tumour necrosis factor alpha (TNFalpha; one is 221 kbp SAMD4A, which a polymerase takes more than 1 h to transcribe. Ten minutes after stimulation, the SAMD4A promoter comes together with other TNFalpha-responsive promoters. Subsequently, these contacts are lost as new downstream ones appear; contacts are invariably between sequences being transcribed. Super-resolution microscopy confirms that nascent transcripts (detected by RNA fluorescence in situ hybridization co-localize at relevant times. Results are consistent with an alternative view of transcription: polymerases fixed in factories reel in their respective templates, so different parts of the templates transiently lie together.

  3. Radiation sensitivity of messenger RNA

    International Nuclear Information System (INIS)

    Ponta, H.; Pfennig-Yeh, M.L.; Herrlich, P.; Karlsruhe Univ.; Wagner, E.F.; Schweiger, M.

    1979-01-01

    Messenger RNA function is inactivated by irradiation with ultraviolet light. A unit length mRNA (in bases) is 2-3 times more sensitive than a unit length of DNA (in base pairs) with respect to the inactivation of template function. These data stem from four experimental systems all of which do not repair DNA: the translation of E. coli mRNA in rifampicin-treated cells, of T7 mRNA in infected E.coli, of f2 phage RNA in vivo, and of stable mRNA in chromosomeless minicells. The comparison of relative sensitivities to UV is relevant to the technique of UV mapping of transcription units which enjoys increasing popularity in pro- and eukaryotic genetic research. (orig.) [de

  4. Radiation sensitivity of messenger RNA

    Energy Technology Data Exchange (ETDEWEB)

    Ponta, H; Pfennig-Yeh, M L; Herrlich, P [Kernforschungszentrum Karlsruhe G.m.b.H. (Germany, F.R.). Inst. fuer Genetik und Toxikologie von Spaltstoffen; Karlsruhe Univ. (TH) (Germany, F.R.). Inst. fuer Genetik); Wagner, E F; Schweiger, M [Innsbruck Univ. (Austria). Inst. fuer Biochemie

    1979-08-01

    Messenger RNA function is inactivated by irradiation with ultraviolet light. A unit length mRNA (in bases) is 2-3 times more sensitive than a unit length of DNA (in base pairs) with respect to the inactivation of template function. These data stem from four experimental systems all of which do not repair DNA: the translation of E. coli mRNA in rifampicin-treated cells, of T7 mRNA in infected E.coli, of f2 phage RNA in vivo, and of stable mRNA in chromosomeless minicells. The comparison of relative sensitivities to UV is relevant to the technique of UV mapping of transcription units which enjoys increasing popularity in pro- and eukaryotic genetic research.

  5. Potent host-directed small-molecule inhibitors of myxovirus RNA-dependent RNA-polymerases.

    Directory of Open Access Journals (Sweden)

    Stefanie A Krumm

    Full Text Available Therapeutic targeting of host cell factors required for virus replication rather than of pathogen components opens new perspectives to counteract virus infections. Anticipated advantages of this approach include a heightened barrier against the development of viral resistance and a broadened pathogen target spectrum. Myxoviruses are predominantly associated with acute disease and thus are particularly attractive for this approach since treatment time can be kept limited. To identify inhibitor candidates, we have analyzed hit compounds that emerged from a large-scale high-throughput screen for their ability to block replication of members of both the orthomyxovirus and paramyxovirus families. This has returned a compound class with broad anti-viral activity including potent inhibition of different influenza virus and paramyxovirus strains. After hit-to-lead chemistry, inhibitory concentrations are in the nanomolar range in the context of immortalized cell lines and human PBMCs. The compound shows high metabolic stability when exposed to human S-9 hepatocyte subcellular fractions. Antiviral activity is host-cell species specific and most pronounced in cells of higher mammalian origin, supporting a host-cell target. While the compound induces a temporary cell cycle arrest, host mRNA and protein biosynthesis are largely unaffected and treated cells maintain full metabolic activity. Viral replication is blocked at a post-entry step and resembles the inhibition profile of a known inhibitor of viral RNA-dependent RNA-polymerase (RdRp activity. Direct assessment of RdRp activity in the presence of the reagent reveals strong inhibition both in the context of viral infection and in reporter-based minireplicon assays. In toto, we have identified a compound class with broad viral target range that blocks host factors required for viral RdRp activity. Viral adaptation attempts did not induce resistance after prolonged exposure, in contrast to rapid

  6. Liquid foam templating - A route to tailor-made polymer foams.

    Science.gov (United States)

    Andrieux, Sébastien; Quell, Aggeliki; Stubenrauch, Cosima; Drenckhan, Wiebke

    2018-06-01

    Solid foams with pore sizes between a few micrometres and a few millimetres are heavily exploited in a wide range of established and emerging applications. While the optimisation of foam applications requires a fine control over their structural properties (pore size distribution, pore opening, foam density, …), the great complexity of most foaming processes still defies a sound scientific understanding and therefore explicit control and prediction of these parameters. We therefore need to improve our understanding of existing processes and also develop new fabrication routes which we understand and which we can exploit to tailor-make new porous materials. One of these new routes is liquid templating in general and liquid foam templating in particular, to which this review article is dedicated. While all solid foams are generated from an initially liquid(-like) state, the particular notion of liquid foam templating implies the specific condition that the liquid foam has time to find its "equilibrium structure" before it is solidified. In other words, the characteristic time scales of the liquid foam's stability and its solidification are well separated, allowing to build on the vast know-how on liquid foams established over the last 20 years. The dispersed phase of the liquid foam determines the final pore size and pore size distribution, while the continuous phase contains the precursors of the desired porous scaffold. We review here the three key challenges which need to be addressed by this approach: (1) the control of the structure of the liquid template, (2) the matching of the time scales between the stability of the liquid template and solidification, and (3) the preservation of the structure of the template throughout the process. Focusing on the field of polymer foams, this review gives an overview of recent research on the properties of liquid foam templates and summarises a key set of studies in the emerging field of liquid foam templating. It

  7. Perl Template Toolkit

    CERN Document Server

    Chamberlain, Darren; Cross, David; Torkington, Nathan; Diaz, tatiana Apandi

    2004-01-01

    Among the many different approaches to "templating" with Perl--such as Embperl, Mason, HTML::Template, and hundreds of other lesser known systems--the Template Toolkit is widely recognized as one of the most versatile. Like other templating systems, the Template Toolkit allows programmers to embed Perl code and custom macros into HTML documents in order to create customized documents on the fly. But unlike the others, the Template Toolkit is as facile at producing HTML as it is at producing XML, PDF, or any other output format. And because it has its own simple templating language, templates

  8. The RNA synthesis machinery of negative-stranded RNA viruses

    International Nuclear Information System (INIS)

    Ortín, Juan; Martín-Benito, Jaime

    2015-01-01

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes

  9. The RNA synthesis machinery of negative-stranded RNA viruses

    Energy Technology Data Exchange (ETDEWEB)

    Ortín, Juan, E-mail: jortin@cnb.csic.es [Department of Molecular and Cellular Biology, Centro Nacional de Biotecnología (CSIC) and CIBER de Enfermedades Respiratorias (ISCIII), Madrid (Spain); Martín-Benito, Jaime, E-mail: jmartinb@cnb.csic.es [Department of Macromolecular Structures, Centro Nacional de Biotecnología (CSIC), Madrid (Spain)

    2015-05-15

    The group of Negative-Stranded RNA Viruses (NSVs) includes many human pathogens, like the influenza, measles, mumps, respiratory syncytial or Ebola viruses, which produce frequent epidemics of disease and occasional, high mortality outbreaks by transmission from animal reservoirs. The genome of NSVs consists of one to several single-stranded, negative-polarity RNA molecules that are always assembled into mega Dalton-sized complexes by association to many nucleoprotein monomers. These RNA-protein complexes or ribonucleoproteins function as templates for transcription and replication by action of the viral RNA polymerase and accessory proteins. Here we review our knowledge on these large RNA-synthesis machines, including the structure of their components, the interactions among them and their enzymatic activities, and we discuss models showing how they perform the virus transcription and replication programmes. - Highlights: • Overall organisation of NSV RNA synthesis machines. • Structure and function of the ribonucleoprotein components: Atomic structure of the RNA polymerase complex. • Commonalities and differences between segmented- and non-segmented NSVs. • Transcription versus replication programmes.

  10. Small RNA-directed epigenetic natural variation in Arabidopsis thaliana.

    Directory of Open Access Journals (Sweden)

    Jixian Zhai

    2008-04-01

    Full Text Available Progress in epigenetics has revealed mechanisms that can heritably regulate gene function independent of genetic alterations. Nevertheless, little is known about the role of epigenetics in evolution. This is due in part to scant data on epigenetic variation among natural populations. In plants, small interfering RNA (siRNA is involved in both the initiation and maintenance of gene silencing by directing DNA methylation and/or histone methylation. Here, we report that, in the model plant Arabidopsis thaliana, a cluster of approximately 24 nt siRNAs found at high levels in the ecotype Landsberg erecta (Ler could direct DNA methylation and heterochromatinization at a hAT element adjacent to the promoter of FLOWERING LOCUS C (FLC, a major repressor of flowering, whereas the same hAT element in ecotype Columbia (Col with almost identical DNA sequence, generates a set of low abundance siRNAs that do not direct these activities. We have called this hAT element MPF for Methylated region near Promoter of FLC, although de novo methylation triggered by an inverted repeat transgene at this region in Col does not alter its FLC expression. DNA methylation of the Ler allele MPF is dependent on genes in known silencing pathways, and such methylation is transmissible to Col by genetic crosses, although with varying degrees of penetrance. A genome-wide comparison of Ler and Col small RNAs identified at least 68 loci matched by a significant level of approximately 24 nt siRNAs present specifically in Ler but not Col, where nearly half of the loci are related to repeat or TE sequences. Methylation analysis revealed that 88% of the examined loci (37 out of 42 were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes.

  11. Pseudo template synthesis of poly (1-naphthylamine): effect of environment on nanostructured morphology

    International Nuclear Information System (INIS)

    Riaz, Ufana; Ahmad, Sharif; Ashraf, S. M.

    2008-01-01

    A template free approach was adopted to explore the effect of polymerization environment on the synthesis of nanostructured poly (1-naphthylamine) (PNA) using cupric chloride as oxidant and methyl alcohol as medium. The polymerization environment was varied by carrying out the synthesis in the presence of nitrogen and oxygen. The morphology of the synthesized nanostructured PNA was investigated using scanning electron microscopy (SEM), transmission electron microscopy (TEM), UV-vis and FT-IR spectroscopies. PNA nanorods of sizes varying between 50-100 nm were obtained in presence of nitrogen while in presence of oxygen, it formed aggregated globular particles of sizes varying between 80-100 nm. The results provide valuable information on controlling the synthesis of one-dimensional nanostructured conducting polymers that exhibit superior processibility as compared to the conventional conducting polymers.

  12. Structural explanation for the role of Mn2+ in the activity of phi6 RNA-dependent RNA polymerase.

    Science.gov (United States)

    Poranen, Minna M; Salgado, Paula S; Koivunen, Minni R L; Wright, Sam; Bamford, Dennis H; Stuart, David I; Grimes, Jonathan M

    2008-11-01

    The biological role of manganese (Mn(2+)) has been a long-standing puzzle, since at low concentrations it activates several polymerases whilst at higher concentrations it inhibits. Viral RNA polymerases possess a common architecture, reminiscent of a closed right hand. The RNA-dependent RNA polymerase (RdRp) of bacteriophage 6 is one of the best understood examples of this important class of polymerases. We have probed the role of Mn(2+) by biochemical, biophysical and structural analyses of the wild-type enzyme and of a mutant form with an altered Mn(2+)-binding site (E491 to Q). The E491Q mutant has much reduced affinity for Mn(2+), reduced RNA binding and a compromised elongation rate. Loss of Mn(2+) binding structurally stabilizes the enzyme. These data and a re-examination of the structures of other viral RNA polymerases clarify the role of manganese in the activation of polymerization: Mn(2+) coordination of a catalytic aspartate is necessary to allow the active site to properly engage with the triphosphates of the incoming NTPs. The structural flexibility caused by Mn(2+) is also important for the enzyme dynamics, explaining the requirement for manganese throughout RNA polymerization.

  13. Smart Contract Templates: foundations, design landscape and research directions

    OpenAIRE

    Clack, Christopher D.; Bakshi, Vikram A.; Braine, Lee

    2016-01-01

    In this position paper, we consider some foundational topics regarding smart contracts (such as terminology, automation, enforceability, and semantics) and define a smart contract as an automatable and enforceable agreement. We explore a simple semantic framework for smart contracts, covering both operational and non-operational aspects, and describe templates and agreements for legally-enforceable smart contracts, based on legal documents. Building upon the Ricardian Contract, we identify op...

  14. Fabrication of large area flexible nanoplasmonic templates with flow coating

    Science.gov (United States)

    Huang, Qian; Devetter, Brent M.; Roosendaal, Timothy; LaBerge, Max; Bernacki, Bruce E.; Alvine, Kyle J.

    2017-07-01

    We describe the development of a custom-built two-axis flow coater for the deposition of polymeric nanosphere monolayers that could be used in the fabrication of large area nanoplasmonic films. The technique described here has the capability of depositing large areas (up to 7 in. × 10 in.) of self-assembled monolayers of polymeric nanospheres onto polyethylene terephthalate (PET) films. Here, three sets of films consisting of different diameters (ranging from 100 to 300 nm) of polymeric nanospheres were used to demonstrate the capabilities of this instrument. To improve the surface wettability of the PET substrates during wet-deposition, we enhanced the wettability by using a forced air blown-arc plasma treatment system. Both the local microstructure, as confirmed by scanning electron microscopy, describing monolayer and multilayer coverage, and the overall macroscopic uniformity of the resultant nanostructured film were optimized by controlling the relative stage to blade speed and nanosphere concentration. We also show using a smaller nanoparticle template that such monolayers can be used to form nanoplasmonic films. As this flow-coating approach is a scalable technique, large area films such as the ones described here have a variety of crucial emerging applications in areas such as energy, catalysis, and chemical sensing.

  15. Priming and the guidance by visual and categorical templates in visual search

    NARCIS (Netherlands)

    Wilschut, A.M.; Theeuwes, J.; Olivers, C.N.L.

    2014-01-01

    Visual search is thought to be guided by top-down templates that are held in visual working memory. Previous studies have shown that a search-guiding template can be rapidly and strongly implemented from a visual cue, whereas templates are less effective when based on categorical cues. Direct visual

  16. IMP3 RNP Safe Houses Prevent miRNA-Directed HMGA2 mRNA Decay in Cancer and Development

    Directory of Open Access Journals (Sweden)

    Lars Jønson

    2014-04-01

    Full Text Available The IMP3 RNA-binding protein is associated with metastasis and poor outcome in human cancer. Using solid cancer transcriptome data, we found that IMP3 correlates with HMGA2 mRNA expression. Cytoplasmic IMP3 granules contain HMGA2, and IMP3 dose-dependently increases HMGA2 mRNA. HMGA2 is regulated by let-7, and let-7 antagomiRs make HMGA2 refractory to IMP3. Removal of let-7 target sites eliminates IMP3-dependent stabilization, and IMP3-containing bodies are depleted of Ago1-4 and miRNAs. The relationship between Hmga2 mRNA and IMPs also exists in the developing limb bud, where IMP1-deficient embryos show dose-dependent Hmga2 mRNA downregulation. Finally, IMP3 ribonucleoproteins (RNPs contain other let-7 target mRNAs, including LIN28B, and a global gene set enrichment analysis demonstrates that miRNA-regulated transcripts in general are upregulated following IMP3 induction. We conclude that IMP3 RNPs may function as cytoplasmic safe houses and prevent miRNA-directed mRNA decay of oncogenes during tumor progression.

  17. Smart polymeric nanoparticles with pH-responsive and PEG-detachable properties for co-delivering paclitaxel and survivin siRNA to enhance antitumor outcomes

    Directory of Open Access Journals (Sweden)

    Jin M

    2018-04-01

    Full Text Available Mingji Jin,1 Guangming Jin,2 Lin Kang,1 Liqing Chen,1 Zhonggao Gao,1 Wei Huang11State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Institute of Materia Medica, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; 2Department of Diagnostic Radiology 2, Yanbian University Hospital, Yanji, Jilin, China Background: The co-delivery of chemotherapeutic agents and small interfering RNA (siRNA within one cargo can enhance the anticancer outcomes through its synergistic therapeutic effects. Materials and methods: We prepared smart polymeric nanoparticles (NPs with pH-responsive and poly(ethylene glycol (PEG-detachable properties to systemically co-deliver paclitaxel (PTX and siRNA against survivin gene for lung cancer therapy. The cationic polyethyleneimine-block-polylactic acid (PEI-PLA was first synthesized and characterized, with good biocompatibility. PTX was encapsulated into the hydrophobic core of the PEI-PLA polymers by dialysis, and then the survivin siRNA was loaded onto the PTX-loaded NPs (PEI-PLA/PTX through electrostatic interaction between siRNA and PEI block. Finally, the negatively charged poly(ethylene glycol-block-poly(l-aspartic acid sodium salt (PEG-PAsp was coated onto the surface of NPs by electrostatic interaction to form final smart polymeric NPs with mean particle size of 82.4 nm and zeta potential of 4.1 mV. After uptake of NPs by tumor cells, the PEG-PAsp segments became electrically neutral owing to the lower endosome pH and consequently detached from the smart NPs. This process allowed endosomal escape of the NPs through the proton-sponge effect of the exposed PEI moiety. Results: The resulting NPs achieved drug loading of 6.04 wt% and exhibited good dispersibility within 24 h in 10% fetal bovine serum (FBS. At pH 5.5, the NPs presented better drug release and cellular uptake than at pH 7.4. The NPs with survivin siRNA effectively knocked down the expression of

  18. The scenario on the origin of translation in the RNA world: in principle of replication parsimony

    Directory of Open Access Journals (Sweden)

    Ma Wentao

    2010-11-01

    Full Text Available Abstract Background It is now believed that in the origin of life, proteins should have been "invented" in an RNA world. However, due to the complexity of a possible RNA-based proto-translation system, this evolving process seems quite complicated and the associated scenario remains very blurry. Considering that RNA can bind amino acids with specificity, it has been reasonably supposed that initial peptides might have been synthesized on "RNA templates" containing multiple amino acid binding sites. This "Direct RNA Template (DRT" mechanism is attractive because it should be the simplest mechanism for RNA to synthesize peptides, thus very likely to have been adopted initially in the RNA world. Then, how this mechanism could develop into a proto-translation system mechanism is an interesting problem. Presentation of the hypothesis Here an explanation to this problem is shown considering the principle of "replication parsimony" --- genetic information tends to be utilized in a parsimonious way under selection pressure, due to its replication cost (e.g., in the RNA world, nucleotides and ribozymes for RNA replication. Because a DRT would be quite long even for a short peptide, its replication cost would be great. Thus the diversity and the length of functional peptides synthesized by the DRT mechanism would be seriously limited. Adaptors (proto-tRNAs would arise to allow a DRT's complementary strand (called "C-DRT" here to direct the synthesis of the same peptide synthesized by the DRT itself. Because the C-DRT is a necessary part in the DRT's replication, fewer turns of the DRT's replication would be needed to synthesize definite copies of the functional peptide, thus saving the replication cost. Acting through adaptors, C-DRTs could transform into much shorter templates (called "proto-mRNAs" here and substitute the role of DRTs, thus significantly saving the replication cost. A proto-rRNA corresponding to the small subunit rRNA would then emerge

  19. Heparin molecularly imprinted polymer thin flm on gold electrode by plasma-induced graft polymerization for label-free biosensor.

    Science.gov (United States)

    Orihara, Kouhei; Hikichi, Atsushi; Arita, Tomohiko; Muguruma, Hitoshi; Yoshimi, Yasuo

    2018-03-20

    Heparin, a highly sulfated glycosaminoglycan, is an important biomaterial having biological and therapeutic functionalities such as anticoagulation, regeneration, and protein stabilization. This study addresses a label-free quartz crystal microbalance (QCM) biosensor for heparin detection based on a macromolecularly imprinted polymer (MIP) as an artificial recognition element. We demonstrate the novel strategy for MIP in the form of thin film on a gold (Au) electrode with the plasma-induced graft polymerization (PIP) technique. The procedure of PIP is as follows: (i) Hexamethyldisiloxane plasma-polymerized thin film (PPF) as a pre-coating scaffold of active species for PIP (post-polymerization) is deposited on an Au electrode. (ii) The PPF/Au electrode is soaked in an water solution containing heparin (template), (2-(methacryloxy)-ethyl)trimethylammonium chloride acrylamide (functional monomer), acrylamide, and N,N-methylenebisacrylamide (crosslinker). Double bonds of monomer and crosslinker attacked by residually active species in pre-coating PPF cause radical chain reaction. Consequently, a growing polymer network of 20 nm thickness of PIP-MIP thin film is formed and grafted on the PPF/Au surface. (iii) The PIP-MIP/PPF/Au is washed by sodium chloride solution so as to remove the template. Non-imprinted polymer (NIP) is carried out like the same procedure without a template. The AFM, XPS, and QCM measurements show that the PIP process facilitates macromolecularly surface imprinting of template heparin where the template is easily removed and is rapidly rebound to PIP-MIP without a diffusional barrier. The heparin-PIP-MIP specifically binds to heparin compared with heparin analog chondroitin sulfate C (selective factor: 4.0) and a detectable range of heparin in the presence of CS (0.1 wt%) was 0.001-0.1 wt%. The PIP-NIP does not show selectivity between them. The evaluated binding kinetics are association (k a  = 350 ± 100 M -1  s -1

  20. RNA-directed DNA methylation: Mechanisms and functions

    KAUST Repository

    Mahfouz, Magdy M.

    2010-07-01

    Epigenetic RNA based gene silencing mechanisms play a major role in genome stability and control of gene expression. Transcriptional gene silencing via RNA-directed DNA methylation (RdDM) guides the epigenetic regulation of the genome in response to disease states, growth, developmental and stress signals. RdDM machinery is composed of proteins that produce and modify 24-nt- long siRNAs, recruit the RdDM complex to genomic targets, methylate DNA and remodel chromatin. The final DNA methylation pattern is determined by either DNA methyltransferase alone or by the combined action of DNA methyltransferases and demethylases. The dynamic interaction between RdDM and demethylases may render the plant epigenome plastic to growth, developmental, and environmental cues. The epigenome plasticity may allow the plant genome to assume many epigenomes and to have the right epigenome at the right time in response to intracellular or extracellular stimuli. This review discusses recent advances in RdDM research and considers future perspectives.

  1. Graphene Emerges as a Versatile Template for Materials Preparation.

    Science.gov (United States)

    Li, Zhengjie; Wu, Sida; Lv, Wei; Shao, Jiao-Jing; Kang, Feiyu; Yang, Quan-Hong

    2016-05-01

    Graphene and its derivatives are emerging as a class of novel but versatile templates for the controlled preparation and functionalization of materials. In this paper a conceptual review on graphene-based templates is given, highlighting their versatile roles in materials preparation. Graphene is capable of acting as a low-dimensional hard template, where its two-dimensional morphology directs the formation of novel nanostructures. Graphene oxide and other functionalized graphenes are amphiphilic and may be seen as soft templates for formatting the growth or inducing the controlled assembly of nanostructures. In addition, nanospaces in restacked graphene can be used for confining the growth of sheet-like nanostructures, and assemblies of interlinked graphenes can behave either as skeletons for the formation of composite materials or as sacrificial templates for novel materials with a controlled network structure. In summary, flexible graphene and its derivatives together with an increasing number of assembled structures show great potentials as templates for materials production. Many challenges remain, for example precise structural control of such novel templates and the removal of the non-functional remaining templates. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Removal of carbamazepine and clofibric acid from water using double templates-molecularly imprinted polymers.

    Science.gov (United States)

    Dai, Chao-meng; Zhang, Juan; Zhang, Ya-lei; Zhou, Xue-fei; Duan, Yan-ping; Liu, Shu-guang

    2013-08-01

    A novel double templates-molecularly imprinted polymer (MIP) was prepared by precipitation polymerization using carbamazepine (CBZ) and clofibric acid (CA) as the double templates molecular and 2-vinylpyridine as functional monomer. The equilibrium data of MIP was well described by the Freundlich isotherm model. Two kinetic models were adopted to describe the experimental data, and the pseudo second-order model well-described adsorption of CBZ and CA on the MIP. Adsorption experimental results showed that the MIP had good selectivity and adsorption capacity for CBZ and CA in the presence of competitive compounds compared with non-imprinted polymer, commercial powdered activated carbon, and C18 adsorbents. The feasibility of removing CBZ and CA from water by the MIP was demonstrated using tap water, lake water, and river water.

  3. A comparison of stresses in molar teeth restored with inlays and direct restorations, including polymerization shrinkage of composite resin and tooth loading during mastication.

    Science.gov (United States)

    Dejak, Beata; Młotkowski, Andrzej

    2015-03-01

    Polymerization shrinkage of composites is one of the main causes of leakage around dental restorations. Despite the large numbers of studies there is no consensus, what kind of teeth reconstruction--direct or indirect composite restorations are the most beneficial and the most durable. The aim was to compare equivalent stresses and contact adhesive stresses in molar teeth with class II MOD cavities, which were restored with inlays and direct restorations (taking into account polymerization shrinkage of composite resin) during simulated mastication. The study was conducted using the finite elements method with the application of contact elements. Three 3D models of first molars were created: model A was an intact tooth; model B--a tooth with a composite inlay, and model C--a tooth with a direct composite restoration. Polymerization linear shrinkage 0.7% of a direct composite restoration and resin luting cement was simulated (load 1). A computer simulation of mastication was performed (load 2). In these 2 situations, equivalent stresses according to the modified von Mises criterion (mvM) in the materials of mandibular first molar models with different restorations were calculated and compared. Contact stresses in the luting cement-tooth tissue adhesive interface around the restorations were also assessed and analyzed. Equivalent stresses in a tooth with a direct composite restoration (the entire volume of which was affected by polymerization shrinkage) were many times higher than in the tooth restored with a composite inlay (where shrinkage was present only in a thin layer of the luting cement). In dentin and enamel the stress values were 8-14 times higher, and were 13 times higher in the direct restoration than in the inlay. Likewise, contact stresses in the adhesive bond around the direct restoration were 6.5-7.7 times higher compared to an extraorally cured restoration. In the masticatory simulation, shear contact stresses in the adhesive bond around the direct

  4. Direct Synthesis of Telechelic Polyethylene by Selective Insertion Polymerization

    KAUST Repository

    Jian, Zhongbao; Falivene, Laura; Boffa, Giusi; Sá nchez, Sheila Ortega; Caporaso, Lucia; Grassi, Alfonso; Mecking, Stefan

    2016-01-01

    A single-step route to telechelic polyethylene (PE) is enabled by selective insertion polymerization. PdII-catalyzed copolymerization of ethylene and 2-vinylfuran (VF) generates α,ω-di-furan telechelic polyethylene. Orthogonally reactive exclusively

  5. In situ synthesis of molecularly imprinted nanoparticles in porous support membranes using high-viscosity polymerization solvents.

    Science.gov (United States)

    Renkecz, Tibor; László, Krisztina; Horváth, Viola

    2012-06-01

    There is a growing need in membrane separations for novel membrane materials providing selective retention. Molecularly imprinted polymers (MIPs) are promising candidates for membrane functionalization. In this work, a novel approach is described to prepare composite membrane adsorbers incorporating molecularly imprinted microparticles or nanoparticles into commercially available macroporous filtration membranes. The polymerization is carried out in highly viscous polymerization solvents, and the particles are formed in situ in the pores of the support membrane. MIP particle composite membranes selective for terbutylazine were prepared and characterized by scanning electron microscopy and N₂ porosimetry. By varying the polymerization solvent microparticles or nanoparticles with diameters ranging from several hundred nanometers to 1 µm could be embedded into the support. The permeability of the membranes was in the range of 1000 to 20,000 Lm⁻²  hr⁻¹  bar⁻¹. The imprinted composite membranes showed high MIP/NIP (nonimprinted polymer) selectivity for the template in organic media both in equilibrium-rebinding measurements and in filtration experiments. The solid phase extraction of a mixture of the template, its analogs, and a nonrelated compound demonstrated MIP/NIP selectivity and substance selectivity of the new molecularly imprinted membrane. The synthesis technique offers a potential for the cost-effective production of selective membrane adsorbers with high capacity and high throughput. Copyright © 2012 John Wiley & Sons, Ltd.

  6. Crystalline mesoporous tungsten oxide nanoplate monoliths synthesized by directed soft template method for highly sensitive NO{sub 2} gas sensor applications

    Energy Technology Data Exchange (ETDEWEB)

    Hoa, Nguyen Duc, E-mail: ndhoa@itims.edu.vn [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology (HUST) (Viet Nam); Duy, Nguyen Van [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology (HUST) (Viet Nam); Hieu, Nguyen Van, E-mail: hieu@itims.edu.vn [International Training Institute for Materials Science (ITIMS), Hanoi University of Science and Technology (HUST) (Viet Nam)

    2013-02-15

    Graphical abstract: Display Omitted Highlights: ► Mesoporous WO{sub 3} nanoplate monoliths were obtained by direct templating synthesis. ► Enable effective accession of the analytic molecules for the sensor applications. ► The WO{sub 3} sensor exhibited a high performance to NO{sub 2} gas at low temperature. -- Abstract: Controllable synthesis of nanostructured metal oxide semiconductors with nanocrystalline size, porous structure, and large specific surface area is one of the key issues for effective gas sensor applications. In this study, crystalline mesoporous tungsten oxide nanoplate-like monoliths with high specific surface areas were obtained through instant direct-templating synthesis for highly sensitive nitrogen dioxide (NO{sub 2}) sensor applications. The copolymer soft template was converted into a solid carbon framework by heat treatment in an inert gas prior to calcinations in air to sustain the mesoporous structure of tungsten oxide. The multidirectional mesoporous structures of tungsten oxide with small crystalline size, large specific surface area, and superior physical characteristics enabled the rapid and effective accession of analytic gas molecules. As a result, the sensor response was enhanced and the response and recovery times were reduced, in which the mesoporous tungsten oxide based gas sensor exhibited a superior response of 21,155% to 5 ppm NO{sub 2}. In addition, the developed sensor exhibited selective detection of low NO{sub 2} concentration in ammonia and ethanol at a low temperature of approximately 150 °C.

  7. Direct synthesis of carbon-templating mesoporous ZSM-5 using microwave heating

    Czech Academy of Sciences Publication Activity Database

    Koo, J.-B.; Jiang, N.; Saravanamurugan, S.; Voláková, Martina; Musilová, Zuzana; Čejka, Jiří; Park, S.-E.

    2010-01-01

    Roč. 276, č. 2 (2010), s. 327-334 ISSN 0021-9517 Institutional research plan: CEZ:AV0Z40400503 Keywords : mesoporous ZSM-5 * template * microwave irradiation * carbon Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 5.415, year: 2010

  8. On the synthesis of peptide imprinted polymers by a combined suspension-Epitope polymerization method

    International Nuclear Information System (INIS)

    Kotrotsiou, O.; Chaitidou, S.; Kiparissides, C.

    2009-01-01

    In the past, molecularly imprinted polymers (MIPs), prepared by free-radical bulk polymerization, have been used for the selective recognition of small biomolecules (i.e., amino acids and amino acid derivatives). Presently, there is a need for the synthesis of MIPs capable of recognizing larger biomolecules (i.e., peptides and proteins). Moreover, it is highly desirable the production of MIP microparticles with well-defined morphological characteristics (e.g., particle size distribution, porosity, etc.) via particulate polymerization techniques. In the present study, the synthesis of molecularly imprinted microparticles, produced via the suspension and inverse suspension polymerization methods, using the 'epitope approach', is reported. The hydrophobic (i.e., Boc-Trp-Trp-Trp) or hydrophilic (i.e., His-Phe) oligo-peptides were employed as template molecules. The potential of the combined suspension polymerization method with the 'epitope approach' for the production of MIP microparticles is demonstrated, as well as the specificity and selectivity characteristics of the MIP microparticles towards hydrophobic and hydrophilic oligo-peptides. The proposed method appears to be a very promising and efficient technique for separation of proteins.

  9. Molecularly Imprinted Polymer Technology: A Powerful, Generic ...

    African Journals Online (AJOL)

    determined analyte (called template) in a polymeric matrix. The template directs the molecular positioning and orientation of the material's functional monomers. Cross-linking ensures polymer rigidity that “freezes” the 3-D molecular architecture of the ...

  10. Tailoring Lipid and Polymeric Nanoparticles as siRNA Carriers towards the Blood-Brain Barrier - from Targeting to Safe Administration.

    Science.gov (United States)

    Gomes, Maria João; Fernandes, Carlos; Martins, Susana; Borges, Fernanda; Sarmento, Bruno

    2017-03-01

    Blood-brain barrier is a tightly packed layer of endothelial cells surrounding the brain that acts as the main obstacle for drugs enter the central nervous system (CNS), due to its unique features, as tight junctions and drug efflux systems. Therefore, since the incidence of CNS disorders is increasing worldwide, medical therapeutics need to be improved. Consequently, aiming to surpass blood-brain barrier and overcome CNS disabilities, silencing P-glycoprotein as a drug efflux transporter at brain endothelial cells through siRNA is considered a promising approach. For siRNA enzymatic protection and efficient delivery to its target, two different nanoparticles platforms, solid lipid (SLN) and poly-lactic-co-glycolic (PLGA) nanoparticles were used in this study. Polymeric PLGA nanoparticles were around 115 nm in size and had 50 % of siRNA association efficiency, while SLN presented 150 nm and association efficiency close to 52 %. Their surface was functionalized with a peptide-binding transferrin receptor, in a site-oriented manner confirmed by NMR, and their targeting ability against human brain endothelial cells was successfully demonstrated by fluorescence microscopy and flow cytometry. The interaction of modified nanoparticles with brain endothelial cells increased 3-fold compared to non-modified lipid nanoparticles, and 4-fold compared to non-modified PLGA nanoparticles, respectively. These nanosystems, which were also demonstrated to be safe for human brain endothelial cells, without significant cytotoxicity, bring a new hopeful breath to the future of brain diseases therapies.

  11. Stroke from Delayed Embolization of Polymerized Glue Following Percutaneous Direct Injection of a Carotid Body Tumor

    Energy Technology Data Exchange (ETDEWEB)

    Krishnamoorthy, Thamburaj; Gupta, Arun Kumar; Rajan, Jayadevan E; Thomas, Bejoy [Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, Kerala, (India)

    2007-06-15

    Direct percutaneous embolization of hypervascular tumors results in more effective preoperative devascularization. Migration of glue is a well known complication of direct glue injection and it may lead to stroke or cranial nerve deficits. We report here on a case of carotid body tumor in a 52-year-old man; the tumor was mainly embolized by percutaneous injection of 50% glue and this was supported with balloon protection of the internal carotid artery. Thirteen hours later, he developed hemiparesis from delayed migration of glue. The possible mechanisms of this migration are discussed and preventive measures are suggested. Preoperative embolization of hypervascular tumors of the head and neck, including carotid body tumor, is often performed to decrease the amount of blood loss during surgery. Devascularization is mainly performed with particulate agents and by employing the transarterial route. More effective embolization may be achieved by performing percutaneous direct embolization of hypervascular tumors with liquid embolic agents. Even though there are few reports available on direct embolization, complications from glue migration have been reported, and this mainly happens during the procedure when the glue is in a liquid state. We report here on a case of delayed migration of polymerized glue (n-butyl-2-cyanoacrylate [NBCA]), many hours after the procedure, into the intracranial circulation and the final result was stroke. A 52-year-old male with right carotid body tumor underwent direct percutaneous glue (n-butylcyanoacrylate [NBCA]) embolization. Several hours later, he developed left hemiparesis from embolization of the polymerized glue cast. Migration of glue during percutaneous tumor embolization is presumed to occur only in the liquid state, which may lead to stroke or cranial nerve deficits. To the best of our knowledge, this is the first report of delayed glue embolization from a treated hypervascular tumor of the head and neck.

  12. Synthesis of HNTs@PEDOT composites via in situ chemical oxidative polymerization and their application in electrode materials

    Science.gov (United States)

    Wang, Fang; Zhang, Xianhong; Ma, Yuhong; Yang, Wantai

    2018-01-01

    The hybrid composite of poly(3,4-ethylenedioxythiophene) (PEDOT) and halloysite nanotubes (HNTs) was synthesized by a two-step process. First, poly(sodium styrene sulfonate) (PSSNa) was grafted onto HNTs via surface initiated atom transfer radical polymerization. Then with the HNTs-g-PSS as a template and the grafted PSS chains as the counterion dopant, PEDOT was precipitated onto the template via in situ oxidization polymerization of EDOT to form HNTs@PEDOT hybrid composites. The conductivity of HNTs@PEDOT can reach up to 9.35 S/cm with the content of 40% HNTs-g-PSS, which increased almost 78 times than that of pure PEDOT (about 0.12 S/cm) prepared at the similar condition. Further treated with p-toluenesulfonic acid (TsOH) as external dopant, the conductivity of HNTs@PEDOT increased to 24.3 S/cm. The electrochemical properties of the composites were investigated with cyclic voltammetry, galvanostatic charge-discharge and electrochemical impedance spectroscopy with three-electrode cell configuration. The results showed that the capacitance of HNTs@PEDOT composite increased 55% than that of pure PEDOT.

  13. Design of multi-phase dynamic chemical networks

    Science.gov (United States)

    Chen, Chenrui; Tan, Junjun; Hsieh, Ming-Chien; Pan, Ting; Goodwin, Jay T.; Mehta, Anil K.; Grover, Martha A.; Lynn, David G.

    2017-08-01

    Template-directed polymerization reactions enable the accurate storage and processing of nature's biopolymer information. This mutualistic relationship of nucleic acids and proteins, a network known as life's central dogma, is now marvellously complex, and the progressive steps necessary for creating the initial sequence and chain-length-specific polymer templates are lost to time. Here we design and construct dynamic polymerization networks that exploit metastable prion cross-β phases. Mixed-phase environments have been used for constructing synthetic polymers, but these dynamic phases emerge naturally from the growing peptide oligomers and create environments suitable both to nucleate assembly and select for ordered templates. The resulting templates direct the amplification of a phase containing only chain-length-specific peptide-like oligomers. Such multi-phase biopolymer dynamics reveal pathways for the emergence, self-selection and amplification of chain-length- and possibly sequence-specific biopolymers.

  14. An empirical strategy to detect bacterial transcript structure from directional RNA-seq transcriptome data.

    Science.gov (United States)

    Wang, Yejun; MacKenzie, Keith D; White, Aaron P

    2015-05-07

    As sequencing costs are being lowered continuously, RNA-seq has gradually been adopted as the first choice for comparative transcriptome studies with bacteria. Unlike microarrays, RNA-seq can directly detect cDNA derived from mRNA transcripts at a single nucleotide resolution. Not only does this allow researchers to determine the absolute expression level of genes, but it also conveys information about transcript structure. Few automatic software tools have yet been established to investigate large-scale RNA-seq data for bacterial transcript structure analysis. In this study, 54 directional RNA-seq libraries from Salmonella serovar Typhimurium (S. Typhimurium) 14028s were examined for potential relationships between read mapping patterns and transcript structure. We developed an empirical method, combined with statistical tests, to automatically detect key transcript features, including transcriptional start sites (TSSs), transcriptional termination sites (TTSs) and operon organization. Using our method, we obtained 2,764 TSSs and 1,467 TTSs for 1331 and 844 different genes, respectively. Identification of TSSs facilitated further discrimination of 215 putative sigma 38 regulons and 863 potential sigma 70 regulons. Combining the TSSs and TTSs with intergenic distance and co-expression information, we comprehensively annotated the operon organization in S. Typhimurium 14028s. Our results show that directional RNA-seq can be used to detect transcriptional borders at an acceptable resolution of ±10-20 nucleotides. Technical limitations of the RNA-seq procedure may prevent single nucleotide resolution. The automatic transcript border detection methods, statistical models and operon organization pipeline that we have described could be widely applied to RNA-seq studies in other bacteria. Furthermore, the TSSs, TTSs, operons, promoters and unstranslated regions that we have defined for S. Typhimurium 14028s may constitute valuable resources that can be used for

  15. RNA Profiling for Biomarker Discovery: Practical Considerations for Limiting Sample Sizes

    Directory of Open Access Journals (Sweden)

    Danny J. Kelly

    2005-01-01

    Full Text Available We have compared microarray data generated on Affymetrix™ chips from standard (8 micrograms or low (100 nanograms amounts of total RNA. We evaluated the gene signals and gene fold-change estimates obtained from the two methods and validated a subset of the results by real time, polymerase chain reaction assays. The correlation of low RNA derived gene signals to gene signals obtained from standard RNA was poor for less to moderately abundant genes. Genes with high abundance showed better correlation in signals between the two methods. The signal correlation between the low RNA and standard RNA methods was improved by including a reference sample in the microarray analysis. In contrast, the fold-change estimates for genes were better correlated between the two methods regardless of the magnitude of gene signals. A reference sample based method is suggested for studies that would end up comparing gene signal data from a combination of low and standard RNA templates; no such referencing appears to be necessary when comparing fold-changes of gene expression between standard and low template reactions.

  16. Code Generation with Templates

    CERN Document Server

    Arnoldus, Jeroen; Serebrenik, A

    2012-01-01

    Templates are used to generate all kinds of text, including computer code. The last decade, the use of templates gained a lot of popularity due to the increase of dynamic web applications. Templates are a tool for programmers, and implementations of template engines are most times based on practical experience rather than based on a theoretical background. This book reveals the mathematical background of templates and shows interesting findings for improving the practical use of templates. First, a framework to determine the necessary computational power for the template metalanguage is presen

  17. Efficient CRISPR/Cas9-Mediated Genome Editing Using a Chimeric Single-Guide RNA Molecule

    KAUST Repository

    Butt, Haroon; Eid, Ayman; Ali, Zahir; Atia, Mohamed A. M.; Mokhtar, Morad M.; Hassan, Norhan; Lee, Ciaran M.; Bao, Gang; Mahfouz, Magdy M.

    2017-01-01

    used CRISPR/Cas9 to generate targeted double-strand breaks and to deliver an RNA repair template for HDR in rice (Oryza sativa). We used chimeric single-guide RNA (cgRNA) molecules carrying both sequences for target site specificity (to generate

  18. Direct dry transfer of CVD graphene to an optical substrate by in situ photo-polymerization

    Science.gov (United States)

    Kessler, Felipe; Muñoz, Pablo A. R.; Phelan, Ciaran; Romani, Eric C.; Larrudé, Dunieskys R. G.; Freire, Fernando L.; Thoroh de Souza, Eunézio A.; de Matos, Christiano J. S.; Fechine, Guilhermino J. M.

    2018-05-01

    Here, we report on a method that allows graphene produced by chemical vapor deposition (CVD) to be directly transferred to an optically transparent photo resin, by in situ photo-polymerization of the latter, with high efficiency and low contamination. Two photocurable resins, A and B, with different viscosities but essentially the same chemical structure, were used. Raman spectroscopy and surface energy results show that large continuous areas of graphene were transferred with minimal defects to the lower viscosity resin (B), due to the better contact between the resin and graphene. As a proof-of-principle optical experiment, graphene on the polymeric substrate was subjected to high-intensity femtosecond infrared pulses and third-harmonic generation was observed with no noticeable degradation of the sample. A sheet third-order susceptibility χ (3) = 0.71 ×10-28m3V-2 was obtained, matching that of graphene on a glass substrate. These results indicate the suitability of the proposed transfer method, and of the photo resin, for the production of nonlinear photonic components and devices.

  19. An intermediate state of T7 RNA polymerase provides another pathway of nucleotide selection

    International Nuclear Information System (INIS)

    Wang Zhan-Feng; Liu Yu-Ru; Wang Peng-Ye; Xie Ping

    2017-01-01

    Phage T7 RNA polymerase is a single-subunit transcription enzyme, transcribing template DNA to RNA. Nucleoside triphosphate (NTP) selection and translocation are two critical steps of the transcription elongation. Here, using all-atom molecular dynamics simulations, we found that between pre- and post-translocation states of T7 RNA polymerase an intermediate state exists, where the O helix C-terminal residue tyrosine 639, which plays important roles in translocation, locates between its pre- and post-translocation positions and the side chain of the next template DNA nucleotide has moved into the active site. NTP selection in this intermediate state was studied, revealing that the selection in the intermediate state can be achieved relying on the effect of Watson–Crick interaction between NTP and template DNA nucleotide, effect of stability of the components near the active site such as the nascent DNA–RNA hybrid and role of tyrosine 639. This indicates that another NTP-selection pathway can also exist besides the main pathway where NTP selection begins at the post-translocation state upon the entry of NTP. (paper)

  20. Polymeric Micelles with Ionic Cores Containing Biodegradable Crosslinks for Delivery of Chemotherapeutic Agents

    OpenAIRE

    Kim, Jong Oh; Sahay, Gaurav; Kabanov, Alexander V.; Bronich, Tatiana K.

    2010-01-01

    Novel functional polymeric nanocarriers with ionic cores containing biodegradable cross-links were developed for delivery of chemotherapeutic agents. Block ionomer complexes (BIC) of poly(ethylene oxide)-b-poly(methacylic acid) (PEO-b-PMA) and divalent metal cations (Ca2+) were utilized as templates. Disulfide bonds were introduced into the ionic cores by using cystamine as a biodegradable cross-linker. The resulting cross-linked micelles with disulfide bonds represented soft, hydrogel-like n...

  1. Template-mediated, Hierarchical Engineering of Ordered Mesoporous Films and Powders

    Science.gov (United States)

    Tian, Zheng

    Hierarchical control over pore size, pore topology, and meso/mictrostructure as well as material morphology (e.g., powders, monoliths, thin films) is crucial for meeting diverse materials needs among applications spanning next generation catalysts, sensors, batteries, sorbents, etc. The overarching goal of this thesis is to establish fundamental mechanistic insight enabling new strategies for realizing such hierarchical textural control for carbon materials that is not currently achievable with sacrificial pore formation by 'one-pot' surfactant-based 'soft'-templating or multi-step inorganic 'hard-templating. While 'hard'-templating is often tacitly discounted based upon its perceived complexity, it offers potential for overcoming key 'soft'-templating challenges, including bolstering pore stability, accommodating a more versatile palette of replica precursors, realizing ordered/spanning porosity in the case of porous thin films, simplifying formation of bi-continuous pore topologies, and inducing microstructure control within porous replica materials. In this thesis, we establish strategies for hard-templating of hierarchically porous and structured carbon powders and tunable thin films by both multi-step hard-templating and a new 'one-pot' template-replica precursor co-assembly process. We first develop a nominal hard-templating technique to successfully prepare three-dimensionally ordered mesoporous (3DOm) and 3DOm-supported microporous carbon thin films by exploiting our ability to synthesize and assemble size-tunable silica nanoparticles into scalable, colloidal crystalline thin film templates of tunable mono- to multi-layer thickness. This robust thin film template accommodates liquid and/or vapor-phase infiltration, polymerization, and pyrolysis of various carbon sources without pore contraction and/or collapse upon template sacrifice. The result is robust, flexible 3DOm or 3DOm-supported ultra-thin microporous films that can be transferred by stamp

  2. Mechanism for Coordinated RNA Packaging and Genome Replication by Rotavirus Polymerase VP1

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Xiaohui; McDonald, Sarah M.; Tortorici, M. Alejandra; Tao, Yizhi Jane; Vasquez-Del Carpio, Rodrigo; Nibert, Max L.; Patton, John T.; Harrison, Stephen C. (Harvard-Med); (NIH); (CH-Boston)

    2009-04-08

    Rotavirus RNA-dependent RNA polymerase VP1 catalyzes RNA synthesis within a subviral particle. This activity depends on core shell protein VP2. A conserved sequence at the 3' end of plus-strand RNA templates is important for polymerase association and genome replication. We have determined the structure of VP1 at 2.9 {angstrom} resolution, as apoenzyme and in complex with RNA. The cage-like enzyme is similar to reovirus {lambda}3, with four tunnels leading to or from a central, catalytic cavity. A distinguishing characteristic of VP1 is specific recognition, by conserved features of the template-entry channel, of four bases, UGUG, in the conserved 3' sequence. Well-defined interactions with these bases position the RNA so that its 3' end overshoots the initiating register, producing a stable but catalytically inactive complex. We propose that specific 3' end recognition selects rotavirus RNA for packaging and that VP2 activates the autoinhibited VP1/RNA complex to coordinate packaging and genome replication.

  3. Organic or organometallic template mediated clay synthesis

    Science.gov (United States)

    Gregar, Kathleen C.; Winans, Randall E.; Botto, Robert E.

    1994-01-01

    A method for incorporating diverse Varieties of intercalants or templates directly during hydrothermal synthesis of clays such as hectorite or montmorillonite-type layer-silicate clays. For a hectorite layer-silicate clay, refluxing a gel of silica sol, magnesium hydroxide sol and lithium fluoride for two days in the presence of an organic or organometallic intercalant or template results in crystalline products containing either (a) organic dye molecules such as ethyl violet and methyl green, (b) dye molecules such as alcian blue that are based on a Cu(II)-phthalocyannine complex, or (c) transition metal complexes such as Ru(II)phenanthroline and Co(III)sepulchrate or (d) water-soluble porphyrins and metalloporphyrins. Montmorillonite-type clays are made by the method taught by U.S. Pat. No. 3,887,454 issued to Hickson, Jun. 13, 1975; however, a variety of intercalants or templates may be introduced. The intercalants or templates should have (i) water-solubility, (ii) positive charge, and (iii) thermal stability under moderately basic (pH 9-10) aqueous reflux conditions or hydrothermal pressurized conditions for the montmorillonite-type clays.

  4. Direct access to highly crystalline mesoporous nano TiO2 using sterically bulky organic acid templates

    Science.gov (United States)

    Bakre, Pratibha V.; Tilve, S. G.

    2018-05-01

    Sterically bulky monocarboxylic acid templates pivalic acid and phenoxyacetic acid are reported for the first time as organic templates in the sol-gel synthesis of TiO2. Mesoporous nanoparticulates of pure anatase phase and of well defined size were synthesized. The characterization of the materials prepared was done by various methods such as XRD, SEM, TEM, FTIR, UV-DRS, BET, etc. The prepared TiO2 samples were evaluated for the day light photodegradation of methylene blue by comparing with Degussa P25 and templates free synthesized TiO2 and were found to be more efficient.

  5. Template-directed synthesis of MS (M=Cd, Zn) hollow microsphere via hydrothermal method

    Science.gov (United States)

    Wang, Shi-Ming; Wang, Qiong-Sheng; Wan, Qing-Li

    2008-05-01

    CdS, ZnS hollow microspheres were prepared with chitosan as the synthesis template at 140 and 150 °C, respectively, by hydrothermal method. The resultant products were characterized by X-ray diffraction (XRD) measurements in order to determine the crystalline phase of the products. The structural and morphological features of the nanoparticles were investigated by transmission electron microscopy (TEM) and ultraviolet-visible diffuse reflection spectroscopy (DRS). The experimental results indicated that all the nanoparticles aggregated into hollow microspheres and chitosan as a template played an important role in the formation of hollow microspheres. In addition, an intermediate complex structure-controlling possible reaction mechanism was proposed in this paper.

  6. Fabrication of Polymeric Antireflection Film Manufactured by Anodic Aluminum Oxide Template on Dye-Sensitized Solar Cells

    Directory of Open Access Journals (Sweden)

    Jenn-Kai Tsai

    2017-03-01

    Full Text Available In this study, high energy conversion efficient dye-sensitized solar cells (DSSCs were successfully fabricated by attaching a double anti-reflection (AR layer, which is composed of a subwavelength moth-eye structured polymethyl methacrylate (PMMA film and a polydimethylsiloxane (PDMS film. An efficiency of up to 6.79% was achieved. The moth-eye structured PMMA film was fabricated by using an anodic aluminum oxide (AAO template which is simple, low-cost and scalable. The nano-pattern of the AAO template was precisely reproduced onto the PMMA film. The photoanode was composed of Titanium dioxide (TiO2 nanoparticles (NPs with a diameter of 25 nm deposited on the fluorine-doped tin oxide (FTO glass substrate and the sensitizer N3. The double AR layer was proved to effectively improve the short-circuit current density (JSC and conversion efficiency from 14.77 to 15.79 mA/cm2 and from 6.26% to 6.79%, respectively.

  7. Nanoparticles from a controlled polymerization process

    International Nuclear Information System (INIS)

    Tirumala, V.R.; Caneba, G.T.; Dar, Y.; Wang, H.-H.; Mancini, D.C.

    2003-01-01

    Free-radical retrograde precipitation polymerization process in the past has shown excellent control characteristics over reaction rate, molecular weight, and in the entrapment of live radicals for the generation of block copolymers. The same principle has now been extended to study the reaction confinement to a nanoscale region. Nanosized polymer particles have been reported to form from block copolymers, conventional precipitation polymerization methods, or through emulsion polymerization approaches. In this work, we present a new method of generating nanosized polymer particles by polymerizing the monomer in an environment that precipitates the polymer above the lower critical solution temperature. The nanoparticles have been characterized by both tapping-mode atomic force microscopy observations and in situ synchrotron time-resolved small-angle X-ray scattering analysis. The results from both the techniques showed the formation of nanoparticles in the size range of 15-30 nm, directly from the polymerization process.

  8. Research in Water Permeability of Poly(ethylene) Terephthalate Track Membranes Modified by Polymerization of Dimethylaniline under the Action of Direct Current Discharge

    CERN Document Server

    Kravets, L I; Drachev, A I

    2004-01-01

    The properties of poly(ethylene) terephthalate track membranes modified by polymerization of dimethylaniline in a discharge of direct current are investigated. The influence of conditions of plasma treatment on the basic characteristics of the membranes (pore size, wettability, surface charge, water permeability) is studied. It is shown that under the action of discharge, a polymeric layer is formed on the membrane surface that can swell in solutions with low pH values. It has been found that the degree of the swelling stipulated by the conformation transfer of macromolecules of the deposited polymeric layer depends upon the size of relative magnification of the mass of the membrane during its plasma treatment. It is also shown that the obtained membranes can reversibly react to changing the pH of solution and applied pressure.

  9. Remote meta-C-H olefination of phenylacetic acids directed by a versatile U-shaped template.

    Science.gov (United States)

    Deng, Youqian; Yu, Jin-Quan

    2015-01-12

    meta-C-H olefination of phenylacetic acid derivatives has been achieved using a commercially available nitrile-containing template. The identification of N-formyl-protected glycine as the ligand (Formyl-Gly-OH) was crucial for the development of this reaction. Versatility of the template approach in accommodating macrocyclopalladation processes with different ring sizes is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Efficient construction of an inverted minimal H1 promoter driven siRNA expression cassette: facilitation of promoter and siRNA sequence exchange.

    Directory of Open Access Journals (Sweden)

    Hoorig Nassanian

    2007-08-01

    Full Text Available RNA interference (RNAi, mediated by small interfering RNA (siRNA, is an effective method used to silence gene expression at the post-transcriptional level. Upon introduction into target cells, siRNAs incorporate into the RNA-induced silencing complex (RISC. The antisense strand of the siRNA duplex then "guides" the RISC to the homologous mRNA, leading to target degradation and gene silencing. In recent years, various vector-based siRNA expression systems have been developed which utilize opposing polymerase III promoters to independently drive expression of the sense and antisense strands of the siRNA duplex from the same template.We show here the use of a ligase chain reaction (LCR to develop a new vector system called pInv-H1 in which a DNA sequence encoding a specific siRNA is placed between two inverted minimal human H1 promoters (approximately 100 bp each. Expression of functional siRNAs from this construct has led to efficient silencing of both reporter and endogenous genes. Furthermore, the inverted H1 promoter-siRNA expression cassette was used to generate a retrovirus vector capable of transducing and silencing expression of the targeted protein by>80% in target cells.The unique design of this construct allows for the efficient exchange of siRNA sequences by the directional cloning of short oligonucleotides via asymmetric restriction sites. This provides a convenient way to test the functionality of different siRNA sequences. Delivery of the siRNA cassette by retroviral transduction suggests that a single copy of the siRNA expression cassette efficiently knocks down gene expression at the protein level. We note that this vector system can potentially be used to generate a random siRNA library. The flexibility of the ligase chain reaction suggests that additional control elements can easily be introduced into this siRNA expression cassette.

  11. Design and fabrication of polymeric nanocomposites with conducting fillers as electronic nanomaterials

    Science.gov (United States)

    Mushibe, Eliud Kizito

    The growing demand for small, portable and high performance electronic devices has resulted in research activity for embedded electronic components. This offers prospects for the development of flexible electronic components that combines the use of organic and inorganic materials and can be produced on a roll-to-roll process. This dissertation presents advances in the fabrication and characterization of flexible polymeric nanocomposite thin films. Inorganic and synthetic metal nanostructures with high electrical and dielectric properties were employed as filler materials. The processability of these functional filler materials was achieved by dispersion in conventional polymer matrices such as polystyrene (PS), polymethylmethacrylate (PMMA) and poly(vinylidene fluoride) to afford electroactive polymeric composite materials. In the fabrication of inorganic nanostructures, a Tubes by Fiber Template technique was employed to afford submicron metal and metal oxide tubes. Silver and copper nanostructures were fabricated by electroless deposition on electrospun fiber templates. To obtain hollow, submicron tubes, the sacrificial polymer template materials were removed by a combination of solvent dissolution and thermal degradation under an inert atmosphere. Polyaniline thin film deposited on the fiber template was used as a binding interface to enhance uniform and continuous deposition of the metal. This was instrumental in fabricating tubes with varied wall thicknesses ranging from 50 to 300 nm obtained as a function of plating time. By doping electrically conducting polymers such as polyaniline, the conductivity can be modified. We describe the fabrication of highly conducting polyaniline nanostructures via template free synthesis. A novel approach that involves a combination of hydrochloric acid and camphorsulfonic acid dopant at low concentrations was adopted. This approach afforded nanofibers with diameters of 150 ± 50 nm and high electrical conductivity of 4.2

  12. Reduced graphene oxide aerogel networks with soft interfacial template for applications in bone tissue regeneration

    Science.gov (United States)

    Asha, S.; Ananth, A. Nimrodh; Jose, Sujin P.; Rajan, M. A. Jothi

    2018-05-01

    Reduced Graphene Oxide aerogels (A-RGO), functionalized with chitosan, were found to induce and/or accelerate the mineralization of hydroxyapatite. The functionalized chitosan acts as a soft interfacial template on the surface of A-RGO assisting the growth of hydroxyapatite particles. The mineralization on these soft aerogel networks was performed by soaking the aerogels in simulated body fluid, relative to time. Polymer-induced mineralization exhibited an ordered arrangement of hydroxyapatite particles on reduced graphene oxide aerogel networks with a higher crystalline index (IC) of 1.7, which mimics the natural bone formation indicating the importance of the polymeric interfacial template. These mineralized aerogels which mimic the structure and composition of natural bone exhibit relatively higher rate of cell proliferation, osteogenic differentiation and osteoid matrix formation proving it to be a potential scaffold for bone tissue regeneration.

  13. Small interfering RNA delivery through positively charged polymer nanoparticles

    International Nuclear Information System (INIS)

    Dragoni, Luca; Cesana, Alberto; Moscatelli, Davide; Ferrari, Raffaele; Morbidelli, Massimo; Lupi, Monica; Falcetta, Francesca; Ubezio, Paolo; D’Incalci, Maurizio

    2016-01-01

    Small interfering RNA (siRNA) is receiving increasing attention with regard to the treatment of many genetic diseases, both acquired and hereditary, such as cancer and diabetes. Being a high molecular weight (MW) polyanion, siRNA is not able to cross a cell membrane, and in addition it is unstable in physiological conditions. Accordingly, a biocompatible nanocarrier able to deliver siRNA into cells is needed. In this work, we synthesized biocompatible positively charged nanoparticles (NPs) following a two-step process that involves ring opening polymerization (ROP) and emulsion free radical polymerization (EFRP). Firstly, we proved the possibility of fine tuning the NPs’ characteristics (e.g. size and surface charge) by changing the synthetic process parameters. Then the capability in loading and delivering undamaged siRNA into a cancer cell cytoplasm has been shown. This latter process occurs through the biodegradation of the polymer constituting the NPs, whose kinetics can be tuned by adjusting the polymer’s MW. Finally, the ability of NPs to carry siRNA inside the cells in order to inhibit their target gene has been demonstrated using green flourescent protein positive cells. (paper)

  14. Rational design of mesoporous metals and related nanomaterials by a soft-template approach.

    Science.gov (United States)

    Yamauchi, Yusuke; Kuroda, Kazuyuki

    2008-04-07

    We review recent developments in the preparation of mesoporous metals and related metal-based nanomaterials. Among the many types of mesoporous materials, mesoporous metals hold promise for a wide range of potential applications, such as in electronic devices, magnetic recording media, and metal catalysts, owing to their metallic frameworks. Mesoporous metals with highly ordered networks and narrow pore-size distributions have traditionally been produced by using mesoporous silica as a hard template. This method involves the formation of an original template followed by deposition of metals within the mesopores and subsequent removal of the template. Another synthetic method is the direct-template approach from lyotropic liquid crystals (LLCs) made of nonionic surfactants at high concentrations. Direct-template synthesis creates a novel avenue for the production of mesoporous metals as well as related metal-based nanomaterials. Many mesoporous metals have been prepared by the chemical or electrochemical reduction of metal salts dissolved in aqueous LLC domains. As a soft template, LLCs are more versatile and therefore more advantageous than hard templates. It is possible to produce various nanostructures (e.g., lamellar, 2D hexagonal (p6mm), and 3D cubic (Ia\\3d)), nanoparticles, and nanotubes simply by controlling the composition of the reaction bath.

  15. Barbell-shaped stir bar sorptive extraction using dummy template molecularly imprinted polymer coatings for analysis of bisphenol A in water.

    Science.gov (United States)

    Liu, Ruimei; Feng, Feng; Chen, Guolin; Liu, Zhimin; Xu, Zhigang

    2016-07-01

    This study reports the development of a novel dummy template molecularly imprinted polymer (MIP)-coated barbell-shaped stir bar. The MIP stir bar coatings were prepared by using 2,2-bis(4-hydroxyphenyl)butane (BPB), 4,4'-dihydroxydiphenylmethane (BPF), 4-tert-butylphenol (PTBP), and tetrabromobisphenol A (TBBA) as dummy templates using a capillary in situ polymerization method. Uniform coatings can be prepared controllably. The method is simple, easy, and reproducible. The barbell-shaped stir bar was developed by using medical silicone tubes as wheels. The wheels could be removed and reinstalled when necessary; therefore, the barbell-shaped stir bar was easy to disassemble and reassemble. The novel MIP-coated stir bar showed good selectivity for the target analyte, bisphenol A (BPA). The established method is selective and sensitive with a lower detection limit for BPA of 0.003 μg/L. The dummy template MIP-coated stir bar is suitable for trace BPA analysis in real environmental water samples without template leakage. The novel stir bar can be used at least 100 times.

  16. Performance Evaluation of Fusing Protected Fingerprint Minutiae Templates on the Decision Level

    NARCIS (Netherlands)

    Yang, Bian; Busch, C.; Groot, K. de; Xu, H.; Veldhuis, Raymond N.J.

    In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiers results in a decision testing whether both identifiers are derived from the same biometric

  17. Performance evaluation of fusing protected fingerprint minutiae templates on the decision level

    NARCIS (Netherlands)

    Yang, B.; Groot, K.T.J. de; Christoph Busch; Veldhuis, R.N.J.; Xu, H.

    2013-01-01

    In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiersresults in a decision testing whether both identifiers are derived from the same biometric

  18. Templating mesoporous zeolites

    DEFF Research Database (Denmark)

    Egeblad, Kresten; Christensen, Christina Hviid; Kustova, Marina

    2008-01-01

    The application of templating methods to produce zeolite materials with hierarchical bi- or trimodal pore size distributions is reviewed with emphasis on mesoporous materials. Hierarchical zeolite materials are categorized into three distinctly different types of materials: hierarchical zeolite...... crystals, nanosized zeolite crystals, and supported zeolite crystals. For the pure zeolite materials in the first two categories, the additional meso- or macroporosity can be classified as being either intracrystalline or intercrystalline, whereas for supported zeolite materials, the additional porosity...... originates almost exclusively from the support material. The methods for introducing mesopores into zeolite materials are discussed and categorized. In general, mesopores can be templated in zeolite materials by use of solid templating, supramolecular templating, or indirect templating...

  19. Nanoporous polymeric nanofibers based on selectively etched PS-b-PDMS block copolymers.

    Science.gov (United States)

    Demirel, Gokcen B; Buyukserin, Fatih; Morris, Michael A; Demirel, Gokhan

    2012-01-01

    One-dimensional nanoporous polymeric nanofibers have been fabricated within an anodic aluminum oxide (AAO) membrane by a facile approach based on selective etching of poly(dimethylsiloxane) (PDMS) domains in polystyrene-block-poly(dimethylsiloxane) (PS-b-PDMS) block copolymers that had been formed within the AAO template. It was observed that prior to etching, the well-ordered PS-b-PDMS nanofibers are solid and do not have any porosity. The postetched PS nanofibers, on the other hand, had a highly porous structure having about 20-50 nm pore size. The nanoporous polymeric fibers were also employed as a drug carrier for the native, continuous, and pulsatile drug release using Rhodamine B (RB) as a model drug. These studies showed that enhanced drug release and tunable drug dosage can be achieved by using ultrasound irradiation. © 2011 American Chemical Society

  20. Direct 13C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA

    International Nuclear Information System (INIS)

    Fürtig, Boris; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina; Kovacs, Helena; Schwalbe, Harald

    2016-01-01

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond 1 H detection. Here, we develop 13 C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for 13 C direct detection allows correlations of donor–acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed 13 C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.

  1. Dynamics of prebiotic RNA reproduction illuminated by chemical game theory.

    Science.gov (United States)

    Yeates, Jessica A M; Hilbe, Christian; Zwick, Martin; Nowak, Martin A; Lehman, Niles

    2016-05-03

    Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

  2. Dynamics of prebiotic RNA reproduction illuminated by chemical game theory

    Science.gov (United States)

    Yeates, Jessica A. M.; Hilbe, Christian; Zwick, Martin; Nowak, Martin A.; Lehman, Niles

    2016-01-01

    Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock–paper–scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world. PMID:27091972

  3. Patterned Arrays of Functional Lateral Heterostructures via Sequential Template-Directed Printing.

    Science.gov (United States)

    Li, Yifan; Su, Meng; Li, Zheng; Huang, Zhandong; Li, Fengyu; Pan, Qi; Ren, Wanjie; Hu, Xiaotian; Song, Yanlin

    2018-04-30

    The precise integration of microscale dots and lines with controllable interfacing connections is highly important for the fabrication of functional devices. To date, the solution-processible methods are used to fabricate the heterogeneous micropatterns for different materials. However, for increasingly miniaturized and multifunctional devices, it is extremely challenging to engineer the uncertain kinetics of a solution on the microstructures surfaces, resulting in uncontrollable interface connections and poor device performance. Here, a sequential template-directed printing process is demonstrated for the fabrication of arrayed microdots connected by microwires through the regulation of the Rayleigh-Taylor instability of material solution or suspension. Flexibility in the control of fluidic behaviors can realize precise interface connection between the micropatterns, including the microwires traversing, overlapping or connecting the microdots. Moreover, various morphologies such as circular, rhombic, or star-shaped microdots as well as straight, broken or curved microwires can be achieved. The lateral heterostructure printed with two different quantum dots displays bright dichromatic photoluminescence. The ammonia gas sensor printed by polyaniline and silver nanoparticles exhibits a rapid response time. This strategy can construct heterostructures in a facile manner by eliminating the uncertainty of the multimaterials interface connection, which will be promising for the development of novel lateral functional devices. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. The analysis of novel microRNA mimic sequences in cancer cells reveals lack of specificity in stem-loop RT-qPCR-based microRNA detection.

    Science.gov (United States)

    Winata, Patrick; Williams, Marissa; McGowan, Eileen; Nassif, Najah; van Zandwijk, Nico; Reid, Glen

    2017-11-17

    MicroRNAs are frequently downregulated in cancer, and restoring expression has tumour suppressive activity in tumour cells. Our recent phase I clinical trial investigated microRNA-based therapy in patients with malignant pleural mesothelioma. Treatment with TargomiRs, microRNA mimics with novel sequence packaged in EGFR antibody-targeted bacterial minicells, revealed clear signs of clinical activity. In order to detect delivery of microRNA mimics to tumour cells in future clinical trials, we tested hydrolysis probe-based assays specific for the sequence of the novel mimics in transfected mesothelioma cell lines using RT-qPCR. The custom assays efficiently and specifically amplified the consensus mimics. However, we found that these assays gave a signal when total RNA from untransfected and control mimic-transfected cells were used as templates. Further investigation revealed that the reverse transcription step using stem-loop primers appeared to introduce substantial non-specific amplification with either total RNA or synthetic RNA templates. This suggests that reverse transcription using stem-loop primers suffers from an intrinsic lack of specificity for the detection of highly similar microRNAs in the same family, especially when analysing total RNA. These results suggest that RT-qPCR is unlikely to be an effective means to detect delivery of microRNA mimic-based drugs to tumour cells in patients.

  5. Controlling the anodizing conditions in preparation of an nanoporous anodic aluminium oxide template

    Science.gov (United States)

    Nazemi, Azadeh; Abolfazl, Seyed; Sadjadi, Seyed

    2014-12-01

    Porous anodic aluminium oxide (AAO) template is commonly used in the synthesis of one-dimensional nanostructures, such as nanowires and nanorods, due to its simple fabrication process. Controlling the anodizing conditions is important because of their direct influence on the size of AAO template pores; it affects the size of nanostructures that are fabricated in AAO template. In present study, several alumina templates were fabricated by a two-step electrochemical anodization in different conditions, such as the time of first process, its voltage, and electrolyte concentration. The effect of these factors on pore diameters of AAO templates was investigated using scanning electron microscopy (SEM).

  6. Synthesis of CdS nanoparticles based on DNA network templates

    International Nuclear Information System (INIS)

    Yao Yong; Song Yonghai; Wang Li

    2008-01-01

    CdS nanoparticles have been successfully synthesized by using DNA networks as templates. The synthesis was carried out by first dropping a mixture of cadmium acetate and DNA on a mica surface for the formation of the DNA network template and then transferring the sample into a heated thiourea solution. The Cd 2+ reacted with thiourea at high temperature and formed CdS nanoparticles on the DNA network template. UV-vis spectroscopy, photoluminescence, x-ray diffraction and atomic force microscopy (AFM) were used to characterize the CdS nanoparticles in detail. AFM results showed that the resulted CdS nanoparticles were directly aligned on the DNA network templates and that the synthesis and assembly of CdS nanoparticles was realized in one step. CdS nanoparticles fabricated with this method were smaller than those directly synthesized in a thiourea solution and were uniformly aligned on the DNA networks. By adjusting the density of the DNA networks and the concentration of Cd 2+ , the size and density of the CdS nanoparticles could be effectively controlled and CdS nanoparticles could grow along the DNA chains into nanowires. The possible growth mechanism has also been discussed in detail

  7. Preparation and Characterization of Mesoporous Zirconia Made by Using a Poly (methyl methacrylate Template

    Directory of Open Access Journals (Sweden)

    Zhang Chunxiang

    2008-01-01

    Full Text Available AbstractSuperfine powders of poly (methyl methacrylate (PMMA have been prepared by means of an emulsion polymerization method. These have been used as templates in the synthesis of tetragonal phase mesoporous zirconia by the sol–gel method, using zirconium oxychloride and oxalic acid as raw materials. The products have been characterized by infrared spectroscopy, X-ray diffraction analysis, transmission electron microscopy, N2adsorption-desorption isotherms, and pore size distribution. The results indicate that the average pore size was found to be 3.7 nm.

  8. [Investigation of RNA viral genome amplification by multiple displacement amplification technique].

    Science.gov (United States)

    Pang, Zheng; Li, Jian-Dong; Li, Chuan; Liang, Mi-Fang; Li, De-Xin

    2013-06-01

    In order to facilitate the detection of newly emerging or rare viral infectious diseases, a negative-strand RNA virus-severe fever with thrombocytopenia syndrome bunyavirus, and a positive-strand RNA virus-dengue virus, were used to investigate RNA viral genome unspecific amplification by multiple displacement amplification technique from clinical samples. Series of 10-fold diluted purified viral RNA were utilized as analog samples with different pathogen loads, after a series of reactions were sequentially processed, single-strand cDNA, double-strand cDNA, double-strand cDNA treated with ligation without or with supplemental RNA were generated, then a Phi29 DNA polymerase depended isothermal amplification was employed, and finally the target gene copies were detected by real time PCR assays to evaluate the amplification efficiencies of various methods. The results showed that multiple displacement amplification effects of single-strand or double-strand cDNA templates were limited, while the fold increases of double-strand cDNA templates treated with ligation could be up to 6 X 10(3), even 2 X 10(5) when supplemental RNA existed, and better results were obtained when viral RNA loads were lower. A RNA viral genome amplification system using multiple displacement amplification technique was established in this study and effective amplification of RNA viral genome with low load was achieved, which could provide a tool to synthesize adequate viral genome for multiplex pathogens detection.

  9. An oligonucleotide complementary to the SL-B1 domain in the 3'-end of the minus-strand RNA of the hepatitis C virus inhibits in vitro initiation of RNA synthesis by the viral polymerase

    International Nuclear Information System (INIS)

    Reigadas, Sandrine; Ventura, Michel; Andreola, Marie-Line; Michel, Justine; Gryaznov, Sergei; Tarrago-Litvak, Laura; Litvak, Simon; Astier-Gin, Therese

    2003-01-01

    We describe oligonucleotides (ODNs) that inhibit hepatitis C virus (HCV) RNA synthesis in vitro. From a series of 13 ODNs complementary to the 3'-end of the minus-strand HCV RNA, only 4 inhibited RNA synthesis with IC 50 values lower than 1 μM. The inhibition was sequence-specific, since no effect was observed when the ODNs were used with a noncomplementary template. The introduction of a 2'-O-methyl modification increased the inhibitor activity 11-fold (IC 50 = 50 nM) in just 1 (ODN7) of the 4 inhibitory ODNs. ODNs did not inhibit RNA synthesis by interfering with the elongation process as no short RNAs products were detected. We also show that ODN7 did not prevent binding of NS5B to the template or cause polymerase trapping by the duplex RNA/ODN. Our data demonstrate that ODN7 inhibits the initiation process, most probably by modifying structural features present at the 3'-end of the minus-strand RNA

  10. Conductance measurement by two-line probe method of polypyrrole nano-films formed on mica by admicellar polymerization

    Energy Technology Data Exchange (ETDEWEB)

    Mou, C.-Y. [Graduate Institute of Textile Engineering, Feng Chia University, Taichung 40724, Taiwan (China); Yuan, W.-L. [Department of Chemical Engineering, Feng Chia University, Taichung 40724, Taiwan (China)], E-mail: wyuan@fcu.edu.tw; Tsai, I-S. [Graduate Institute of Textile Engineering, Feng Chia University, Taichung 40724, Taiwan (China); O' Rear, Edgar A. [School of Chemical, Biological and Material Engineering, University of Oklahoma, Norman, OK 73019 (United States); Barraza, Harry [Unilever R and D HPC, Quarry Road East, Bebington, Wirral, CH63 3JW (United Kingdom)

    2008-10-01

    Measuring the electrical conductance is of importance in fabricating electronic devices based on semiconducting thin films. In this report, electrically conducting polypyrrole (PPy) nano-films were deposited on insulating mica plates by admicellar polymerization. It becomes difficult to measure such film conductance in the lateral direction due the nanometric thickness which only allows for very low electrical current. In order to understand the effects of surfactant on the film conductivity, morphological studies using atomic force microscopy and conductance measurements with a sub-fA multimeter were performed. Higher conductances were found for PPy thin films made using surfactant templates, than that of a bare mica surface. Using the two-line probe method by drawing two lines of silver glue 8 mm apart on the sample surface, the current-voltage curves of bare mica surface yielded a lateral conductance of 6.0 x 10{sup -13} S. In comparison, PPy thin films made using sodium dodecyl sulfate (SDS) and cetyl trimethyl ammonium bromide (CTAB) as surfactant templates showed conductances of 1.2 x 10{sup -11} S and 7.7 x 10{sup -12} S, respectively. The higher conductances indicate tunneling, hopping, and percolation of charge carriers throughout the films. The lower-bound conductivities were calculated as 4.0 x 10{sup -3} S/cm and 2.6 x 10{sup -3} S/cm, measured based on the average thickness 2.3 nm for the SDS-PPy films and 2.4 nm for the CTAB-PPy films. Conductivities for both SDS and CTAB template PPy films are found to be of the same order.

  11. Conductance measurement by two-line probe method of polypyrrole nano-films formed on mica by admicellar polymerization

    International Nuclear Information System (INIS)

    Mou, C.-Y.; Yuan, W.-L.; Tsai, I-S.; O'Rear, Edgar A.; Barraza, Harry

    2008-01-01

    Measuring the electrical conductance is of importance in fabricating electronic devices based on semiconducting thin films. In this report, electrically conducting polypyrrole (PPy) nano-films were deposited on insulating mica plates by admicellar polymerization. It becomes difficult to measure such film conductance in the lateral direction due the nanometric thickness which only allows for very low electrical current. In order to understand the effects of surfactant on the film conductivity, morphological studies using atomic force microscopy and conductance measurements with a sub-fA multimeter were performed. Higher conductances were found for PPy thin films made using surfactant templates, than that of a bare mica surface. Using the two-line probe method by drawing two lines of silver glue 8 mm apart on the sample surface, the current-voltage curves of bare mica surface yielded a lateral conductance of 6.0 x 10 -13 S. In comparison, PPy thin films made using sodium dodecyl sulfate (SDS) and cetyl trimethyl ammonium bromide (CTAB) as surfactant templates showed conductances of 1.2 x 10 -11 S and 7.7 x 10 -12 S, respectively. The higher conductances indicate tunneling, hopping, and percolation of charge carriers throughout the films. The lower-bound conductivities were calculated as 4.0 x 10 -3 S/cm and 2.6 x 10 -3 S/cm, measured based on the average thickness 2.3 nm for the SDS-PPy films and 2.4 nm for the CTAB-PPy films. Conductivities for both SDS and CTAB template PPy films are found to be of the same order

  12. MiRNA-directed regulation of VEGF and other angiogenic factors under hypoxia.

    Directory of Open Access Journals (Sweden)

    Zhong Hua

    Full Text Available MicroRNAs (miRNAs are a class of 20-24 nt non-coding RNAs that regulate gene expression primarily through post-transcriptional repression or mRNA degradation in a sequence-specific manner. The roles of miRNAs are just beginning to be understood, but the study of miRNA function has been limited by poor understanding of the general principles of gene regulation by miRNAs. Here we used CNE cells from a human nasopharyngeal carcinoma cell line as a cellular system to investigate miRNA-directed regulation of VEGF and other angiogenic factors under hypoxia, and to explore the principles of gene regulation by miRNAs. Through computational analysis, 96 miRNAs were predicted as putative regulators of VEGF. But when we analyzed the miRNA expression profile of CNE and four other VEGF-expressing cell lines, we found that only some of these miRNAs could be involved in VEGF regulation, and that VEGF may be regulated by different miRNAs that were differentially chosen from 96 putative regulatory miRNAs of VEGF in different cells. Some of these miRNAs also co-regulate other angiogenic factors (differential regulation and co-regulation principle. We also found that VEGF was regulated by multiple miRNAs using different combinations, including both coordinate and competitive interactions. The coordinate principle states that miRNAs with independent binding sites in a gene can produce coordinate action to increase the repressive effect of miRNAs on this gene. By contrast, the competitive principle states when multiple miRNAs compete with each other for a common binding site, or when a functional miRNA competes with a false positive miRNA for the same binding site, the repressive effects of miRNAs may be decreased. Through the competitive principle, false positive miRNAs, which cannot directly repress gene expression, can sometimes play a role in miRNA-mediated gene regulation. The competitive principle, differential regulation, multi-miRNA binding sites, and false

  13. Direct assembly of in situ templated CdSe quantum dots via crystalline lamellae structure of polyamide 66

    Energy Technology Data Exchange (ETDEWEB)

    Cheval, Nicolas; Brooks, Richard [University of Nottingham, Division of Materials, Mechanics and Structures, Faculty of Engineering (United Kingdom); Fahmi, Amir, E-mail: Amir.Fahmi@hochschule-Rhein-waal.de [Rhein-Waal University of Applied Sciences, Faculty of Technology and Bionics (Germany)

    2012-03-15

    A simple concept is proposed for templating in situ synthesised CdSe quantum dots (QDs) into an organised nano-pattern using the crystalline lamellae structure of polyamide 66 (PA66). The morphology obtained for PA66 and the hybrid material on Si/SiO{sub x} solid substrate was characterised by means of atomic force microscope. Controlling the PA66 concentration in solution and the organic-inorganic interactions are found to be the keys factors to direct the assembly of CdSe QDs along the PA66 linear crystalline structure. This simple approach could be opened a new avenue for a large spectrum of innovative high-tech applications.

  14. Report Template

    DEFF Research Database (Denmark)

    Bjørn, Anders; Laurent, Alexis; Owsianiak, Mikołaj

    2018-01-01

    To ensure consistent reporting of life cycle assessment (LCA), we provide a report template. The report includes elements of an LCA study as recommended but the ILCD Handbook. Illustrative case study reported according to this template is presented in Chap. 39 ....

  15. Origin of the RNA world: The fate of nucleobases in warm little ponds

    Science.gov (United States)

    Pearce, Ben K. D.; Pudritz, Ralph E.; Semenov, Dmitry A.; Henning, Thomas K.

    2017-10-01

    Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet–dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth's early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (less than a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean, but this increasing availability of “targets” for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods, mean that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet–dry cycles. Under these conditions, RNA polymers likely appeared before 4.17 billion years ago.

  16. Origin of the RNA world: The fate of nucleobases in warm little ponds.

    Science.gov (United States)

    Pearce, Ben K D; Pudritz, Ralph E; Semenov, Dmitry A; Henning, Thomas K

    2017-10-24

    Before the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favorable environments on early Earth. At this time, meteorites and interplanetary dust particles delivered organics such as nucleobases (the characteristic molecules of nucleotides) to warm little ponds whose wet-dry cycles promoted rapid polymerization. We build a comprehensive numerical model for the evolution of nucleobases in warm little ponds leading to the emergence of the first nucleotides and RNA. We couple Earth's early evolution with complex prebiotic chemistry in these environments. We find that RNA polymers must have emerged very quickly after the deposition of meteorites (less than a few years). Their constituent nucleobases were primarily meteoritic in origin and not from interplanetary dust particles. Ponds appeared as continents rose out of the early global ocean, but this increasing availability of "targets" for meteorites was offset by declining meteorite bombardment rates. Moreover, the rapid losses of nucleobases to pond seepage during wet periods, and to UV photodissociation during dry periods, mean that the synthesis of nucleotides and their polymerization into RNA occurred in just one to a few wet-dry cycles. Under these conditions, RNA polymers likely appeared before 4.17 billion years ago.

  17. Large Scale Laser Two-Photon Polymerization Structuring for Fabrication of Artificial Polymeric Scaffolds for Regenerative Medicine

    International Nuclear Information System (INIS)

    Malinauskas, M.; Purlys, V.; Zukauskas, A.; Rutkauskas, M.; Danilevicius, P.; Paipulas, D.; Bickauskaite, G.; Gadonas, R.; Piskarskas, A.; Bukelskis, L.; Baltriukiene, D.; Bukelskiene, V.; Sirmenis, R.; Gaidukeviciute, A.; Sirvydis, V.

    2010-01-01

    We present a femtosecond Laser Two-Photon Polymerization (LTPP) system of large scale three-dimensional structuring for applications in tissue engineering. The direct laser writing system enables fabrication of artificial polymeric scaffolds over a large area (up to cm in lateral size) with sub-micrometer resolution which could find practical applications in biomedicine and surgery. Yb:KGW femtosecond laser oscillator (Pharos, Light Conversion. Co. Ltd.) is used as an irradiation source (75 fs, 515 nm (frequency doubled), 80 MHz). The sample is mounted on wide range linear motor driven stages having 10 nm sample positioning resolution (XY--ALS130-100, Z--ALS130-50, Aerotech, Inc.). These stages guarantee an overall travelling range of 100 mm into X and Y directions and 50 mm in Z direction and support the linear scanning speed up to 300 mm/s. By moving the sample three-dimensionally the position of laser focus in the photopolymer is changed and one is able to write complex 3D (three-dimensional) structures. An illumination system and CMOS camera enables online process monitoring. Control of all equipment is automated via custom made computer software ''3D-Poli'' specially designed for LTPP applications. Structures can be imported from computer aided design STereoLihography (stl) files or programmed directly. It can be used for rapid LTPP structuring in various photopolymers (SZ2080, AKRE19, PEG-DA-258) which are known to be suitable for bio-applications. Microstructured scaffolds can be produced on different substrates like glass, plastic and metal. In this paper, we present microfabricated polymeric scaffolds over a large area and growing of adult rabbit myogenic stem cells on them. Obtained results show the polymeric scaffolds to be applicable for cell growth practice. It exhibit potential to use it for artificial pericardium in the experimental model in the future.

  18. Large Scale Laser Two-Photon Polymerization Structuring for Fabrication of Artificial Polymeric Scaffolds for Regenerative Medicine

    Science.gov (United States)

    Malinauskas, M.; Purlys, V.; Žukauskas, A.; Rutkauskas, M.; Danilevičius, P.; Paipulas, D.; Bičkauskaitė, G.; Bukelskis, L.; Baltriukienė, D.; Širmenis, R.; Gaidukevičiutė, A.; Bukelskienė, V.; Gadonas, R.; Sirvydis, V.; Piskarskas, A.

    2010-11-01

    We present a femtosecond Laser Two-Photon Polymerization (LTPP) system of large scale three-dimensional structuring for applications in tissue engineering. The direct laser writing system enables fabrication of artificial polymeric scaffolds over a large area (up to cm in lateral size) with sub-micrometer resolution which could find practical applications in biomedicine and surgery. Yb:KGW femtosecond laser oscillator (Pharos, Light Conversion. Co. Ltd.) is used as an irradiation source (75 fs, 515 nm (frequency doubled), 80 MHz). The sample is mounted on wide range linear motor driven stages having 10 nm sample positioning resolution (XY—ALS130-100, Z—ALS130-50, Aerotech, Inc.). These stages guarantee an overall travelling range of 100 mm into X and Y directions and 50 mm in Z direction and support the linear scanning speed up to 300 mm/s. By moving the sample three-dimensionally the position of laser focus in the photopolymer is changed and one is able to write complex 3D (three-dimensional) structures. An illumination system and CMOS camera enables online process monitoring. Control of all equipment is automated via custom made computer software "3D-Poli" specially designed for LTPP applications. Structures can be imported from computer aided design STereoLihography (stl) files or programmed directly. It can be used for rapid LTPP structuring in various photopolymers (SZ2080, AKRE19, PEG-DA-258) which are known to be suitable for bio-applications. Microstructured scaffolds can be produced on different substrates like glass, plastic and metal. In this paper, we present microfabricated polymeric scaffolds over a large area and growing of adult rabbit myogenic stem cells on them. Obtained results show the polymeric scaffolds to be applicable for cell growth practice. It exhibit potential to use it for artificial pericardium in the experimental model in the future.

  19. Numerical study of the thermal degradation of isotropic and anisotropic polymeric materials

    Energy Technology Data Exchange (ETDEWEB)

    Soler, E. [Departamento de Lenguajes y Ciencias de la Computacion, ETSI Informatica, Universidad de Malaga, 29071 Malaga (Spain); Ramos, J.I. [Room I-320-D, ETS Ingenieros Industriales, Universidad de Malaga, Plaza El Ejido, s/n, 29013 Malaga (Spain)

    2005-08-01

    The thermal degradation of two-dimensional isotropic, orthotropic and anisotropic polymeric materials is studied numerically by means of a second-order accurate (in both space and time) linearly implicit finite difference formulation which results in linear algebraic equations at each time step. It is shown that, for both isotropic and orthotropic composites, the monomer mass diffusion tensor plays a role in initiating the polymerization kinetics, the formation of a polymerization kernel and the initial front propagation, whereas the later stages of the polymerization are nearly independent of the monomer mass diffusion tensor. In anisotropic polymeric composites, it has been found that the monomer mass diffusion tensor plays a paramount role in determining the initial stages of the polymerization and the subsequent propagation of the polymerization front, the direction and speed of propagation of which are found to be related to the principal directions of both the monomer mass and the heat diffusion tensors. It is also shown that the polymerization time and temperatures depend strongly on the anisotropy of the mass and heat diffusion tensors. (authors)

  20. Pentafluorosulfanyl Substituents in Polymerization Catalysis.

    Science.gov (United States)

    Kenyon, Philip; Mecking, Stefan

    2017-10-04

    Highly electron-withdrawing pentafluorosulfanyl groups were probed as substituents in an organometallic catalyst. In Ni(II) salicylaldiminato complexes as an example case, these highly electron-withdrawing substituents allow for polymerization of ethylene to higher molecular weights with reduced branching due to significant reductions in β-hydrogen elimination. Combined with the excellent functional group tolerance of neutral Ni(II) complexes, this suppression of β-hydrogen elimination allows for the direct polymerization of ethylene in water to nanocrystal dispersions of disentangled, ultrahigh-molecular-weight linear polyethylene.

  1. Influenza virus gene expression: viral RNA replication in vivo and in vitro

    International Nuclear Information System (INIS)

    Shapiro, G.I.

    1987-01-01

    To develop an overall scheme for the control of influenza virus gene expression, single-stranded M13 DNAs specific for the various genomic segments were used to analyze the synthesis of virus-specific RNAs in infected cells. The results showed that virus infection is divided into two distinct phases. During the early phase, the syntheses of specific virion RNAs (vRNAs), viral mRNAs, and viral proteins were coupled. This phase lasted for 2.5 hours in BHK-21 cells, the time when the rate of synthesis of all the viral mRNAs was maximal. During the late phase, the synthesis of all the vRNAs remained at or near maximum, whereas the rate of synthesis of all the viral mRNAs declined dramatically. Viral mRNA and protein syntheses were also not coupled, as the synthesis of all the viral proteins continued at maximum levels, indicating that protein synthesis during this phase was directed principally by previously synthesized viral mRNAs. Pulses with [ 3 H]uridine and nonaqueous fractionation of cells were used to show that influenza vRNA, like viral mRNAs, are synthesized in the nucleus and efficiently transported to the cytoplasm. In contrast, the full-length transcripts of the vRNAs, the templates for new vRNA synthesis, were synthesized only at early times, and remained sequestered in the nucleus to direct vRNA synthesis throughout infection

  2. [Clinical application of individualized three-dimensional printing implant template in multi-tooth dental implantation].

    Science.gov (United States)

    Wang, Lie; Chen, Zhi-Yuan; Liu, Rong; Zeng, Hao

    2017-08-01

    To study the value and satisfaction of three-dimensional printing implant template and conventional implant template in multi-tooth dental implantation. Thirty cases (83 teeth) with missing teeth needing to be implanted were randomly divided into conventional implant template group (CIT group, 15 cases, 42 teeth) and 3D printing implant template group (TDPIT group, 15 cases, 41 teeth). Patients in CIT group were operated by using conventional implant template, while patients in TDPIT group were operated by using three-dimensional printing implant template. The differences of implant neck and tip deviation, implant angle deviation and angle satisfaction between the two groups were compared. The difference of probing depth and bone resorption of implant were compared 1 year after operation between the two groups. The difference of success rate and satisfaction of dental implantation were compared 1 year after operation between the two groups. SPSS19.0 software package was used for statistical analysis. The deviation direction of the neck and the tip in disto-mesial, bucco-palatal, vertical direction and angle of implants in disto-mesial and bucco-palatal direction in TDPIT group were significantly lower than in CIT group (P0.05). The difference of the cumulative success rate in dental implantation at 3 months and 6 months between the two groups were not significant (P>0.05), but the cumulative success rate of TDPIT group was significantly higher than CIT group at 9 months and 1 year (90.48% vs 100%,P=0.043). The patients' satisfaction rate of dental implantation in TDPIT group was significantly higher than in CIT group (86.67% vs 53.33%, P=0.046). Using three-dimensional printing implant template can obtain better accuracy of implant, higher implant success rate and better patients' satisfaction than using conventional implant template. It is suitable for clinical application.

  3. Welding template

    International Nuclear Information System (INIS)

    Ben Venue, R.J. of.

    1976-01-01

    A welding template is described which is used to weld strip material into a cellular grid structure for the accommodation of fuel elements in a nuclear reactor. On a base plate the template carries a multitude of cylindrical pins whose upper half is narrower than the bottom half and only one of which is attached to the base plate. The others are arrested in a hexagonal array by oblong webs clamped together by chuck jaws which can be secured by means of screws. The parts are ground very accurately. The template according to the invention is very easy to make. (UWI) [de

  4. Template assisted solid state electrochemical growth of silver micro- and nanowires

    International Nuclear Information System (INIS)

    Peppler, Klaus; Janek, Juergen

    2007-01-01

    We report on a template based solid state electrochemical method for fabricating silver nanowires with predefined diameter, depending only on the pore diameter of the template. As templates we used porous silicon with pore diameters in the μm range and porous alumina with pore diameters in the nm range. The template pores were filled with silver sulfide (a mixed silver cation and electronic conductor) by direct chemical reaction of silver and sulfur. The filled template was then placed between a silver foil as anode (bottom side) and a microelectrode (top side) as cathode. An array of small cylindrical transference cells with diameters in the range of either micro- or nanometers was thus obtained. By applying a cathodic voltage to the microelectrode silver in the form of either micro- or nanowires was deposited at about 150 deg. C. The growth rate is controllable by the electric current

  5. Sacrificial template method of fabricating a nanotube

    Science.gov (United States)

    Yang, Peidong [Berkeley, CA; He, Rongrui [Berkeley, CA; Goldberger, Joshua [Berkeley, CA; Fan, Rong [El Cerrito, CA; Wu, Yi-Ying [Albany, CA; Li, Deyu [Albany, CA; Majumdar, Arun [Orinda, CA

    2007-05-01

    Methods of fabricating uniform nanotubes are described in which nanotubes were synthesized as sheaths over nanowire templates, such as using a chemical vapor deposition process. For example, single-crystalline zinc oxide (ZnO) nanowires are utilized as templates over which gallium nitride (GaN) is epitaxially grown. The ZnO templates are then removed, such as by thermal reduction and evaporation. The completed single-crystalline GaN nanotubes preferably have inner diameters ranging from 30 nm to 200 nm, and wall thicknesses between 5 and 50 nm. Transmission electron microscopy studies show that the resultant nanotubes are single-crystalline with a wurtzite structure, and are oriented along the direction. The present invention exemplifies single-crystalline nanotubes of materials with a non-layered crystal structure. Similar "epitaxial-casting" approaches could be used to produce arrays and single-crystalline nanotubes of other solid materials and semiconductors. Furthermore, the fabrication of multi-sheath nanotubes are described as well as nanotubes having multiple longitudinal segments.

  6. Synthesis and characterization of templated ion exchange resins for the selective complexation of actinide ions. 1998 annual progress report

    International Nuclear Information System (INIS)

    Murray, G.M.; Uy, O.M.

    1998-01-01

    'The purpose of this research is to develop polymeric extractants for the selective complexation of uranyl ions (and subsequently other actinyl and actinide ions) from aqueous solutions (lakes, streams, waste tanks and body fluids). Selectivity for a specific actinide ion is obtained by providing polymers with cavities lined with complexing ligands so arranged as to match the charge, coordination number, coordination geometry, and size of the actinide metal ion. These cavity-containing polymers will be produced using a specific actinide ion (or surrogate) as a template around which monomeric complexing ligands will be polymerized. The polymers will provide useful sequestering agents for removing actinide ions from wastes and will form the basis for a variety of analytical techniques for actinide determinations.'

  7. Programmed self-assembly of DNA/RNA for biomedical applications

    Science.gov (United States)

    Wang, Pengfei

    Three self-assembly strategies were utilized for assembly of novel functional DNA/RNA nanostructures. RNA-DNA hybrid origami method was developed to fabricate nano-objects (ribbon, rectangle, and triangle) with precisely controlled geometry. Unlike conventional DNA origami which use long DNA single strand as scaffold, a long RNA single strand was used instead, which was folded by short DNA single strands (staples) into prescribed objects through sequence specific hybridization between RNA and DNA. Single stranded tiles (SST) and RNA-DNA hybrid origami were utilized to fabricate a variety of barcode-like nanostructures with unique patterns by expanding a plain rectangle via introducing spacers (10-bp dsDNA segment) between parallel duplexes. Finally, complex 2D array and 3D polyhedrons with multiple patterns within one structure were assembled from simple DNA motifs. Two demonstrations of biomedical applications of DNA nanotechnology were presented. Firstly, lambda-DNA was used as template to direct the fabrication of multi-component magnetic nanoparticle chains. Nuclear magnetic relaxation (NMR) characterization showed superb magnetic relaxativity of the nanoparticle chains which have large potential to be utilized as MRI contrast agents. Secondly, DNA nanotechnology was introduced into the conformational study of a routinely used catalytic DNAzyme, the RNA-cleaving 10-23 DNAzyme. The relative angle between two flanking duplexes of the catalytic core was determined (94.8°), which shall be able to provide a clue to further understanding of the cleaving mechanism of this DNAzyme from a conformational perspective.

  8. Synthesis of PLGA-Lipid Hybrid Nanoparticles for siRNA Delivery Using the Emulsion Method PLGA-PEG-Lipid Nanoparticles for siRNA Delivery.

    Science.gov (United States)

    Wang, Lei; Griffel, Benjamin; Xu, Xiaoyang

    2017-01-01

    The effective delivery of small interfering RNA (siRNA) to tumor cells remains a challenge for applications in cancer therapy. The development of polymeric nanoparticles with high siRNA loading efficacy has shown great potential for cancer targets. Double emulsion solvent evaporation technique is a useful tool for encapsulation of hydrophilic molecules (e.g., siRNA). Here we describe a versatile platform for siRNA delivery based on PLGA-PEG-cationic lipid nanoparticles by using the double emulsion method. The resulting nanoparticles show high encapsulation efficiency for siRNA (up to 90%) and demonstrate effective downregulation of the target genes in vitro and vivo.

  9. Distributed biotin-streptavidin transcription roadblocks for mapping cotranscriptional RNA folding.

    Science.gov (United States)

    Strobel, Eric J; Watters, Kyle E; Nedialkov, Yuri; Artsimovitch, Irina; Lucks, Julius B

    2017-07-07

    RNA folding during transcription directs an order of folding that can determine RNA structure and function. However, the experimental study of cotranscriptional RNA folding has been limited by the lack of easily approachable methods that can interrogate nascent RNA structure at nucleotide resolution. To address this, we previously developed cotranscriptional selective 2΄-hydroxyl acylation analyzed by primer extension sequencing (SHAPE-Seq) to simultaneously probe all intermediate RNA transcripts during transcription by stalling elongation complexes at catalytically dead EcoRIE111Q roadblocks. While effective, the distribution of elongation complexes using EcoRIE111Q requires laborious PCR using many different oligonucleotides for each sequence analyzed. Here, we improve the broad applicability of cotranscriptional SHAPE-Seq by developing a sequence-independent biotin-streptavidin (SAv) roadblocking strategy that simplifies the preparation of roadblocking DNA templates. We first determine the properties of biotin-SAv roadblocks. We then show that randomly distributed biotin-SAv roadblocks can be used in cotranscriptional SHAPE-Seq experiments to identify the same RNA structural transitions related to a riboswitch decision-making process that we previously identified using EcoRIE111Q. Lastly, we find that EcoRIE111Q maps nascent RNA structure to specific transcript lengths more precisely than biotin-SAv and propose guidelines to leverage the complementary strengths of each transcription roadblock in cotranscriptional SHAPE-Seq. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Programmable imprint lithography template

    Science.gov (United States)

    Cardinale, Gregory F [Oakland, CA; Talin, Albert A [Livermore, CA

    2006-10-31

    A template for imprint lithography (IL) that reduces significantly template production costs by allowing the same template to be re-used for several technology generations. The template is composed of an array of spaced-apart moveable and individually addressable rods or plungers. Thus, the template can be configured to provide a desired pattern by programming the array of plungers such that certain of the plungers are in an "up" or actuated configuration. This arrangement of "up" and "down" plungers forms a pattern composed of protruding and recessed features which can then be impressed onto a polymer film coated substrate by applying a pressure to the template impressing the programmed configuration into the polymer film. The pattern impressed into the polymer film will be reproduced on the substrate by subsequent processing.

  11. Macroporous 'bubble' graphene film via template-directed ordered-assembly for high rate supercapacitors.

    Science.gov (United States)

    Chen, Cheng-Meng; Zhang, Qiang; Huang, Chun-Hsien; Zhao, Xiao-Chen; Zhang, Bing-Sen; Kong, Qing-Qiang; Wang, Mao-Zhang; Yang, Yong-Gang; Cai, Rong; Sheng Su, Dang

    2012-07-21

    A three-dimensional bubble graphene film, with controllable and uniform macropores and tailorable microstructure, was fabricated by a facile hard templating strategy and exhibit extraordinary electrochemical capacitance with high rate capability (1.0 V s(-1)).

  12. Direct {sup 13}C-detected NMR experiments for mapping and characterization of hydrogen bonds in RNA

    Energy Technology Data Exchange (ETDEWEB)

    Fürtig, Boris, E-mail: fuertig@nmr.uni-frankfurt.de; Schnieders, Robbin; Richter, Christian; Zetzsche, Heidi; Keyhani, Sara; Helmling, Christina [Johann Wolfgang Goethe Universität Frankfurt, Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology (Germany); Kovacs, Helena [Bruker BioSpin (Switzerland); Schwalbe, Harald, E-mail: schwalbe@nmr.uni-frankfurt.de [Johann Wolfgang Goethe Universität Frankfurt, Center for Biomolecular Magnetic Resonance (BMRZ), Institute of Organic Chemistry and Chemical Biology (Germany)

    2016-03-15

    In RNA secondary structure determination, it is essential to determine whether a nucleotide is base-paired and not. Base-pairing of nucleotides is mediated by hydrogen bonds. The NMR characterization of hydrogen bonds relies on experiments correlating the NMR resonances of exchangeable protons and can be best performed for structured parts of the RNA, where labile hydrogen atoms are protected from solvent exchange. Functionally important regions in RNA, however, frequently reveal increased dynamic disorder which often leads to NMR signals of exchangeable protons that are broadened beyond {sup 1}H detection. Here, we develop {sup 13}C direct detected experiments to observe all nucleotides in RNA irrespective of whether they are involved in hydrogen bonds or not. Exploiting the self-decoupling of scalar couplings due to the exchange process, the hydrogen bonding behavior of the hydrogen bond donor of each individual nucleotide can be determined. Furthermore, the adaption of HNN-COSY experiments for {sup 13}C direct detection allows correlations of donor–acceptor pairs and the localization of hydrogen-bond acceptor nucleotides. The proposed {sup 13}C direct detected experiments therefore provide information about molecular sites not amenable by conventional proton-detected methods. Such information makes the RNA secondary structure determination by NMR more accurate and helps to validate secondary structure predictions based on bioinformatics.

  13. A 9-vinyladenine-based molecularly imprinted polymeric membrane for the efficient recognition of plant hormone 1H-indole-3-acetic acid

    International Nuclear Information System (INIS)

    Chen Changbao; Chen Yanjun; Zhou Jie; Wu Chunhui

    2006-01-01

    9-Vinyladenine was synthesized as a novel functional monomer for molecular imprinting techniques and its structure was established with elemental analysis and 1 H NMR spectroscopy. The binding mechanism between this functional monomer 9-vinyladenine and the plant hormone 1 H-indole-3-acetic acid in acetonitrile was studied with UV-vis spectrophotometry. Based on this study, using 1 H-indole-3-acetic acid as a template molecule, a specific 9-vinyladenine-based molecularly imprinted polymeric membrane was prepared. Then, the resultant polymeric membrane morphologies were visualized with scanning electron microscopy, and the membrane permselectivity for 1 H-indole-3-acetic acid, 1 H-indole-3-butyric acid and kinetin was tested with separate experiments and competitive diffusion experiments. These results showed that the imprinted polymeric membrane prepared with 9-vinyladenine exhibited higher transport selectivity for the template molecule 1 H-indole-3-acetic acid than 1 H-indole-3-butyric acid or kinetin. The membrane prepared with 9-vinyladenine also took on higher permselectivity for 1 H-indole-3-acetic acid in comparison with the imprinted membrane made with methacrylic acid. It is predicted that the 9-vinyladenine-based molecularly imprinted membrane may be applicable to the assay of 1 H-indole-3-acetic acid or for the preparation of a molecularly imprinted polymer sensor for the analysis of 1 H-indole-3-acetic acid in plant samples

  14. Analysis of diverse direct arylation polymerization (DArP) conditions toward the efficient synthesis of polymers converging with stille polymers in organic solar cells

    DEFF Research Database (Denmark)

    Livi, Francesco; Gobalasingham, Nemal S.; Thompson, Barry C.

    2016-01-01

    Despite the emergence of direct arylation polymerization (DArP) as an alternative method to traditional cross-coupling routes like Stille polymerization, the exploration of DArP polymers in practical applications like polymer solar cells (PSCs) is limited. DArP polymers tend to have a reputation...... for being marginally inferior to Stille counterparts due to the increased presence of defects that result from unwanted side reactions in direct arylation, such as unselective C-H bond activation and homocoupling. We report ten DArP protocols across the three major classes of DArP to generate poly[(2,5-bis...... was synthesized in superheated THF with Cs2CO3, neodecanoic acid, and P(o-anisyl)3, it generated polymers of exceptional quality that performed comparably to Stille counterparts in both roll coated ITO-free and spin-coated ITO devices....

  15. Mimicking the Nanostructure of Bone: Comparison of Polymeric Process-Directing Agents

    Directory of Open Access Journals (Sweden)

    Laurie B. Gower

    2010-12-01

    Full Text Available The nanostructure of bone has been replicated using a polymer-induced liquid-precursor (PILP mineralization process. This polymer-mediated crystallization process yields intrafibrillar mineralization of collagen with uniaxially-oriented hydroxyapatite crystals. The process-directing agent, an anionic polymer which we propose mimics the acidic non-collagenous proteins associated with bone formation, sequesters calcium and phosphate ions to form amorphous precursor droplets that can infiltrate the interstices of collagen fibrils. In search of a polymeric agent that produces the highest mineral content in the shortest time, we have studied the influence of various acidic polymers on the in vitro mineralization of collagen scaffolds via the PILP process. Among the polymers investigated were poly-L-aspartic acid (PASP, poly-L-glutamic acid (PGLU, polyvinylphosphonic acid (PVPA, and polyacrylic acid (PAA. Our data indicate that PASP and the combination of PGLU/PASP formed stable mineralization solutions, and yielded nano-structured composites with the highest mineral content. Such studies contribute to our goal of preparing biomimetic bone graft substitutes with composition and structure that mimic bone.

  16. Long-chain amine-templated synthesis of gallium sulfide and gallium selenide nanotubes

    Science.gov (United States)

    Seral-Ascaso, A.; Metel, S.; Pokle, A.; Backes, C.; Zhang, C. J.; Nerl, H. C.; Rode, K.; Berner, N. C.; Downing, C.; McEvoy, N.; Muñoz, E.; Harvey, A.; Gholamvand, Z.; Duesberg, G. S.; Coleman, J. N.; Nicolosi, V.

    2016-06-01

    We describe the soft chemistry synthesis of amine-templated gallium chalcogenide nanotubes through the reaction of gallium(iii) acetylacetonate and the chalcogen (sulfur, selenium) using a mixture of long-chain amines (hexadecylamine and dodecylamine) as a solvent. Beyond their role as solvent, the amines also act as a template, directing the growth of discrete units with a one-dimensional multilayer tubular nanostructure. These new materials, which broaden the family of amine-stabilized gallium chalcogenides, can be tentatively classified as direct large band gap semiconductors. Their preliminary performance as active material for electrodes in lithium ion batteries has also been tested, demonstrating great potential in energy storage field even without optimization.We describe the soft chemistry synthesis of amine-templated gallium chalcogenide nanotubes through the reaction of gallium(iii) acetylacetonate and the chalcogen (sulfur, selenium) using a mixture of long-chain amines (hexadecylamine and dodecylamine) as a solvent. Beyond their role as solvent, the amines also act as a template, directing the growth of discrete units with a one-dimensional multilayer tubular nanostructure. These new materials, which broaden the family of amine-stabilized gallium chalcogenides, can be tentatively classified as direct large band gap semiconductors. Their preliminary performance as active material for electrodes in lithium ion batteries has also been tested, demonstrating great potential in energy storage field even without optimization. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr01663d

  17. Priming and the guidance by visual and categorical templates in visual search

    Directory of Open Access Journals (Sweden)

    Anna eWilschut

    2014-02-01

    Full Text Available Visual search is thought to be guided by top-down templates that are held in visual working memory. Previous studies have shown that a search-guiding template can be rapidly and strongly implemented from a visual cue, whereas templates are less effective when based on categorical cues. Direct visual priming from cue to target may underlie this difference. In two experiments we first asked observers to remember two possible target colors. A postcue then indicated which of the two would be the relevant color. The task was to locate a briefly presented and masked target of the cued color among irrelevant distractor items. Experiment 1 showed that overall search accuracy improved more rapidly on the basis of a direct visual postcue that carried the target color, compared to a neutral postcue that pointed to the memorized color. However, selectivity towards the target feature, i.e. the extent to which observers searched selectively among items of the cued versus uncued color, was found to be relatively unaffected by the presence of the visual signal. In Experiment 2 we compared search that was based on either visual or categorical information, but now controlled for direct visual priming. This resulted in no differences in overall performance nor selectivity. Altogether the results suggest that perceptual processing of visual search targets is facilitated by priming from visual cues, whereas attentional selectivity is enhanced by a working memory template that can formed from both visual and categorical input. Furthermore, if the priming is controlled for, categorical- and visual-based templates similarly enhance search guidance.

  18. Priming and the guidance by visual and categorical templates in visual search.

    Science.gov (United States)

    Wilschut, Anna; Theeuwes, Jan; Olivers, Christian N L

    2014-01-01

    Visual search is thought to be guided by top-down templates that are held in visual working memory. Previous studies have shown that a search-guiding template can be rapidly and strongly implemented from a visual cue, whereas templates are less effective when based on categorical cues. Direct visual priming from cue to target may underlie this difference. In two experiments we first asked observers to remember two possible target colors. A postcue then indicated which of the two would be the relevant color. The task was to locate a briefly presented and masked target of the cued color among irrelevant distractor items. Experiment 1 showed that overall search accuracy improved more rapidly on the basis of a direct visual postcue that carried the target color, compared to a neutral postcue that pointed to the memorized color. However, selectivity toward the target feature, i.e., the extent to which observers searched selectively among items of the cued vs. uncued color, was found to be relatively unaffected by the presence of the visual signal. In Experiment 2 we compared search that was based on either visual or categorical information, but now controlled for direct visual priming. This resulted in no differences in overall performance nor selectivity. Altogether the results suggest that perceptual processing of visual search targets is facilitated by priming from visual cues, whereas attentional selectivity is enhanced by a working memory template that can formed from both visual and categorical input. Furthermore, if the priming is controlled for, categorical- and visual-based templates similarly enhance search guidance.

  19. Peptide-enhanced mRNA transfection in cultured mouse cardiac fibroblasts and direct reprogramming towards cardiomyocyte-like cells

    Directory of Open Access Journals (Sweden)

    Lee K

    2015-03-01

    Full Text Available Kunwoo Lee,1,2 Pengzhi Yu,3 Nithya Lingampalli,1 Hyun Jin Kim,1 Richard Tang,1 Niren Murthy1,2 1Department of Bioengineering, University of California, Berkeley, CA, USA; 2UC Berkeley and UCSF Joint Graduate Program in Bioengineering, Berkeley/San Francisco, CA, USA; 3Gladstone Institute of Cardiovascular Disease, San Francisco, CA, USA Abstract: The treatment of myocardial infarction is a major challenge in medicine due to the inability of heart tissue to regenerate. Direct reprogramming of endogenous cardiac fibroblasts into functional cardiomyocytes via the delivery of transcription factor mRNAs has the potential to regenerate cardiac tissue and to treat heart failure. Even though mRNA delivery to cardiac fibroblasts has the therapeutic potential, mRNA transfection in cardiac fibroblasts has been challenging. Herein, we develop an efficient mRNA transfection in cultured mouse cardiac fibroblasts via a polyarginine-fused heart-targeting peptide and lipofectamine complex, termed C-Lipo and demonstrate the partial direct reprogramming of cardiac fibroblasts towards cardiomyocyte cells. C-Lipo enabled the mRNA-induced direct cardiac reprogramming due to its efficient transfection with low toxicity, which allowed for multiple transfections of Gata4, Mef2c, and Tbx5 (GMT mRNAs for a period of 2 weeks. The induced cardiomyocyte-like cells had α-MHC promoter-driven GFP expression and striated cardiac muscle structure from a-actinin immunohistochemistry. GMT mRNA transfection of cultured mouse cardiac fibroblasts via C-Lipo significantly increased expression of the cardiomyocyte marker genes, Actc1, Actn2, Gja1, Hand2, and Tnnt2, after 2 weeks of transfection. Moreover, this study provides the first direct evidence that the stoichiometry of the GMT reprogramming factors influence the expression of cardiomyocyte marker genes. Our results demonstrate that mRNA delivery is a potential approach for cardiomyocyte generation. Keywords: direct cardiac

  20. Microwave-assisted RAFT polymerization of well-constructed magnetic surface molecularly imprinted polymers for specific recognition of benzimidazole residues

    Science.gov (United States)

    Chen, Fangfang; Wang, Jiayu; Chen, Huiru; Lu, Ruicong; Xie, Xiaoyu

    2018-03-01

    Magnetic nanoparticles have been widely used as support core for fast separation, which could be directly separated from complicated matrices using an external magnet in few minutes. Surface imprinting based on magnetic core has shown favorable adsorption and separation performance, including good adsorption capacity, fast adsorption kinetics and special selectivity adsorption. Reversible addition-fragmentation chain transfer (RAFT) is an ideal choice for producing well-defined complex architecture with mild reaction conditions. We herein describe the preparation of well-constructed magnetic molecularly imprinted polymers (MMIPs) for the recognition of benzimidazole (BMZ) residues via the microwave-assisted RAFT polymerization. The merits of RAFT polymerization assisting with microwave heating allowed successful and more efficient preparation of well-constructed imprinted coats. Moreover, the polymerization time dramatically shortened and was just 1/24th of the time taken by conventional heating. The results indicated that a uniform nanoscale imprinted layer was formed on the Fe3O4 core successfully, and enough saturation magnetization of MMIPs (16.53 emu g-1) was got for magnetic separation. The desirable adsorption capacity (30.18 μmol g-1) and high selectivity toward template molecule with a selectivity coefficient (k) of 13.85 of MMIPs were exhibited by the adsorption isothermal assay and competitive binding assay, respectively. A solid phase extraction enrichment approach was successfully established for the determination of four BMZ residues from apple samples using MMIPs coupled to HPLC. Overall, this study provides a versatile approach for highly efficient fabrication of well-constructed MMIPs for enrichment and determination of target molecules from complicated samples.

  1. Direct activation of microcrystalline zeolites

    NARCIS (Netherlands)

    Ortiz-Iniesta, Maria Jesus; Heeres, Hero Jan; Melian-Cabrera, Ignacio

    2013-01-01

    In this work a direct activation route of zeolites is assessed. It consists of NH4-exchanging the as-synthesized solids before removing the organic template. Calcination afterwards serves to combust the organic template and creates the Bronsted sites directly; thus applying merely a single thermal

  2. Synthesis of ZnO micro-pompons by soft template-directed wet chemical method and their application in electrochemical biosensors

    International Nuclear Information System (INIS)

    Zhou, Yu; Wang, Lei; Ye, Zhizhen; Zhao, Minggang; Huang, Jingyun

    2014-01-01

    Highlights: •ZnO micro-pompons (MPs) are synthesized by a controlled soft template-directed route. •ZnO MPs are composed of radial robust nanowires built of numerous nanoparticles. •The structure is ideal for the immobilization of enzymes to maintain their activity. •ZnO MPs are favorable for electron transfer and liquid mobilization. •Good performance of H 2 O 2 biosensor indicates ZnO MPs are promising in biosensing. -- Abstract: ZnO micro-pompons are fabricated by a controlled synthesis route via a soft template-directed wet chemical method followed by a subsequent calcination in air. The achieved ZnO micro-pompons with several hundred micrometers in diameter are composed of a great number of robust nanowires built of numerous nanoparticles. This unique structure is accessible for enzymes to sequester or bind, and the tightly connected nanoparticles facilitate the transmission of electrons, what's more, the large spaces between the nanowires are favorable for the mobilization of the liquid with target substance. In addition, the high electron communication features of ZnO and the tightly connected nanoparticles of the structure also promote the electron transfer between the active sites of proteins and the electrode. The enzymatic electrode fabricated with Horseradish peroxidase immobilized on ZnO micro-pompons along with chitosan covering outside exhibits excellent response for detecting H 2 O 2 with a wide linear range of 0.2–3.4 mM and a high sensitivity of 1395.64 (μA/mM cm 2 ), indicating a great potential in fabricating electrochemical biosensors

  3. RNA Catalysis, Thermodynamics and the Origin of Life

    Directory of Open Access Journals (Sweden)

    William G. Scott

    2014-04-01

    Full Text Available The RNA World Hypothesis posits that the first self-replicating molecules were RNAs. RNA self-replicases are, in general, assumed to have employed nucleotide 5ʹ-polyphosphates (or their analogues as substrates for RNA polymerization. The mechanism by which these substrates might be synthesized with sufficient abundance to supply a growing and evolving population of RNAs is problematic for evolutionary hypotheses because non-enzymatic synthesis and assembly of nucleotide 5ʹ-triphosphates (or other analogously activated phosphodiester species is inherently difficult. However, nucleotide 2ʹ,3ʹ-cyclic phosphates are also phosphodiesters, and are the natural and abundant products of RNA degradation. These have previously been dismissed as viable substrates for prebiotic RNA synthesis. We propose that the arguments for their dismissal are based on a flawed assumption, and that nucleotide 2ʹ,3ʹ-cyclic phosphates in fact possess several significant, advantageous properties that indeed make them particularly viable substrates for prebiotic RNA synthesis. An RNA World hypothesis based upon the polymerization of nucleotide 2ʹ,3ʹ-cyclic phosphates possesses additional explanatory power in that it accounts for the observed ribozyme “fossil record”, suggests a viable mechanism for substrate transport across lipid vesicle boundaries of primordial proto-cells, circumvents the problems of substrate scarcity and implausible synthetic pathways, provides for a primitive but effective RNA replicase editing mechanism, and definitively explains why RNA, rather than DNA, must have been the original catalyst. Finally, our analysis compels us to propose that a fundamental and universal property that drives the evolution of living systems, as well as pre-biotic replicating molecules (be they composed of RNA or protein, is that they exploit chemical reactions that already possess competing kinetically-preferred and thermodynamically-preferred pathways in a

  4. Click polymerization for the synthesis of reduction-responsive polymeric prodrug

    Science.gov (United States)

    Zhang, Xiaojin; Wang, Hongquan; Dai, Yu

    2018-05-01

    Click polymerization is a powerful polymerization technique for the construction of new macromolecules with well-defined structures and multifaceted functionalities. Here, we synthesize reduction-responsive polymeric prodrug PEG- b-(PSS- g-MTX)- b-PEG containing disulfide bonds and pendant methotrexate (MTX) via two-step click polymerization followed by conjugating MTX to pendant hydroxyl. MTX content in polymeric prodrug is 13.5%. Polymeric prodrug is able to form polymeric micelles by self-assembly in aqueous solution. Polymeric micelles are spherical nanoparticles with tens of nanometers in size. Of note, polymeric micelles are reduction-responsive due to disulfide bonds in the backbone of PEG- b-(PSS- g-MTX)- b-PEG and could release pendant drugs in the presence of the reducing agents such as dl-dithiothreitol (DTT).

  5. Receptor-targeted aptamer-siRNA conjugate-directed transcriptional regulation of HIV-1

    Science.gov (United States)

    Zhou, Jiehua; Lazar, Daniel; Li, Haitang; Xia, Xin; Satheesan, Sangeetha; Charlins, Paige; O'Mealy, Denis; Akkina, Ramesh; Saayman, Sheena; Weinberg, Marc S.; Rossi, John J.; Morris, Kevin V.

    2018-01-01

    Gene-based therapies represent a promising therapeutic paradigm for the treatment of HIV-1, as they have the potential to maintain sustained viral inhibition with reduced treatment interventions. Such an option may represent a long-term treatment alternative to highly active antiretroviral therapy. Methods: We previously described a therapeutic approach, referred to as transcriptional gene silencing (TGS), whereby small noncoding RNAs directly inhibit the transcriptional activity of HIV-1 by targeting sites within the viral promoter, specifically the 5' long terminal repeat (LTR). TGS differs from traditional RNA interference (RNAi) in that it is characterized by concomitant silent-state epigenetic marks on histones and DNA. To deliver TGS-inducing RNAs, we developed functional RNA conjugates based on the previously reported dual function of the gp120 (A-1) aptamer conjugated to 27-mer Dicer-substrate anti-HIV-1 siRNA (dsiRNA), LTR-362. Results: We demonstrate here that high levels of processed guide RNAs localize to the nucleus in infected T lymphoblastoid CEM cell line and primary human CD4+ T-cells. Treatment of the aptamer-siRNA conjugates induced TGS with an ~10-fold suppression of viral p24 levels as measured at day 12 post infection. To explore the silencing efficacy of aptamer-siRNA conjugates in vivo, HIV-1-infected humanized NOD/SCID/IL2 rγnull mice (hu-NSG) were treated with the aptamer-siRNA conjugates. Systemic delivery of the A-1-stick-LTR-362 27-mer siRNA conjugates suppressed HIV-1 infection and protected CD4+ T cell levels in viremia hu-NSG mice. Principle conclusions: Collectively these data suggest that the gp120 aptamer-dsiRNA conjugate design is suitable for systemic delivery of small RNAs that can be used to suppress HIV-1. PMID:29556342

  6. Pulsed-laser polymerization in compartmentalized liquids. 1. Polymerization in vesicles

    NARCIS (Netherlands)

    Jung, M.; Casteren, van I.A.; Monteiro, M.J.; Herk, van A.M.; German, A.L.

    2000-01-01

    Polymerization in vesicles is a novel type of polymerization in heterogeneous media, leading to parachute-like vesicle-polymer hybrid morphologies. To explore the kinetics of vesicle polymerizations and to learn more about the actual locus of polymerization we applied the pulsed-laser polymerization

  7. Computing layouts with deformable templates

    KAUST Repository

    Peng, Chi-Han

    2014-07-22

    In this paper, we tackle the problem of tiling a domain with a set of deformable templates. A valid solution to this problem completely covers the domain with templates such that the templates do not overlap. We generalize existing specialized solutions and formulate a general layout problem by modeling important constraints and admissible template deformations. Our main idea is to break the layout algorithm into two steps: a discrete step to lay out the approximate template positions and a continuous step to refine the template shapes. Our approach is suitable for a large class of applications, including floorplans, urban layouts, and arts and design. Copyright © ACM.

  8. Computing layouts with deformable templates

    KAUST Repository

    Peng, Chi-Han; Yang, Yongliang; Wonka, Peter

    2014-01-01

    In this paper, we tackle the problem of tiling a domain with a set of deformable templates. A valid solution to this problem completely covers the domain with templates such that the templates do not overlap. We generalize existing specialized solutions and formulate a general layout problem by modeling important constraints and admissible template deformations. Our main idea is to break the layout algorithm into two steps: a discrete step to lay out the approximate template positions and a continuous step to refine the template shapes. Our approach is suitable for a large class of applications, including floorplans, urban layouts, and arts and design. Copyright © ACM.

  9. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives.

    Science.gov (United States)

    Bujarski, Jozef J

    2013-01-01

    RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

  10. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives

    Directory of Open Access Journals (Sweden)

    Jozef Julian Bujarski

    2013-03-01

    Full Text Available RNA recombination is one of the driving forces of genetic variability in (+-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings along with nonreplicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (i How various factors modulate the ability of viral replicase to switch templates, (ii What is the intracellular location of RNA-RNA template switchings, (iii Mechanisms and factors responsible for non-replicative RNA recombination, (iv Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (v What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.

  11. Studying RNA-protein interactions in vivo by RNA immunoprecipitation

    DEFF Research Database (Denmark)

    Selth, Luke A; Close, Pierre; Svejstrup, Jesper Q

    2011-01-01

    and have significant effects on gene expression. RNA immunoprecipitation (RIP) is a powerful technique used to detect direct and indirect interactions between individual proteins and specific RNA molecules in vivo. Here, we describe RIP methods for both yeast and mammalian cells.......The crucial roles played by RNA-binding proteins in all aspects of RNA metabolism, particularly in the regulation of transcription, have become increasingly evident. Moreover, other factors that do not directly interact with RNA molecules can nevertheless function proximally to RNA polymerases...

  12. Direct application of radioiodinated aminoacyl tRNA for radiolabeling nascent proteins

    International Nuclear Information System (INIS)

    Scherberg, N.H.; Barokas, K.; Murata, Y.; Refetoff, S.

    1985-01-01

    A two-step procedure to incorporate 125 I-iodotyrosine into protein synthesized in a reticulocyte lysate is described. In the first step, the iodination of tyrosyl tRNA was catalyzed by a solid-state glycouril compound. More than one-third of 200 microCi of radioiodine became bound to 70 micrograms of aminoacyl tRNA after 15 min at 0 degrees C. The isotope was distributed in a three-to-one ratio of monoiodotyrosine to di-iodotyrosine. In the second step, the soluble product of the radioiodination was transferred directly into a nuclease-treated reticulocyte lysate coded with RNA isolated from the human hepatoma cell line Hep G2. Fractional recovery of radioiodine in nascent protein was maximally 7.6%. Reaction of the product of translation with antibody against alpha-antitrypsin separated an 125 I-containing protein having a molecular weight estimated as 47,000. The synthesis of unprocessed alpha-antitrypsin was confirmed by cleavage of the labeled protein with leader peptidase and by its displacement from immunocomplex formation with purified alpha-antitrypsin. The amount of 125 I incorporated into alpha-antitrypsin was proportionate to iodinated tRNA additions up to a concentration of 70 micrograms/ml. The synthesis of alpha-antitrypsin as detected in radioautograms after gel electrophoresis was more than twice as sensitive using radioiodinated aminoacyl tRNA as compared with [ 35 S]methionine. Iodine labeling of thyroxine-binding globulin was also demonstrated in the translation product of Hep G2 RNA. Since the specific activity of the radioiodine is high and the means for detection of the isotope efficient, the method described can facilitate the demonstration of quantitatively minor translation products

  13. Polymerisation of activated RNA in eutectic ice phases

    DEFF Research Database (Denmark)

    Dörr, Mark; Maurer, Sarah Elisabeth; Monnard, Pierre-Alain

    , metal catalyzed condensation reactions (s. micrograph, right). With a new, non-radioactive ex-perimental essay we are selectively monitoring the 5'-3' and 5'-2' elongation of 5'-fluorescence labeled RNA oligomers. At - 18.5 °C the polymerization reaction and its selectivity is expected to be much higher...... than at room temperature. In the case of a mixed dimer or oligomer experiment this might lead to a particular sequence distribution. The concurrence between polymerization and degradation seen in the previous work shall be further investigated, focusing on possible sequences stabilizing and increasing...... (“cooperative sequences”) or degrading (“parasitic sequences”) the RNA population. These eutectic phases in water-ice are plausible prebiotic micro-environments that should help to overcome the dilution problem in origin of life scenarios. They might have supported the production of libraries...

  14. Facile template-directed synthesis of carbon-coated SnO2 nanotubes with enhanced Li-storage capabilities

    International Nuclear Information System (INIS)

    Zhu, Xiaoshu; Zhu, Jingyi; Yao, Yinan; Zhou, Yiming; Tang, Yawen; Wu, Ping

    2015-01-01

    Herein, a novel type of carbon-coated SnO 2 nanotubes has been designed and synthesized through a facile two-step hydrothermal approach by using ZnO nanorods as templates. During the synthetic route, SnO 2 nanocrystals and carbon layer have been uniformly deposited on the rod-like templates in sequence, meanwhile ZnO nanorods could be in situ dissolved owing to the generated alkaline and acidic environments during hydrothermal coating of SnO 2 nanocrystals and hydrothermal carbonization of glucose, respectively. When utilized as an anode material in lithium-ion batteries, the carbon-coated SnO 2 nanotubes manifests markedly enhanced Li-storage capabilities in terms of specific capacity and cycling stability in comparison with bare SnO 2 nanocrystals. - Graphical abstract: Display Omitted - Highlights: • C-coated SnO 2 nanotubes prepared via facile ZnO-nanorod-templated hydrothermal route. • Unique morphological and structural features toward lithium storage. • Enhanced Li-storage performance in terms of specific capacity and cycling stability

  15. A Deformable Template Model, with Special Reference to Elliptical Templates

    DEFF Research Database (Denmark)

    Hobolth, Asger; Pedersen, Jan; Jensen, Eva Bjørn Vedel

    2002-01-01

    This paper suggests a high-level continuous image model for planar star-shaped objects. Under this model, a planar object is a stochastic deformation of a star-shaped template. The residual process, describing the difference between the radius-vector function of the template and the object...

  16. The use of Trametes versicolor laccase for the polymerization of aniline in the presence of vesicles as templates.

    Science.gov (United States)

    Junker, Katja; Kissner, Reinhard; Rakvin, Boris; Guo, Zengwei; Willeke, Martin; Busato, Stephan; Weber, Thomas; Walde, Peter

    2014-02-05

    The enzymatic polymerization of aniline to polyaniline (PANI) with Trametes versicolor laccase (TvL) as catalyst and dioxygen (O₂) as oxidant was investigated in an aqueous medium containing unilamellar vesicles with an average diameter of about 80 nm formed from AOT (=sodium bis(2-ethylhexyl) sulfosuccinate). Compared to the same reaction carried out with horseradish peroxidase isoenzyme C (HRPC) as catalyst and hydrogen peroxide (H₂O₂) as oxidant, notable differences were found in the kinetics of the reaction, as well as in the characteristics of the PANI obtained. Under comparable optimal conditions, which are pH 3.5 for TvL/O₂ and pH 4.3 for HRPC/H₂O₂, the reaction with TvL/O₂ was much slower than with HRPC/H₂O₂, i.e. ≈27 days vs. 1 day reaction time to reach equilibrium with >90% yield at 25 °C. Although in both cases, aniline monomer coupling occurred mainly via the carbon atom in para position of aniline, UV-vis-NIR absorption and EPR measurements indicate that the reaction with TvL/O₂ yielded mainly overoxidized products (with λ(max)=730 nm). These products had a lower amount of unpaired electrons if compared with the products obtained with HRPC/H₂O₂ (with λ(max)≈1000 nm, which is characteristic for the polaron state of PANI-ES, the emeraldine salt form of PANI). Similarly to previous findings with HRPC/H₂O₂, enzyme inactivation occurred during the polymerization also in the case of TvL/O₂. Since the aqueous PANI-vesicle suspensions obtained are of high colloidal stability, they can be used directly as ink in a conventional thermal inkjet printer for printing on paper or on surface treated polyimide films. Printed PANI-ES patterns on paper changed colour from green (emeraldine salt) to blue (emeraldine base) upon exposure to ammonia gas, demonstrating the expected ammonia sensing properties. Copyright © 2013 Elsevier Inc. All rights reserved.

  17. The emergence of DNA in the RNA world: an in silico simulation study of genetic takeover.

    Science.gov (United States)

    Ma, Wentao; Yu, Chunwu; Zhang, Wentao; Wu, Sanmao; Feng, Yu

    2015-12-07

    It is now popularly accepted that there was an "RNA world" in early evolution of life. This idea has a direct consequence that later on there should have been a takeover of genetic material - RNA by DNA. However, since genetic material carries genetic information, the "source code" of all living activities, it is actually reasonable to question the plausibility of such a "revolutionary" transition. Due to our inability to model relevant "primitive living systems" in reality, it is as yet impossible to explore the plausibility and mechanisms of the "genetic takeover" by experiments. Here we investigated this issue by computer simulation using a Monte-Carlo method. It shows that an RNA-by-DNA genetic takeover may be triggered by the emergence of a nucleotide reductase ribozyme with a moderate activity in a pure RNA system. The transition is unstable and limited in scale (i.e., cannot spread in the population), but can get strengthened and globalized if certain parameters are changed against RNA (i.e., in favor of DNA). In relation to the subsequent evolution, an advanced system with a larger genome, which uses DNA as genetic material and RNA as functional material, is modeled - the system cannot sustain if the nucleotide reductase ribozyme is "turned off" (thus, DNA cannot be synthesized). Moreover, the advanced system cannot sustain if only DNA's stability, template suitability or replication fidelity (any of the three) is turned down to the level of RNA's. Genetic takeover should be plausible. In the RNA world, such a takeover may have been triggered by the emergence of some ribozyme favoring the formation of deoxynucleotides. The transition may initially have been "weak", but could have been reinforced by environmental changes unfavorable to RNA (such as temperature or pH rise), and would have ultimately become irreversible accompanying the genome's enlargement. Several virtues of DNA (versus RNA) - higher stability against hydrolysis, greater suitability as

  18. CRISPR/Cas9 cleavages in budding yeast reveal templated insertions and strand-specific insertion/deletion profiles.

    Science.gov (United States)

    Lemos, Brenda R; Kaplan, Adam C; Bae, Ji Eun; Ferrazzoli, Alexander E; Kuo, James; Anand, Ranjith P; Waterman, David P; Haber, James E

    2018-02-27

    Harnessing CRISPR-Cas9 technology provides an unprecedented ability to modify genomic loci via DNA double-strand break (DSB) induction and repair. We analyzed nonhomologous end-joining (NHEJ) repair induced by Cas9 in budding yeast and found that the orientation of binding of Cas9 and its guide RNA (gRNA) profoundly influences the pattern of insertion/deletions (indels) at the site of cleavage. A common indel created by Cas9 is a 1-bp (+1) insertion that appears to result from Cas9 creating a 1-nt 5' overhang that is filled in by a DNA polymerase and ligated. The origin of +1 insertions was investigated by using two gRNAs with PAM sequences located on opposite DNA strands but designed to cleave the same sequence. These templated +1 insertions are dependent on the X-family DNA polymerase, Pol4. Deleting Pol4 also eliminated +2 and +3 insertions, which are biased toward homonucleotide insertions. Using inverted PAM sequences, we also found significant differences in overall NHEJ efficiency and repair profiles, suggesting that the binding of the Cas9:gRNA complex influences subsequent NHEJ processing. As with events induced by the site-specific HO endonuclease, CRISPR-Cas9-mediated NHEJ repair depends on the Ku heterodimer and DNA ligase 4. Cas9 events are highly dependent on the Mre11-Rad50-Xrs2 complex, independent of Mre11's nuclease activity. Inspection of the outcomes of a large number of Cas9 cleavage events in mammalian cells reveals a similar templated origin of +1 insertions in human cells, but also a significant frequency of similarly templated +2 insertions.

  19. A novel ethanol templating synthesis of ordered lamellar superstructured crystalline zirconia

    International Nuclear Information System (INIS)

    Liu Chao; Wang Bin; Ji Xiujie; Zhao Shanshan; Wu Jie; Jia Jianlong; Ma Dongxia

    2012-01-01

    Soft template technique has attracted great interest, because it is a facile, inexpensive and efficient synthesis strategy for ordered superstructural systems. Here, a novel ethanol template was used to synthesize the ordered lamellar superstructured crystalline zirconia (Lα-ZrO 2 ) without post-treatments and surfactants. ZrOCl 2 and NaOH were served as Zr source and precipitant, respectively. XRD analysis showed that Lα-ZrO 2 is crystalline. XPS spectra indicated the physical adsorption of ethanol molecules in Lα-ZrO 2 . TEM further observed and proved the 1.36-nm period of superstructure detected and calculated by SAXRD (1.35 nm), which is composed of 0.68-nm thick ZrO 2 and pore alternatively. In contrast, the template-free ZrO 2 (TF-ZrO 2 ) presents no superstructure and is poorly crystallized. As a soft template, ethanol presents the roles of (i) inducing the growth of zirconia layers, (ii) directing the self-assembly of ordered lamellar superstructure, and (iii) decreasing the crystallization temperature. The possible mechanism of ethanol serving as a soft template was proposed and discussed in thermodynamics.

  20. Biotechnological applications of mobile group II introns and their reverse transcriptases: gene targeting, RNA-seq, and non-coding RNA analysis.

    Science.gov (United States)

    Enyeart, Peter J; Mohr, Georg; Ellington, Andrew D; Lambowitz, Alan M

    2014-01-13

    high processivity and fidelity of group II intron reverse transcriptases along with their novel template-switching activity, which can directly link RNA-seq adaptor sequences to cDNAs during reverse transcription, open new approaches for RNA-seq and the identification and profiling of non-coding RNAs, with potentially wide applications in research and biotechnology.

  1. Developmental regulation of Xenopus 5S RNA genes

    International Nuclear Information System (INIS)

    Wormington, W.M.; Schlissel, M.; Brown, D.D.

    1983-01-01

    In this paper it is demonstrated that the actively transcribed fraction of somatic 5S RNA genes in somatic-cell chromatin is complexed stably with all required factors, so that the addition of only purified RNA polymerase III is needed to support somatic 5S RNA synthesis in vitro. Oocyte 5S RNA genes in somatic-cell chromatin appear to lack these factors, since their activation in salt-washed somatic-cell chromatin depends on exogeneous transciption factors in addition to RNA polymerase III. The developmental control of 5S RNA genes is established over a period beginning with the onset of 5S RNA synthesis in late blastula embryos, and this control is reproduced in vitro using chromatin templates isolated from appropriate stages. We propose that a decreasing concentration of the 5S-specific transcription factor during embryogenesis contributes to the inactivation of oocyte 5S RNA genes. 12 references, 4 figures, 1 table

  2. Transcriptomic-Wide Discovery of Direct and Indirect HuR RNA Targets in Activated CD4+ T Cells.

    Directory of Open Access Journals (Sweden)

    Patsharaporn Techasintana

    Full Text Available Due to poor correlation between steady state mRNA levels and protein product, purely transcriptomic profiling methods may miss genes posttranscriptionally regulated by RNA binding proteins (RBPs and microRNAs (miRNAs. RNA immunoprecipitation (RIP methods developed to identify in vivo targets of RBPs have greatly elucidated those mRNAs which may be regulated via transcript stability and translation. The RBP HuR (ELAVL1 and family members are major stabilizers of mRNA. Many labs have identified HuR mRNA targets; however, many of these analyses have been performed in cell lines and oftentimes are not independent biological replicates. Little is known about how HuR target mRNAs behave in conditional knock-out models. In the present work, we performed HuR RIP-Seq and RNA-Seq to investigate HuR direct and indirect targets using a novel conditional knock-out model of HuR genetic ablation during CD4+ T activation and Th2 differentiation. Using independent biological replicates, we generated a high coverage RIP-Seq data set (>160 million reads that was analyzed using bioinformatics methods specifically designed to find direct mRNA targets in RIP-Seq data. Simultaneously, another set of independent biological replicates were sequenced by RNA-Seq (>425 million reads to identify indirect HuR targets. These direct and indirect targets were combined to determine canonical pathways in CD4+ T cell activation and differentiation for which HuR plays an important role. We show that HuR may regulate genes in multiple canonical pathways involved in T cell activation especially the CD28 family signaling pathway. These data provide insights into potential HuR-regulated genes during T cell activation and immune mechanisms.

  3. An RNA secondary structure bias for non-homologous reverse transcriptase-mediated deletions in vivo

    DEFF Research Database (Denmark)

    Duch, Mogens; Carrasco, Maria L; Jespersen, Thomas

    2004-01-01

    Murine leukemia viruses harboring an internal ribosome entry site (IRES)-directed translational cassette are able to replicate, but undergo loss of heterologous sequences upon continued passage. While complete loss of heterologous sequences is favored when these are flanked by a direct repeat......, deletion mutants with junction sites within the heterologous cassette may also be retrieved, in particular from vectors without flanking repeats. Such deletion mutants were here used to investigate determinants of reverse transcriptase-mediated non-homologous recombination. Based upon previous structural...... result from template switching during first-strand cDNA synthesis and that the choice of acceptor sites for non-homologous recombination are guided by non-paired regions. Our results may have implications for recombination events taking place within structured regions of retroviral RNA genomes...

  4. Radiation polymerization of tetrafluoroethylene in freon-22

    International Nuclear Information System (INIS)

    Schnautz, N.G.; Thompson, J.C.

    1979-02-01

    The radiation-induced solution-polymerization of tetrafluoroethylene in Freon-22 has been investigated over a temperature range of - 62 degrees celcius to 0 degrees celcius. The rate of polymerization for the in-source process was found to be directly propertional to monomer concentration and an activation energy of only 7,66 kj/mole was calculated. The number-average molecular mass of the product PTFE ranged from 2X10 4 to 6X10 4 and was relatively independent of the usual reaction parameters. The rate of postpolymerization was also found to be directly proportional to monomer concentration. The postpolyerization process did not result in any enchancement of the initial PTFE molecular mass [af

  5. The Human Nuclear Exosome Targeting Complex Is Loaded onto Newly Synthesized RNA to Direct Early Ribonucleolysis

    Directory of Open Access Journals (Sweden)

    Michal Lubas

    2015-01-01

    Full Text Available The RNA exosome complex constitutes the major nuclear eukaryotic 3′-5′ exonuclease. Outside of nucleoli, the human nucleoplasmic exosome is directed to some of its substrates by the nuclear exosome targeting (NEXT complex. How NEXT targets RNA has remained elusive. Using an in vivo crosslinking approach, we report global RNA binding sites of RBM7, a key component of NEXT. RBM7 associates broadly with RNA polymerase II-derived RNA, including pre-mRNA and short-lived exosome substrates such as promoter upstream transcripts (PROMPTs, enhancer RNAs (eRNAs, and 3′-extended products from snRNA and replication-dependent histone genes. Within pre-mRNA, RBM7 accumulates at the 3′ ends of introns, and pulse-labeling experiments demonstrate that RBM7/NEXT defines an early exosome-targeting pathway for 3′-extended snoRNAs derived from such introns. We propose that RBM7 is generally loaded onto newly synthesized RNA to accommodate exosome action in case of available unprotected RNA 3′ ends.

  6. Template-directed covalent conjugation of DNA to native antibodies, transferrin and other metal-binding proteins

    Science.gov (United States)

    Rosen, Christian B.; Kodal, Anne L. B.; Nielsen, Jesper S.; Schaffert, David H.; Scavenius, Carsten; Okholm, Anders H.; Voigt, Niels V.; Enghild, Jan J.; Kjems, Jørgen; Tørring, Thomas; Gothelf, Kurt V.

    2014-09-01

    DNA-protein conjugates are important in bioanalytical chemistry, molecular diagnostics and bionanotechnology, as the DNA provides a unique handle to identify, functionalize or otherwise manipulate proteins. To maintain protein activity, conjugation of a single DNA handle to a specific location on the protein is often needed. However, preparing such high-quality site-specific conjugates often requires genetically engineered proteins, which is a laborious and technically challenging approach. Here we demonstrate a simpler method to create site-selective DNA-protein conjugates. Using a guiding DNA strand modified with a metal-binding functionality, we directed a second DNA strand to the vicinity of a metal-binding site of His6-tagged or wild-type metal-binding proteins, such as serotransferrin, where it subsequently reacted with lysine residues at that site. This method, DNA-templated protein conjugation, facilitates the production of site-selective protein conjugates, and also conjugation to IgG1 antibodies via a histidine cluster in the constant domain.

  7. Use of Polymeric and Natural Materials for the Removal of Irradiated Direct and acid Dyes from Effluents

    International Nuclear Information System (INIS)

    Dessouki, A.M.; Abdel-Aal, S.E.; Gad, Y.H.

    2000-01-01

    Wastewater effluents from textile plants typically contain appreciable quantities of organic dyes that are resistant to degrade by ordinary treatment processes and constitute a highly visible form of pollution in the receiving waters. Carbon absorption as well as ionizing radiation are used as treatment processes. However, each method alone did not achieve the complete removal of these pollutants. A combined treatment is more effective. The two direct dyes(Direct orange S, Isma fast yellow Rl) were degraded by radiation 76% and 70% ,respectively. Also, the acid dye Sandolane Rubanole E-3 GSL (Acid red 37) was degraded almost to the same extent. Addition of O 2 or H 2 O-2 resulted in a remarkable enhancement in the degradation process. The effect of ph, gamma-dose and dye concentration was studied. Polymeric ion exchangers proved to be more effective in the removal process than clays. However, granular activated carbon (GAC) was the best adsorbent for the direct dyes. Clays proved to be very good adsorbents for two basic dyes than their weak adsorption behavior of the direct ones

  8. An In Vitro RNA Synthesis Assay for Rabies Virus Defines Ribonucleoprotein Interactions Critical for Polymerase Activity.

    Science.gov (United States)

    Morin, Benjamin; Liang, Bo; Gardner, Erica; Ross, Robin A; Whelan, Sean P J

    2017-01-01

    We report an in vitro RNA synthesis assay for the RNA-dependent RNA polymerase (RdRP) of rabies virus (RABV). We expressed RABV large polymerase protein (L) in insect cells from a recombinant baculovirus vector and the phosphoprotein cofactor (P) in Escherichia coli and purified the resulting proteins by affinity and size exclusion chromatography. Using chemically synthesized short RNA corresponding to the first 19 nucleotides (nt) of the rabies virus genome, we demonstrate that L alone initiates synthesis on naked RNA and that P serves to enhance the initiation and processivity of the RdRP. The L-P complex lacks full processivity, which we interpret to reflect the lack of the viral nucleocapsid protein (N) on the template. Using this assay, we define the requirements in P for stimulation of RdRP activity as residues 11 to 50 of P and formally demonstrate that ribavirin triphosphate (RTP) inhibits the RdRP. By comparing the properties of RABV RdRP with those of the related rhabdovirus, vesicular stomatitis virus (VSV), we demonstrate that both polymerases can copy the heterologous promoter sequence. The requirements for engagement of the N-RNA template of VSV by its polymerase are provided by the C-terminal domain (CTD) of P. A chimeric RABV P protein in which the oligomerization domain (OD) and the CTD were replaced by those of VSV P stimulated RABV RdRP activity on naked RNA but was insufficient to permit initiation on the VSV N-RNA template. This result implies that interactions between L and the template N are also required for initiation of RNA synthesis, extending our knowledge of ribonucleoprotein interactions that are critical for gene expression. The current understanding of the structural and functional significance of the components of the rabies virus replication machinery is incomplete. Although structures are available for the nucleocapsid protein in complex with RNA, and also for portions of P, information on both the structure and function of the L

  9. The ribosome structure controls and directs mRNA entry, translocation and exit dynamics

    International Nuclear Information System (INIS)

    Kurkcuoglu, Ozge; Doruker, Pemra; Jernigan, Robert L; Sen, Taner Z; Kloczkowski, Andrzej

    2008-01-01

    The protein-synthesizing ribosome undergoes large motions to effect the translocation of tRNAs and mRNA; here, the domain motions of this system are explored with a coarse-grained elastic network model using normal mode analysis. Crystal structures are used to construct various model systems of the 70S complex with/without tRNA, elongation factor Tu and the ribosomal proteins. Computed motions reveal the well-known ratchet-like rotational motion of the large subunits, as well as the head rotation of the small subunit and the high flexibility of the L1 and L7/L12 stalks, even in the absence of ribosomal proteins. This result indicates that these experimentally observed motions during translocation are inherently controlled by the ribosomal shape and only partially dependent upon GTP hydrolysis. Normal mode analysis further reveals the mobility of A- and P-tRNAs to increase in the absence of the E-tRNA. In addition, the dynamics of the E-tRNA is affected by the absence of the ribosomal protein L1. The mRNA in the entrance tunnel interacts directly with helicase proteins S3 and S4, which constrain the mRNA in a clamp-like fashion, as well as with protein S5, which likely orients the mRNA to ensure correct translation. The ribosomal proteins S7, S11 and S18 may also be involved in assuring translation fidelity by constraining the mRNA at the exit site of the channel. The mRNA also interacts with the 16S 3' end forming the Shine–Dalgarno complex at the initiation step; the 3' end may act as a 'hook' to reel in the mRNA to facilitate its exit

  10. Monte Carlo simulation of non-linear free radical polymerization using a percolation kinetic gelation model (I): free radical homo polymerization

    International Nuclear Information System (INIS)

    Ghiass, M.; Dabir, B.; Nikazar, M.; Rey, A.D.; Mirzadeh, H.

    2001-01-01

    A kinetic gelation model that incorporates the kinetics of free radical homo polymerization is implemented to determine the effects of kinetics on polymerization statistics and microstructures. The simulation is performed on a simple cubic lattice that has 100 sites in each direction. A new algorithm for random selecting of the next step in a self-avoiding random walk and very efficient mechanisms of mobility of components are introduced to improve the generality of the predictions by removing commonly accruing deficiencies due to early trapping of radicals. A first order kinetics is considered for decomposition of initiator that enables us to consider the effect of temperature on polymerization reaction. Better understanding of microstructural evolution during polymerization and providing a framework to produce a realistic system of highly packed random chains within polymer network are among the benefits of model

  11. Liquid as template for next generation micro devices

    International Nuclear Information System (INIS)

    Charmet, Jerome; Haquette, Henri; Laux, Edith; Keppner, Herbert; Gorodyska, Ganna; Textor, Marcus; Durante, Guido Spinola; Portuondo-Campa, Erwin; Knapp, Helmut; Bitterli, Roland; Noell, Wilfried

    2009-01-01

    Liquids have fascinated generations of scientists and engineers. Since ancient Greece, the perfect natural shape of liquids has been used to create optical systems. Nowadays, the natural shape of liquid is used in the fabrication of microlens arrays that rely on the melting of glass or photoresist to generate high quality lenses. However shrinkage normally associated to the liquid to solid phase transition will affect the initial shape and quality of the liquid structure. In this contribution, a novel fabrication technique that enables the encapsulation and replication of liquid templates without affecting their natural shape is presented. The SOLID (SOlid on LIquid Deposition) process allows for a transparent solid film to be deposited and grown onto a liquid template (droplet, film, line) in a way that the liquid shapes the overgrowing solid layer. The resulting configuration of the SOLID devices is chemically and mechanically stable and is the base of a huge variety of new micro-nano systems in the field of microfluidics, biomedical devices and micro-optics among others. The SOLID process enables in a one step process the encapsulation of liquid microlenses, fluidics channels, drug reservoir or any naturally driven liquid structure. The phenomenon and solid-liquid interface resulting from the SOLID process is new and still unexploited. The solid layer used for the SOLID process chosen in this paper is poly-para-xylylene called Parylene, a transparent biocompatible polymer with excellent mechanical and chemical properties. Moreover, as the solid layer is growing over a liquid template, atomically smooth surfaces channels can be obtained. The polymerization of Parylene does not exert stress and does not change the shape of the liquid; this latter aspect is particularly interesting for manufacturing naturally driven liquid structures. In this paper the authors explore the limits of this new method by testing different designs of SOLID encapsulated structures and

  12. Cross-catalytic peptide nucleic acid (PNA) replication based on templated ligation

    DEFF Research Database (Denmark)

    Singhal, Abhishek; Nielsen, Peter E

    2014-01-01

    We report the first PNA self-replicating system based on template directed cross-catalytic ligation, a process analogous to biological replication. Using two template PNAs and four pentameric precursor PNAs, all four possible carbodiimide assisted amide ligation products were detected...... precursors. Cross-catalytic product formation followed product inhibited kinetics, but approximately two replication rounds were observed. Analogous but less efficient replication was found for a similar tetrameric system. These results demonstrate that simpler nucleobase replication systems than natural...

  13. Biometric Template Security

    Directory of Open Access Journals (Sweden)

    Abhishek Nagar

    2008-03-01

    Full Text Available Biometric recognition offers a reliable solution to the problem of user authentication in identity management systems. With the widespread deployment of biometric systems in various applications, there are increasing concerns about the security and privacy of biometric technology. Public acceptance of biometrics technology will depend on the ability of system designers to demonstrate that these systems are robust, have low error rates, and are tamper proof. We present a high-level categorization of the various vulnerabilities of a biometric system and discuss countermeasures that have been proposed to address these vulnerabilities. In particular, we focus on biometric template security which is an important issue because, unlike passwords and tokens, compromised biometric templates cannot be revoked and reissued. Protecting the template is a challenging task due to intrauser variability in the acquired biometric traits. We present an overview of various biometric template protection schemes and discuss their advantages and limitations in terms of security, revocability, and impact on matching accuracy. A template protection scheme with provable security and acceptable recognition performance has thus far remained elusive. Development of such a scheme is crucial as biometric systems are beginning to proliferate into the core physical and information infrastructure of our society.

  14. In situ and real-time small-angle neutron scattering studies of living anionic polymerization process and polymerization-induced self-assembly of block copolymers

    International Nuclear Information System (INIS)

    Tanaka, H.; Yamauchi, K.; Hasegawa, H.; Miyamoto, N.; Koizumi, S.; Hashimoto, T.

    2006-01-01

    We have studied a simultaneous living anionic polymerization process of isoprene and deuterated styrene in deuterated benzene with sec-buthyl lithium as an initiator into polyisoprene-block-poly(styrene-d 8 ) and the polymerization-induced self-assembling process. This polymerization-induced self-assembling process was directly observed by an in situ and real-time small-angle neutron scattering (SANS) experiment. The time-resolved SANS studies enabled us to explore a time evolution of hierarchical structures induced by a time evolution of the primary structure (linear sequential connection of two monomers)

  15. Ferritin-Templated Quantum-Dots for Quantum Logic Gates

    Science.gov (United States)

    Choi, Sang H.; Kim, Jae-Woo; Chu, Sang-Hyon; Park, Yeonjoon; King, Glen C.; Lillehei, Peter T.; Kim, Seon-Jeong; Elliott, James R.

    2005-01-01

    Quantum logic gates (QLGs) or other logic systems are based on quantum-dots (QD) with a stringent requirement of size uniformity. The QD are widely known building units for QLGs. The size control of QD is a critical issue in quantum-dot fabrication. The work presented here offers a new method to develop quantum-dots using a bio-template, called ferritin, that ensures QD production in uniform size of nano-scale proportion. The bio-template for uniform yield of QD is based on a ferritin protein that allows reconstitution of core material through the reduction and chelation processes. One of the biggest challenges for developing QLG is the requirement of ordered and uniform size of QD for arrays on a substrate with nanometer precision. The QD development by bio-template includes the electrochemical/chemical reconsitution of ferritins with different core materials, such as iron, cobalt, manganese, platinum, and nickel. The other bio-template method used in our laboratory is dendrimers, precisely defined chemical structures. With ferritin-templated QD, we fabricated the heptagonshaped patterned array via direct nano manipulation of the ferritin molecules with a tip of atomic force microscope (AFM). We also designed various nanofabrication methods of QD arrays using a wide range manipulation techniques. The precise control of the ferritin-templated QD for a patterned arrangement are offered by various methods, such as a site-specific immobilization of thiolated ferritins through local oxidation using the AFM tip, ferritin arrays induced by gold nanoparticle manipulation, thiolated ferritin positioning by shaving method, etc. In the signal measurements, the current-voltage curve is obtained by measuring the current through the ferritin, between the tip and the substrate for potential sweeping or at constant potential. The measured resistance near zero bias was 1.8 teraohm for single holoferritin and 5.7 teraohm for single apoferritin, respectively.

  16. Performance Evaluation of Fusing Protected Fingerprint Minutiae Templates on the Decision Level

    Directory of Open Access Journals (Sweden)

    Raymond N. J. Veldhuis

    2012-04-01

    Full Text Available In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiers results in a decision testing whether both identifiers are derived from the same biometric characteristic. Compared to an unprotected system, most existing biometric template protection methods cause to a certain extent degradation in biometric performance. Fusion is therefore a promising way to enhance the biometric performance in template-protected biometric systems. Compared to feature level fusion and score level fusion, decision level fusion has not only the least fusion complexity, but also the maximum interoperability across different biometric features, template protection and recognition algorithms, templates formats, and comparison score rules. However, performance improvement via decision level fusion is not obvious. It is influenced by both the dependency and the performance gap among the conducted tests for fusion. We investigate in this paper several fusion scenarios (multi-sample, multi-instance, multi-sensor, multi-algorithm, and their combinations on the binary decision level, and evaluate their biometric performance and fusion efficiency on a multi-sensor fingerprint database with 71,994 samples.

  17. Performance Evaluation of Fusing Protected Fingerprint Minutiae Templates on the Decision Level

    Science.gov (United States)

    Yang, Bian; Busch, Christoph; de Groot, Koen; Xu, Haiyun; Veldhuis, Raymond N. J.

    2012-01-01

    In a biometric authentication system using protected templates, a pseudonymous identifier is the part of a protected template that can be directly compared. Each compared pair of pseudonymous identifiers results in a decision testing whether both identifiers are derived from the same biometric characteristic. Compared to an unprotected system, most existing biometric template protection methods cause to a certain extent degradation in biometric performance. Fusion is therefore a promising way to enhance the biometric performance in template-protected biometric systems. Compared to feature level fusion and score level fusion, decision level fusion has not only the least fusion complexity, but also the maximum interoperability across different biometric features, template protection and recognition algorithms, templates formats, and comparison score rules. However, performance improvement via decision level fusion is not obvious. It is influenced by both the dependency and the performance gap among the conducted tests for fusion. We investigate in this paper several fusion scenarios (multi-sample, multi-instance, multi-sensor, multi-algorithm, and their combinations) on the binary decision level, and evaluate their biometric performance and fusion efficiency on a multi-sensor fingerprint database with 71,994 samples. PMID:22778583

  18. Optimization of Water/Oil/Surfactant System for Preparation of Medium-Chain-Length Poly-3-Hydroxyalkanoates (mcl-PHA)-Incorporated Nanoparticles via Nanoemulsion Templating Technique.

    Science.gov (United States)

    Ishak, K A; Annuar, M Suffian M; Ahmad, N

    2017-12-01

    Polymeric nanoparticles gain a widespread interest in food and pharmaceutical industries as delivery systems that encapsulate, protect, and release lipophilic compounds such as omega-3 fatty acids, fat-soluble vitamins, carotenoids, carvedilol, cyclosporine, and ketoprofen. In this study, medium-chain-length poly-3-hydroxyalkanoate (mcl-PHA)-incorporated nanoparticle was developed via facile organic solvent-free nanoemulsion templating technique. The water content (W/surfactant-to-oil (S/O)), S/O, and Cremophor EL-to-Span 80 (Cremo/Sp80) ratios were first optimized using response surface methodology (RSM) to obtain nanoemulsion template prior to incorporation of mcl-PHA. Their effects on nanoemulsion formation were investigated. The mcl-PHA-incorporated nanoparticle system showed a good preservation capability of β-carotene and extended storage stability.

  19. Nanostructured Ceramic Photocatalytic Membrane Modified with a Polymer Template for Textile Wastewater Treatment

    Directory of Open Access Journals (Sweden)

    Rizwan Ahmad

    2017-12-01

    Full Text Available Photocatalytic ceramic membranes have attracted considerable attention for industrial wastewater treatment. However, morphological control of the membrane surface to improve its photocatalytic reactivity for the degradation of organic pollutants remains a challenge. Herein, we report a new nanostructured TiO2/Al2O3 composite ceramic membrane prepared from a poly(oxyethylene methacrylate (POEM template through a sol–gel method and its photocatalytic performance in the treatment of a model dye compound. The POEM polymeric template allowed the homogeneous distribution of catalytic sites, i.e., the TiO2 layer, on the Al2O3 membrane surface, resulting in improved organic dye degradation along with effective fouling mitigation. The immobilization of a TiO2 layer on the Al2O3 membrane support also significantly enhanced the membrane adsorption capacity toward dye organic compounds. An organic removal efficiency of over 96% was achieved with the TiO2/Al2O3 composite membrane under Ultraviolet (UV irradiation. In addition, the self-cleaning efficiency of the TiO2/Al2O3 composite membrane was remarkably improved by the degradation of organic foulants on the membrane under UV illumination.

  20. Templates, Numbers & Watercolors.

    Science.gov (United States)

    Clemesha, David J.

    1990-01-01

    Describes how a second-grade class used large templates to draw and paint five-digit numbers. The lesson integrated artistic knowledge and vocabulary with their mathematics lesson in place value. Students learned how draftspeople use templates, and they studied number paintings by Charles Demuth and Jasper Johns. (KM)

  1. RNA-dependent RNA polymerase of hepatitis C virus binds to its coding region RNA stem-loop structure, 5BSL3.2, and its negative strand.

    Science.gov (United States)

    Kanamori, Hiroshi; Yuhashi, Kazuhito; Ohnishi, Shin; Koike, Kazuhiko; Kodama, Tatsuhiko

    2010-05-01

    The hepatitis C virus NS5B RNA-dependent RNA polymerase (RdRp) is a key enzyme involved in viral replication. Interaction between NS5B RdRp and the viral RNA sequence is likely to be an important step in viral RNA replication. The C-terminal half of the NS5B-coding sequence, which contains the important cis-acting replication element, has been identified as an NS5B-binding sequence. In the present study, we confirm the specific binding of NS5B to one of the RNA stem-loop structures in the region, 5BSL3.2. In addition, we show that NS5B binds to the complementary strand of 5BSL3.2 (5BSL3.2N). The bulge structure of 5BSL3.2N was shown to be indispensable for tight binding to NS5B. In vitro RdRp activity was inhibited by 5BSL3.2N, indicating the importance of the RNA element in the polymerization by RdRp. These results suggest the involvement of the RNA stem-loop structure of the negative strand in the replication process.

  2. Charge patterns as templates for the assembly of layered biomolecular structures.

    Science.gov (United States)

    Naujoks, Nicola; Stemmer, Andreas

    2006-08-01

    Electric fields are used to guide the assembly of biomolecules in predefined geometric patterns on solid substrates. Local surface charges serve as templates to selectively position proteins on thin-film polymeric electret layers, thereby creating a basis for site-directed layered assembly of biomolecular structures. Charge patterns are created using the lithographic capabilities of an atomic force microscope, namely by applying voltage pulses between a conductive tip and the sample. Samples consist of a poly(methyl methacrylate) layer on a p-doped silicon support. Subsequently, the sample is developed in a water-in-oil emulsion, consisting of a dispersed aqueous phase containing biotin-modified immunoglobulinG molecules, and a continuous nonpolar, insulating oil phase. The electrostatic fields cause a net force of (di)electrophoretic nature on the droplet, thereby guiding the proteins to the predefined locations. Due to the functionalization of the immunoglobulinG molecules with biotin-groups, these patterns can now be used to initiate the localized layer-by-layer assembly of biomolecules based on the avidin-biotin mechanism. By binding 40 nm sized biotin-labelled beads to the predefined locations via a streptavidin linker, we verify the functionality of the previously deposited immunoglobulinG-biotin. All assembly steps following the initial deposition of the immunoglobulinG from emulsion can conveniently be conducted in aqueous solutions. Results show that pattern definition is maintained after immersion into aqueous solution.

  3. New insights into siRNA amplification and RNAi.

    Science.gov (United States)

    Zhang, Chi; Ruvkun, Gary

    2012-08-01

    In the nematode Caenorhabditis elegans (C. elegans), gene inactivation by RNA interference can achieve remarkable potency due to the amplification of initial silencing triggers by RNA-dependent RNA polymerases (RdRPs). RdRPs catalyze the biogenesis of an abundant species of secondary small interfering RNAs (siRNAs) using the target mRNA as template. The interaction between primary siRNAs derived from the exogenous double-stranded RNA (dsRNA) trigger and the target mRNA is required for the recruitment of RdRPs. Other genetic requirements for RdRP activities have not been characterized. Recent studies have identified the RDE-10/RDE-11 complex which interacts with the primary siRNA bound target mRNA and acts upstream of the RdRPs. rde-10 and rde-11 mutants show an RNAi defective phenotype because the biogenesis of secondary siRNAs is completely abolished. In addition, the RDE-10/RDE-11 complex plays a similar role in the endogenous RNAi pathway for the biogenesis of a subset of siRNAs targeting recently acquired, duplicated genes.

  4. Direct peptide bioconjugation/PEGylation at tyrosine with linear and branched polymeric diazonium salts.

    Science.gov (United States)

    Jones, Mathew W; Mantovani, Giuseppe; Blindauer, Claudia A; Ryan, Sinead M; Wang, Xuexuan; Brayden, David J; Haddleton, David M

    2012-05-02

    Direct polymer conjugation at peptide tyrosine residues is described. In this study Tyr residues of both leucine enkephalin and salmon calcitonin (sCT) were targeted using appropriate diazonium salt-terminated linear monomethoxy poly(ethylene glycol)s (mPEGs) and poly(mPEG) methacrylate prepared by atom transfer radical polymerization. Judicious choice of the reaction conditions-pH, stoichiometry, and chemical structure of diazonium salt-led to a high degree of site-specificity in the conjugation reaction, even in the presence of competitive peptide amino acid targets such as histidine, lysines, and N-terminal amine. In vitro studies showed that conjugation of mPEG(2000) to sCT did not affect the peptide's ability to increase intracellular cAMP induced in T47D human breast cancer cells bearing sCT receptors. Preliminary in vivo investigation showed preserved ability to reduce [Ca(2+)] plasma levels by mPEG(2000)-sCT conjugate in rat animal models. © 2012 American Chemical Society

  5. Template removal via Boudouard equilibrium allows for synthesis of mesostructured molybdenum compounds

    Energy Technology Data Exchange (ETDEWEB)

    Schieder, Martin; Bojer, Carina; Koch, Sebastian; Martin, Thomas; Breu, Josef [Lehrstuhl fuer Anorganische Chemie I, Universitaet Bayreuth (Germany); Stein, Julia vom [Abteilung fuer Heterogene Katalyse, Max-Planck-Institut fuer Kohlenforschung, Muelheim a.d. Ruhr (Germany); Schmalz, Holger [Lehrstuhl fuer Makromolekulare Chemie II, Universitaet Bayreuth (Germany); Lunkenbein, Thomas [Abteilung fuer Anorganische Chemie, Fritz-Haber-Institut, Max-Planck-Gesellschaft, Berlin (Germany)

    2017-11-06

    Oxidative thermal removal of the polymeric templates is not trivial for molybdenum oxides and hampers mesostructuring of this material. At ambient oxygen fugacity, Mo{sup VI} is the thermodynamically stable oxidation state and sublimation of MoO{sub 3} leads to a quick loss of the mesostructure through Oswald ripening. Taking advantage of the Boudouard equilibrium allows to fix the oxygen fugacity at a level where non-volatile MoO{sub 2-x} is stable while carbonaceous material may be oxidized by CO{sub 2}. Mesostructured MoO{sub 2-x} can be chemically converted into MoO{sub 3} or MoN under retention of the mesostructure. (copyright 2017 Wiley-VCH Verlag GmbH and Co. KGaA, Weinheim)

  6. RNA polymerase activity of Ustilago maydis virus

    Energy Technology Data Exchange (ETDEWEB)

    Yie, S.W.

    1986-01-01

    Ustilago maydis virus has an RNA polymerase enzyme which is associated with virion capsids. In the presence of Mg/sup 2 +/ ion and ribonucleotide triphosphate, the enzyme catalyzes the in vitro synthesis of mRNA by using dsRNA as a template. The products of the UmV RNA polymerase were both ssRNA and dsRNA. The dsRNA was determined by characteristic mobilities in gel electrophoresis, lack of sensitivity to RNase, and specific hybridization tests. The ssRNAs were identified by elution from a CF-11 column and by their RNase sensitivity. On the basis of the size of ssRNAs, it was concluded that partial transcripts were produced from H dsRNA segments, and full length transcripts were produced from M and L dsRNA segments. The following observations indicates that transcription occurs by strand displacement; (1) Only the positive strand of M2 dsRNA was labeled by the in vitro reaction. (2) The M2 dsRNA which had been labeled with /sup 32/''P-UTP in vitro could be chased from dsRNA with unlabeled UTP. The transcription products of three UmV strains were compared, and the overall pattern of transcription was very similar among them.

  7. A novel ethanol templating synthesis of ordered lamellar superstructured crystalline zirconia

    Energy Technology Data Exchange (ETDEWEB)

    Liu Chao, E-mail: liuchao_tj@yahoo.com; Wang Bin [Key Laboratory for New Type of Functional Materials in Hebei Province, Hebei University of Technology (China); Ji Xiujie, E-mail: jxjchem@yahoo.com [State Key Laboratory of Hollow Fiber Membrane Materials and Processes, Tianjin Polytechnic University (China); Zhao Shanshan; Wu Jie; Jia Jianlong; Ma Dongxia [Key Laboratory for New Type of Functional Materials in Hebei Province, Hebei University of Technology (China)

    2012-03-15

    Soft template technique has attracted great interest, because it is a facile, inexpensive and efficient synthesis strategy for ordered superstructural systems. Here, a novel ethanol template was used to synthesize the ordered lamellar superstructured crystalline zirconia (L{alpha}-ZrO{sub 2}) without post-treatments and surfactants. ZrOCl{sub 2} and NaOH were served as Zr source and precipitant, respectively. XRD analysis showed that L{alpha}-ZrO{sub 2} is crystalline. XPS spectra indicated the physical adsorption of ethanol molecules in L{alpha}-ZrO{sub 2}. TEM further observed and proved the 1.36-nm period of superstructure detected and calculated by SAXRD (1.35 nm), which is composed of 0.68-nm thick ZrO{sub 2} and pore alternatively. In contrast, the template-free ZrO{sub 2} (TF-ZrO{sub 2}) presents no superstructure and is poorly crystallized. As a soft template, ethanol presents the roles of (i) inducing the growth of zirconia layers, (ii) directing the self-assembly of ordered lamellar superstructure, and (iii) decreasing the crystallization temperature. The possible mechanism of ethanol serving as a soft template was proposed and discussed in thermodynamics.

  8. Cheating the Business Template: Filling in the Blanks

    Science.gov (United States)

    Mechenbier, Mahli Xuan

    2011-01-01

    Business professionals often use standard templates when composing documents, and teachers of business writing direct students to textbook examples to use as sample formats. Good instructors do want to provide their students with informative examples of what is expected, especially in an online course environment where students cannot raise their…

  9. Multiple isoelectric forms of poliovirus RNA-dependent RNA polymerase: Evidence for phosphorylation

    International Nuclear Information System (INIS)

    Ransone, L.J.; Dasgupta, A.

    1989-01-01

    Poliovirus-specific RNA-dependent RNA polymerase (3Dpol) was purified to apparent homogeneity. A single polypeptide of an apparent molecular weight of 63,000 catalyzes the synthesis of dimeric and monomeric RNA products in response to the poliovirion RNA template. Analysis of purified 3Dpol by two-dimensional electrophoresis showed multiple forms of 3Dpol, suggesting posttranslational modification of the protein in virus-infected cells. The two major forms of 3Dpol appear to have approximate pI values of 7.1 and 7.4. Incubation of purified 3Dpol with calf intestinal phosphatase resulted in almost complete disappearance of the pI 7.1 form and a concomitant increase in the intensity of the pI 7.4 form of 3Dpol. Addition of 32P-labeled Pi during infection of HeLa cells with poliovirus resulted in specific labeling of 3Dpol and 3CD, a viral protein which contains the entire 3Dpol sequence. Both 3Dpol and 3CD appear to be phosphorylated at serine residues. Ribosomal salt washes prepared from both mock- and poliovirus-infected cells contain phosphatases capable of dephosphorylating quantitatively the phosphorylated form (pI 7.1) of 3Dpol

  10. Determination of gene expression patterns using high-throughput RNA in situ hybridizaion to whole-mount Drosophila embryos

    Energy Technology Data Exchange (ETDEWEB)

    Weiszmann, R.; Hammonds, A.S.; Celniker, S.E.

    2009-04-09

    We describe a high-throughput protocol for RNA in situ hybridization (ISH) to Drosophila embryos in a 96-well format. cDNA or genomic DNA templates are amplified by PCR and then digoxigenin-labeled ribonucleotides are incorporated into antisense RNA probes by in vitro transcription. The quality of each probe is evaluated before ISH using a RNA probe quantification (dot blot) assay. RNA probes are hybridized to fixed, mixed-staged Drosophila embryos in 96-well plates. The resulting stained embryos can be examined and photographed immediately or stored at 4oC for later analysis. Starting with fixed, staged embryos, the protocol takes 6 d from probe template production through hybridization. Preparation of fixed embryos requires a minimum of 2 weeks to collect embryos representing all stages. The method has been used to determine the expression patterns of over 6,000 genes throughout embryogenesis.

  11. Paraspeckles: Where Long Noncoding RNA Meets Phase Separation.

    Science.gov (United States)

    Fox, Archa H; Nakagawa, Shinichi; Hirose, Tetsuro; Bond, Charles S

    2018-02-01

    Long noncoding RNA (lncRNA) molecules are some of the newest and least understood players in gene regulation. Hence, we need good model systems with well-defined RNA and protein components. One such system is paraspeckles - protein-rich nuclear organelles built around a specific lncRNA scaffold. New discoveries show how paraspeckles are formed through multiple RNA-protein and protein-protein interactions, some of which involve extensive polymerization, and others with multivalent interactions driving phase separation. Once formed, paraspeckles influence gene regulation through sequestration of component proteins and RNAs, with subsequent depletion in other compartments. Here we focus on the dual aspects of paraspeckle structure and function, revealing an emerging role for these dynamic bodies in a multitude of cellular settings. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Multi-template polymerase chain reaction.

    Science.gov (United States)

    Kalle, Elena; Kubista, Mikael; Rensing, Christopher

    2014-12-01

    PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

  13. Double displacement: An improved bioorthogonal reaction strategy for templated nucleic acid detection.

    Science.gov (United States)

    Kleinbaum, Daniel J; Miller, Gregory P; Kool, Eric T

    2010-06-16

    Quenched autoligation probes have been employed previously in a target-templated nonenzymatic ligation strategy for detecting nucleic acids in cells by fluorescence. A common source of background signal in such probes is the undesired reaction with water and other cellular nucleophiles. Here, we describe a new class of self-ligating probes, double displacement (DD) probes, that rely on two displacement reactions to fully unquench a nearby fluorophore. Three potential double displacement architectures, all possessing two fluorescence quencher/leaving groups (dabsylate groups), were synthesized and evaluated for templated reaction with nucleophile (phosphorothioate) probes both in vitro and in intact bacterial cells. All three DD probe designs provided substantially better initial quenching than a single-Dabsyl control. In isothermal templated reactions in vitro, double displacement probes yielded considerably lower background signal than previous single displacement probes; investigation into the mechanism revealed that one dabsylate acts as a sacrificial leaving group, reacting nonspecifically with water, but yielding little signal because another quencher group remains. Templated reaction with the specific nucleophile probe is required to activate a signal. The double displacement probes provided a ca. 80-fold turn-on signal and yielded a 2-4-fold improvement in signal/background over single Dabsyl probes. The best-performing probe architecture was demonstrated in a two-color, FRET-based two-allele discrimination system in vitro and was shown to be capable of discriminating between two closely related species of bacteria differing by a single nucleotide at an rRNA target site.

  14. Synthesis and Evaluation of Molecularly Imprinted Polymeric Microspheres for Chloramphenicol by Aqueous Suspension Polymerization as a High Performance Liquid Chromatography Stationary Phase

    International Nuclear Information System (INIS)

    Zhang, Yan; Lei, Jiandu

    2013-01-01

    Molecularly imprinted microsphere for chloramphenicol (CAP) with high adsorption capacity and excellent selectivity is prepared by aqueous suspension polymerization, in which chloramphenicol is used as template molecule and ethyl acetate as porogen. The CAP-imprinted microspheres are used as high performance liquid chromatography (HPLC) stationary phase and packed into stainless steel column (150 mm Χ 4.6 mm i. d.) for selective separation of chloramphenicol. HPLC analysis suggests that chloramphenicol can be distinguished from not only its structural analogs but also other broad-spectrum antibiotic such as erythromycin and tetracycline. In addition, the binding experiments of CAP-imprinted microspheres are carried out in ethanol/water (1:4, V:V), the results indicate that the maximum apparent static binding capacity of molecularly imprinted microspheres is up to 66.64 mg g -1 according to scatchard model

  15. Plasma-polymerized alkaline anion-exchange membrane: Synthesis and structure characterization

    International Nuclear Information System (INIS)

    Hu Jue; Meng Yuedong; Zhang Chengxu; Fang Shidong

    2011-01-01

    After-glow discharge plasma polymerization was developed for alkaline anion-exchange membranes synthesis using vinylbenzyl chloride as monomer. X-ray photoelectron spectroscopy and attenuated total reflection Fourier transform infrared spectroscopy were used to characterize the chemical structure properties of plasma-polymerized membranes. Ion-exchange capacities of quaternized poly(vinylbenzyl chloride) (QPVBC) membranes were measured to evaluate their capability of hydroxyl ion transport. A mechanism of plasma polymerization using VBC as monomer that accounts for the competitive effects of free radicals polymerization and plasma ablation in the plasma polymerization process was proposed. Our results indicate that plasma discharge power influences the contents of functional groups and the structure of the plasma polymer membranes, which attribute to the coactions of polymerization and ablation. The properties of uniform morphology, good adhesion to the substrate, high thermal stability and satisfying anion conduction level suggest the potential application of QPVBC membrane deposited at discharge power of 20 W in alkaline direct methanol fuel cells.

  16. Emergency department documentation templates: variability in template selection and association with physical examination and test ordering in dizziness presentations

    Directory of Open Access Journals (Sweden)

    Meurer William J

    2011-03-01

    Full Text Available Abstract Background Clinical documentation systems, such as templates, have been associated with process utilization. The T-System emergency department (ED templates are widely used but lacking are analyses of the templates association with processes. This system is also unique because of the many different template options available, and thus the selection of the template may also be important. We aimed to describe the selection of templates in ED dizziness presentations and to investigate the association between items on templates and process utilization. Methods Dizziness visits were captured from a population-based study of EDs that use documentation templates. Two relevant process outcomes were assessed: head computerized tomography (CT scan and nystagmus examination. Multivariable logistic regression was used to estimate the probability of each outcome for patients who did or did not receive a relevant-item template. Propensity scores were also used to adjust for selection effects. Results The final cohort was 1,485 visits. Thirty-one different templates were used. Use of a template with a head CT item was associated with an increase in the adjusted probability of head CT utilization from 12.2% (95% CI, 8.9%-16.6% to 29.3% (95% CI, 26.0%-32.9%. The adjusted probability of documentation of a nystagmus assessment increased from 12.0% (95%CI, 8.8%-16.2% when a nystagmus-item template was not used to 95.0% (95% CI, 92.8%-96.6% when a nystagmus-item template was used. The associations remained significant after propensity score adjustments. Conclusions Providers use many different templates in dizziness presentations. Important differences exist in the various templates and the template that is used likely impacts process utilization, even though selection may be arbitrary. The optimal design and selection of templates may offer a feasible and effective opportunity to improve care delivery.

  17. Generation of RNA in abiotic conditions.

    Science.gov (United States)

    di Mauro, Ernesto

    Generation of RNA in abiotic conditions. Ernesto Di Mauro Dipartimento di Genetica Bi-ologia Molecolare, Universit` "Sapienza" Roma, Italy. a At least four conditions must be satisfied for the spontaneous generation of (pre)-genetic poly-mers: 1) availability of precursors that are activated enough to spontaneously polymerize. Preliminary studies showed that (a) nucleic bases and acyclonucleosides can be synthesized from formamide H2NCOH by simply heating with prebiotically available mineral catalysts [last reviewed in (1)], and that b) nucleic bases can be phosphorylated in every possible posi-tion [2'; 3'; 5'; cyclic 2',3'; cyclic 3',5' (2)]. The higher stability of the cyclic forms allows their accumulation. 2) A polymerization mechanism. A reaction showing the formation of RNA polymers starting from prebiotically plausible precursors (3',5' cyclic GMP and 3', 5'cyclic AMP) was recently reported (3). Polymerization in these conditions is thermodynamically up-hill and an equilibrium is attained that limits the maximum length of the polymer produced to about 40 nucleotides for polyG and 100 nucleotides for polyA. 3) Ligation of the synthesized oligomers. If this type of reaction could occur according to a terminal-joining mechanism and could generate canonical 3',5' phosphodiester bonds, exponential growth would be obtained of the generated oligomers. This type of reaction has been reported (4) , limited to homogeneous polyA sequences and leading to the production of polyA dimers and tetramers. What is still missing are: 4) mechanisms that provide the proof of principle for the generation of sequence complexity. We will show evidence for two mechanisms providing this proof of principle for simple complementary sequences. Namely: abiotic sequence complementary-driven terminal ligation and sequence-complementary terminal growth. In conclusion: all the steps leading to the generation of RNA in abiotic conditions are satisfied. (1) R Saladino, C Crestini, F

  18. In-situ polymerization PLOT columns I: divinylbenzene

    Science.gov (United States)

    Shen, T. C.

    1992-01-01

    A novel method for preparation of porous-layer open-tubular (PLOT) columns is described. The method involves a simple and reproducible, straight-forward in-situ polymerization of monomer directly on the metal tube.

  19. Dual-cyclical nucleic acid strand-displacement polymerization based signal amplification system for highly sensitive determination of p53 gene.

    Science.gov (United States)

    Xu, Jianguo; Wu, Zai-Sheng; Li, Hongling; Wang, Zhenmeng; Le, Jingqing; Zheng, Tingting; Jia, Lee

    2016-12-15

    In the present study, we proposed a novel dual-cyclical nucleic acid strand-displacement polymerization (dual-CNDP) based signal amplification system for highly sensitive determination of tumor suppressor genes. The system primarily consisted of a signaling hairpin probe (SHP), a label-free hairpin probe (LHP) and an initiating primer (IP). The presence of target DNA was able to induce one CNDP through continuous process of ligation, polymerization and nicking, leading to extensively accumulation of two nicked triggers (NT1 and NT2). Intriguingly, the NT1 could directly hybridize SHP, while the NT2 could act as the target analog to induce another CNDP. The resulting dual-CNDP contributed the striking signal amplification, and only a very weak blank noise existed since the ligation template of target was not involved. In this case, the target could be detected in a wide linear range (5 orders of magnitude), and a low detection limit (78 fM) was obtained, which is superior to most of the existing fluorescent methods. Moreover, the dual-CNDP sensing system provided a high selectivity towards target DNA against mismatched target and was successfully applied to analysis of target gene extracted from cancer cells or in human serum-contained samples, indicating its great potential for practical applications. Copyright © 2016 Elsevier B.V. All rights reserved.

  20. Glycine Polymerization on Oxide Minerals

    Science.gov (United States)

    Kitadai, Norio; Oonishi, Hiroyuki; Umemoto, Koichiro; Usui, Tomohiro; Fukushi, Keisuke; Nakashima, Satoru

    2017-06-01

    It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH3 + group of adsorbed Gly to the nucleophilic NH2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.

  1. Glycine Polymerization on Oxide Minerals.

    Science.gov (United States)

    Kitadai, Norio; Oonishi, Hiroyuki; Umemoto, Koichiro; Usui, Tomohiro; Fukushi, Keisuke; Nakashima, Satoru

    2017-06-01

    It has long been suggested that mineral surfaces played an important role in peptide bond formation on the primitive Earth. However, it remains unclear which mineral species was key to the prebiotic processes. This is because great discrepancies exist among the reported catalytic efficiencies of minerals for amino acid polymerizations, owing to mutually different experimental conditions. This study examined polymerization of glycine (Gly) on nine oxide minerals (amorphous silica, quartz, α-alumina and γ-alumina, anatase, rutile, hematite, magnetite, and forsterite) using identical preparation, heating, and analytical procedures. Results showed that a rutile surface is the most effective site for Gly polymerization in terms of both amounts and lengths of Gly polymers synthesized. The catalytic efficiency decreased as rutile > anatase > γ-alumina > forsterite > α- alumina > magnetite > hematite > quartz > amorphous silica. Based on reported molecular-level information for adsorption of Gly on these minerals, polymerization activation was inferred to have arisen from deprotonation of the NH 3 + group of adsorbed Gly to the nucleophilic NH 2 group, and from withdrawal of electron density from the carboxyl carbon to the surface metal ions. The orientation of adsorbed Gly on minerals is also a factor influencing the Gly reactivity. The examination of Gly-mineral interactions under identical experimental conditions has enabled the direct comparison of various minerals' catalytic efficiencies and has made discussion of polymerization mechanisms and their relative influences possible Further systematic investigations using the approach reported herein (which are expected to be fruitful) combined with future microscopic surface analyses will elucidate the role of minerals in the process of abiotic peptide bond formation.

  2. Applications of polymeric micelles with tumor targeted in chemotherapy

    International Nuclear Information System (INIS)

    Ding Hui; Wang Xiaojun; Zhang Song; Liu Xinli

    2012-01-01

    Polymeric micelles (PMs) have gained more progress as a carrier system with the quick development of biological and nanoparticle techniques. In particular, PMs with smart targeting can deliver anti-cancer drugs directly into tumor cells at a sustained rate. PMs with core–shell structure (with diameters of 10 ∼ 100 nm) have been prepared by a variety of biodegradable and biocompatible polymers via a self-assembly process. The preparation of polymeric micelles with stimuli-responsive block copolymers or modification of target molecules on polymeric micelles’ surface are able to significantly improve the efficiency of drug delivery. Polymeric micelles, which have been considered as a novel promising drug carrier for cancer therapeutics, are rapidly evolving and being introduced in an attempt to overcome several limitations of traditional chemotherapeutics, including water solubility, tumor-specific accumulation, anti-tumor efficacy, and non-specific toxicity. This review describes the preparation of polymeric micelles and the targeted modification which greatly enhance the effects of chemotherapeutic agents.

  3. Pulmonary Delivery of siRNA via Polymeric Vectors as Therapies of Asthma.

    Science.gov (United States)

    Xie, Yuran; Merkel, Olivia M

    2015-10-01

    Asthma is a chronic inflammatory disease. Despite the fact that current therapies, such as the combination of inhaled corticosteroids and β2-agonists, can control the symptoms of asthma in most patients, there is still an urgent need for an alternative anti-inflammatory therapy for patients who suffer from severe asthma but lack acceptable response to conventional therapies. Many molecular factors are involved in the inflammatory process in asthma, and thus blocking the function of these factors could efficiently alleviate airway inflammation. RNA interference (RNAi) is often thought to be the answer in the search for more efficient and biocompatible treatments. However, difficulties of efficient delivery of small interference RNA (siRNA), the key factor in RNAi, to target cells and tissues have limited its clinical application. In this review, we summarize cytokines and chemokines, transcription factors, tyrosine kinases, and costimulatory factors that have been reported as targets of siRNA-mediated treatment in experimental asthma. Additionally, we conclude several targeted delivery systems of siRNA to specific cells such as T cells, macrophages, and dendritic cells, which could potentially be applied in asthma therapy. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  4. Synthesis and characterization of TiO2/Ag/polymer ternary nanoparticles via surface-initiated atom transfer radical polymerization

    International Nuclear Information System (INIS)

    Park, Jung Tae; Koh, Joo Hwan; Seo, Jin Ah; Cho, Yong Soo; Kim, Jong Hak

    2011-01-01

    We report on the novel ternary hybrid materials consisting of semiconductor (TiO 2 ), metal (Ag) and polymer (poly(oxyethylene methacrylate) (POEM)). First, a hydrophilic polymer, i.e. POEM, was grafted from TiO 2 nanoparticles via the surface-initiated atom transfer radical polymerization (ATRP) technique. These TiO 2 -POEM brush nanoparticles were used to template the formation of Ag nanoparticles by introduction of a AgCF 3 SO 3 precursor and a NaBH 4 aqueous solution for reduction process. Successful grafting of polymeric chains from the surface of TiO 2 nanoparticles and the in situ formation of Ag nanoparticles within the polymeric chains were confirmed using transmission electron microscopy (TEM), UV-vis spectroscopy, X-ray diffraction (XRD) and X-ray photoelectron spectroscopy (XPS). FT-IR spectroscopy also revealed the specific interaction of Ag nanoparticles with the C=O groups of POEM brushes. This study presents a simple route for the in situ synthesis of both metal and polymer confined within the semiconductor, producing ternary hybrid inorganic-organic nanomaterials.

  5. The RNA Template Channel of the RNA-Dependent RNA Polymerase as a Target for Development of Antiviral Therapy of Multiple Genera within a Virus Family

    NARCIS (Netherlands)

    van der Linden, Lonneke; Vives-Adrián, Laia; Selisko, Barbara; Ferrer-Orta, Cristina; Liu, Xinran; Lanke, Kjerstin; Ulferts, Rachel; De Palma, Armando M; Tanchis, Federica; Goris, Nesya; Lefebvre, David; De Clercq, Kris; Leyssen, Pieter; Lacroix, Céline; Pürstinger, Gerhard; Coutard, Bruno; Canard, Bruno; Boehr, David D; Arnold, Jamie J; Cameron, Craig E; Verdaguer, Nuria; Neyts, Johan; van Kuppeveld, Frank J M

    2015-01-01

    The genus Enterovirus of the family Picornaviridae contains many important human pathogens (e.g., poliovirus, coxsackievirus, rhinovirus, and enterovirus 71) for which no antiviral drugs are available. The viral RNA-dependent RNA polymerase is an attractive target for antiviral therapy.

  6. Multi-template polymerase chain reaction

    Directory of Open Access Journals (Sweden)

    Elena Kalle

    2014-12-01

    Full Text Available PCR is a formidable and potent technology that serves as an indispensable tool in a wide range of biological disciplines. However, due to the ease of use and often lack of rigorous standards many PCR applications can lead to highly variable, inaccurate, and ultimately meaningless results. Thus, rigorous method validation must precede its broad adoption to any new application. Multi-template samples possess particular features, which make their PCR analysis prone to artifacts and biases: multiple homologous templates present in copy numbers that vary within several orders of magnitude. Such conditions are a breeding ground for chimeras and heteroduplexes. Differences in template amplification efficiencies and template competition for reaction compounds undermine correct preservation of the original template ratio. In addition, the presence of inhibitors aggravates all of the above-mentioned problems. Inhibitors might also have ambivalent effects on the different templates within the same sample. Yet, no standard approaches exist for monitoring inhibitory effects in multitemplate PCR, which is crucial for establishing compatibility between samples.

  7. Hard template synthesis of metal nanowires

    Science.gov (United States)

    Kawamura, Go; Muto, Hiroyuki; Matsuda, Atsunori

    2014-11-01

    Metal nanowires (NWs) have attracted much attention because of their high electron conductivity, optical transmittance and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production of composite devices. The resulting NWs are immobilized and spatially arranged, as dictated by the ordered porous structure of the template. This avoids the NWs from aggregating, which is common for NWs prepared with soft templates in solution. Herein, the hard template synthesis of metal NWs is reviewed, and the resulting structures, properties and potential applications are discussed.

  8. Radical-Mediated Enzymatic Polymerizations

    Science.gov (United States)

    Zavada, Scott R.; Battsengel, Tsatsral; Scott, Timothy F.

    2016-01-01

    Polymerization reactions are commonly effected by exposing monomer formulations to some initiation stimulus such as elevated temperature, light, or a chemical reactant. Increasingly, these polymerization reactions are mediated by enzymes―catalytic proteins―owing to their reaction efficiency under mild conditions as well as their environmental friendliness. The utilization of enzymes, particularly oxidases and peroxidases, for generating radicals via reduction-oxidation mechanisms is especially common for initiating radical-mediated polymerization reactions, including vinyl chain-growth polymerization, atom transfer radical polymerization, thiol–ene step-growth polymerization, and polymerization via oxidative coupling. While enzyme-mediated polymerization is useful for the production of materials intended for subsequent use, it is especially well-suited for in situ polymerizations, where the polymer is formed in the place where it will be utilized. Such polymerizations are especially useful for biomedical adhesives and for sensing applications. PMID:26848652

  9. Construction of Au@Pt core—satellite nanoparticles based on in-situ reduction of polymeric ionic liquid protected gold nanoparticles

    Science.gov (United States)

    Wu, Wenlan; Li, Junbo; Zou, Sheng; Guo, Jinwu; Zhou, Huiyun

    2017-03-01

    A method of in-situ reduction to prepare Au@Pt core-satellite nanoparticles (NPs) is described by using Au NPs coating poly[1-methyl 3-(2-methacryloyloxy propylimidazolium bromine)] (PMMPImB-@-Au NPs) as the template. After electrostatic complex chloroplatinic acid with PMMPImB shell, the composite NP was directly reduced with N2H4 to produce Au@Pt core-satellite NPs. The characterization of composite and core-satellite NPs under different amounts of chloroplatinic acid were studied by DLS, UV-vis absorption spectrum and TEM. The satellite Pt NPs with a small size ( 2 nm) dotted around Au core, and the resulting Au@Pt core-satellite NPs showed a red-shift surface plasmon resonance (SPR) and a good dispersion due to effectively electrostatic repulsion providing by the polymeric ionic liquid (PIL) shell. Finally, Au@Pt core-satellite NPs exhibit an enhanced catalytic activity and cycled catalytic capability for the reduction of p-nitrophenol with NaBH4.

  10. Cellular mRNA decay factors involved in the hepatitis C virus life cycle

    OpenAIRE

    Mina Ibarra, Leonardo Bruno

    2010-01-01

    The group of positive strand RNA ((+)RNA) viruses includes numerous plant, animal and human pathogens such as the hepatitis C virus (HCV). Their viral genomes mimic cellular mRNAs, however, besides acting as messengers for translation of viral proteins, they also act as templates for viral replication. Since these two functions are mutually exclusive, a key step in the replication of all (+) RNA viruses is the regulated exit of the genomic RNAs from the cellular translation machinery to the v...

  11. High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide.

    Science.gov (United States)

    Marichy, Catherine; Muller, Nicolas; Froufe-Pérez, Luis S; Scheffold, Frank

    2016-02-25

    Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO2 based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect specular reflectance, a transmission dip close to the detection limit and a Bragg length comparable to the lattice constant.

  12. iTemplate: A template-based eye movement data analysis approach.

    Science.gov (United States)

    Xiao, Naiqi G; Lee, Kang

    2018-02-08

    Current eye movement data analysis methods rely on defining areas of interest (AOIs). Due to the fact that AOIs are created and modified manually, variances in their size, shape, and location are unavoidable. These variances affect not only the consistency of the AOI definitions, but also the validity of the eye movement analyses based on the AOIs. To reduce the variances in AOI creation and modification and achieve a procedure to process eye movement data with high precision and efficiency, we propose a template-based eye movement data analysis method. Using a linear transformation algorithm, this method registers the eye movement data from each individual stimulus to a template. Thus, users only need to create one set of AOIs for the template in order to analyze eye movement data, rather than creating a unique set of AOIs for all individual stimuli. This change greatly reduces the error caused by the variance from manually created AOIs and boosts the efficiency of the data analysis. Furthermore, this method can help researchers prepare eye movement data for some advanced analysis approaches, such as iMap. We have developed software (iTemplate) with a graphic user interface to make this analysis method available to researchers.

  13. Poly(glycidyl methacrylate)-A soft template for the facile preparation of poly(glycidyl methacrylate) core-copper nanoparticle shell nanocomposite

    Science.gov (United States)

    Mohammed Safiullah, S.; Abdul Wasi, K.; Anver Basha, K.

    2015-12-01

    Poly(glycidyl methacrylate) core/copper nanoparticle shell nanocomposite (PGMA/Cu nanohybrid) was prepared by simple two step method (i) The synthesis of poly(glycidyl methacrylate) (PGMA) beads by free radical suspension polymerization followed by (ii) direct deposition of copper nanoparticles (CuNPs) on activated PGMA beads. The PGMA beads were used as a soft template to host the CuNPs without surface modification of it. In this method the CuNPs were formed by chemical reduction of copper salts using sodium borohydride in water medium and deposited directly on the activated PGMA. Two different concentrations of copper salts were employed to know the effect of concentration on the shape and size of nanoparticles. The results showed that, the different sizes and shapes of CuNPs were deposited on the PGMA matrix. The X-ray Diffraction study results showed that the CuNPs were embedded on the surface of the PGMA matrix. The scanning electron microscopic images revealed that the fabrication of CuNPs on the PGMA matrix possess different shapes and changes the morphology and nature of PGMA beads significantly. The fluorescent micrograph also confirmed that the CuNPs were doped on the PGMA surface. The thermal studies have demonstrated that the CuNPs deposition on the surface of PGMA beads had a significant effect.

  14. Metallic nickel nanorod arrays embedded into ordered block copolymer templates

    International Nuclear Information System (INIS)

    Seifarth, O.; Krenek, R.; Tokarev, I.; Burkov, Y.; Sidorenko, A.; Minko, S.; Stamm, M.; Schmeisser, D.

    2007-01-01

    We report on metallic Nickel nanorods prepared by utilizing a mask of ordered nanostructured hollow channels in a block copolymer matrix. These polymeric templates were formed by a self organized process in block copolymer supramolecular assemblies. Nickel was filled into with two different techniques, electrodeposition and washing in. We monitor the formation process of these nanorods by means of atomic force microscopy and synchrotron radiation soft X-ray based photoelectron emission microscopy. The oxidation state of the nickelrods is evaluated with X-ray absorption spectroscopy and X-ray photoelectron spectroscopy at the Ni L edges and lateral distributions of the Ni nanorods were detected with micrometer resolved X-ray absorption spectroscopy. The finding is that the Ni rods were metallic despite their preparation under ambient conditions, inside the particles no hints for NiO complexes were found. This indicates that the polymer protects Ni nanoparticles against oxidation

  15. A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis

    KAUST Repository

    Law, Julie A.; Ausí n, Israel; Johnson, Lianna M.; Vashisht, Ajay  A Amar; Zhu, Jian-Kang; Wohlschlegel, James  A A.; Jacobsen, Steven E.

    2010-01-01

    DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM) [1, 2]. Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts [3]. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) [4] and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3) [5, 6], we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that RDM1, like DRD1 [3] and DMS3 [7], is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V. © 2010 Elsevier Ltd. All rights reserved.

  16. A Protein Complex Required for Polymerase V Transcripts and RNA- Directed DNA Methylation in Arabidopsis

    KAUST Repository

    Law, Julie A.

    2010-05-01

    DNA methylation is an epigenetic modification associated with gene silencing. In Arabidopsis, DNA methylation is established by DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2), which is targeted by small interfering RNAs through a pathway termed RNA-directed DNA methylation (RdDM) [1, 2]. Recently, RdDM was shown to require intergenic noncoding (IGN) transcripts that are dependent on the Pol V polymerase. These transcripts are proposed to function as scaffolds for the recruitment of downstream RdDM proteins, including DRM2, to loci that produce both siRNAs and IGN transcripts [3]. However, the mechanism(s) through which Pol V is targeted to specific genomic loci remains largely unknown. Through affinity purification of two known RdDM components, DEFECTIVE IN RNA-DIRECTED DNA METHYLATION 1 (DRD1) [4] and DEFECTIVE IN MERISTEM SILENCING 3 (DMS3) [5, 6], we found that they copurify with each other and with a novel protein, RNA-DIRECTED DNA METHYLATION 1 (RDM1), forming a complex we term DDR. We also found that DRD1 copurified with Pol V subunits and that RDM1, like DRD1 [3] and DMS3 [7], is required for the production of Pol V-dependent transcripts. These results suggest that the DDR complex acts in RdDM at a step upstream of the recruitment or activation of Pol V. © 2010 Elsevier Ltd. All rights reserved.

  17. Influence of major-groove chemical modifications of DNA on transcription by bacterial RNA polymerases.

    Science.gov (United States)

    Raindlová, Veronika; Janoušková, Martina; Slavíčková, Michaela; Perlíková, Pavla; Boháčová, Soňa; Milisavljevič, Nemanja; Šanderová, Hana; Benda, Martin; Barvík, Ivan; Krásný, Libor; Hocek, Michal

    2016-04-20

    DNA templates containing a set of base modifications in the major groove (5-substituted pyrimidines or 7-substituted 7-deazapurines bearing H, methyl, vinyl, ethynyl or phenyl groups) were prepared by PCR using the corresponding base-modified 2'-deoxyribonucleoside triphosphates (dNTPs). The modified templates were used in an in vitro transcription assay using RNA polymerase from Bacillus subtilis and Escherichia coli Some modified nucleobases bearing smaller modifications (H, Me in 7-deazapurines) were perfectly tolerated by both enzymes, whereas bulky modifications (Ph at any nucleobase) and, surprisingly, uracil blocked transcription. Some middle-sized modifications (vinyl or ethynyl) were partly tolerated mostly by the E. colienzyme. In all cases where the transcription proceeded, full length RNA product with correct sequence was obtained indicating that the modifications of the template are not mutagenic and the inhibition is probably at the stage of initiation. The results are promising for the development of bioorthogonal reactions for artificial chemical switching of the transcription. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

  18. Hard template synthesis of metal nanowires

    Directory of Open Access Journals (Sweden)

    Go eKawamura

    2014-11-01

    Full Text Available Metal nanowires (NWs have attracted much attention because of their high electron conductivity, optical transmittance and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production of composite devices. The resulting NWs are immobilized and spatially arranged, as dictated by the ordered porous structure of the template. This avoids the NWs from aggregating, which is common for NWs prepared with soft templates in solution. Herein, the hard template synthesis of metal NWs is reviewed, and the resulting structures, properties and potential applications are discussed.

  19. On-substrate fabrication of porous Al2O3 templates with tunable pore diameters and interpore distances

    DEFF Research Database (Denmark)

    Berger, Nele; Rubahn, Horst-Günter; habouti, salah

    2016-01-01

    This work is focused on the on-substrate fabrication of porous aluminum oxide templates by anodization of a thin aluminum film deposited directly on the substrate using different concentrations of oxalic acid. These on-substrate templates are used for fabricating supported, free-standing nanorod...

  20. Catalyst-Free Vapor-Phase Method for Direct Integration of Gas Sensing Nanostructures with Polymeric Transducing Platforms

    Directory of Open Access Journals (Sweden)

    Stella Vallejos

    2014-01-01

    Full Text Available Tungsten oxide nanoneedles (NNs are grown and integrated directly with polymeric transducing platforms for gas sensors via aerosol-assisted chemical vapor deposition (AACVD method. Material analysis shows the feasibility to grow highly crystalline nanomaterials in the form of NNs with aspect ratios between 80 and 200 and with high concentration of oxygen vacancies at the surface, whereas gas testing demonstrates moderate sensing responses to hydrogen at concentrations between 10 ppm and 50 ppm, which are comparable with results for tungsten oxide NNs grown on silicon transducing platforms. This method is demonstrated to be an attractive route to fabricate next generation of gas sensors devices, provided with flexibility and functionality, with great potential in a cost effective production for large-scale applications.

  1. Transcription arrest caused by long nascent RNA chains

    DEFF Research Database (Denmark)

    Bentin, Thomas; Cherny, Dmitry; Larsen, H Jakob

    2004-01-01

    on transcription. Using phage T3 RNA polymerase (T3 RNAP) and covalently closed circular (cccDNA) DNA templates that did not contain any strong termination signal, transcription was severely inhibited after a short period of time. Less than approximately 10% residual transcriptional activity remained after 10 min......The transcription process is highly processive. However, specific sequence elements encoded in the nascent RNA may signal transcription pausing and/or termination. We find that under certain conditions nascent RNA chains can have a strong and apparently sequence-independent inhibitory effect...... of incubation. The addition of RNase A almost fully restored transcription in a dose dependent manner. Throughout RNase A rescue, an elongation rate of approximately 170 nt/s was maintained and this velocity was independent of RNA transcript length, at least up to 6 kb. Instead, RNase A rescue increased...

  2. Natural RNA circles function as efficient microRNA sponges

    DEFF Research Database (Denmark)

    Hansen, Thomas Birkballe; Jensen, Trine I; Clausen, Bettina Hjelm

    2013-01-01

    MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called comp......MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so......-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more...... sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA....

  3. High-temperature synthesis of highly hydrothermal stable mesoporous silica and Fe-SiO2 using ionic liquid as a template

    International Nuclear Information System (INIS)

    Liu, Hong; Wang, Mengyang; Hu, Hongjiu; Liang, Yuguang; Wang, Yong; Cao, Weiran; Wang, Xiaohong

    2011-01-01

    Mesoporous silicas and Fe-SiO 2 with worm-like structures have been synthesized using a room temperature ionic liquid, 1-hexadecane-3-methylimidazolium bromide, as a template at a high aging temperature (150-190 o C) with the assistance of NaF. The hydrothermal stability of mesoporous silica was effectively improved by increasing the aging temperature and adding NaF to the synthesis gel. High hydrothermally stable mesoporous silica was obtained after being aged at 190 o C in the presence of NaF, which endured the hydrothermal treatment in boiling water at least for 10 d or steam treatment at 600 o C for 6 h. The ultra hydrothermal stability could be attributed to its high degree of polymerization of silicate. Furthermore, highly hydrothermal stable mesoporous Fe-SiO 2 has been synthesized, which still remained its mesostructure after being hydrothermally treated at 100 o C for 12 d or steam-treated at 600 o C for 6 h. -- Graphical abstract: Worm-like mesoporous silica and Fe-SiO 2 with high hydrothermal stability have been synthesized using ionic liquid 1-hexadecane-3-methylimidazolium bromide as a template under the assistance of NaF at high temperature. Display Omitted Research highlights: → Increasing aging temperature improved the hydrothermal stability of materials. →Addition of NaF enhanced the polymerization degree of silicates. → Mesoporous SiO 2 and Fe-SiO 2 obtained have remarkable hydrothermal stability.

  4. Non-equilibrium supramolecular polymerization.

    Science.gov (United States)

    Sorrenti, Alessandro; Leira-Iglesias, Jorge; Markvoort, Albert J; de Greef, Tom F A; Hermans, Thomas M

    2017-09-18

    Supramolecular polymerization has been traditionally focused on the thermodynamic equilibrium state, where one-dimensional assemblies reside at the global minimum of the Gibbs free energy. The pathway and rate to reach the equilibrium state are irrelevant, and the resulting assemblies remain unchanged over time. In the past decade, the focus has shifted to kinetically trapped (non-dissipative non-equilibrium) structures that heavily depend on the method of preparation (i.e., pathway complexity), and where the assembly rates are of key importance. Kinetic models have greatly improved our understanding of competing pathways, and shown how to steer supramolecular polymerization in the desired direction (i.e., pathway selection). The most recent innovation in the field relies on energy or mass input that is dissipated to keep the system away from the thermodynamic equilibrium (or from other non-dissipative states). This tutorial review aims to provide the reader with a set of tools to identify different types of self-assembled states that have been explored so far. In particular, we aim to clarify the often unclear use of the term "non-equilibrium self-assembly" by subdividing systems into dissipative, and non-dissipative non-equilibrium states. Examples are given for each of the states, with a focus on non-dissipative non-equilibrium states found in one-dimensional supramolecular polymerization.

  5. Elektroaktive polymerer

    DEFF Research Database (Denmark)

    West, K.

    Traditionelt tænker vi på polymerer (plastik) som elektrisk isolerende materialer - det som er udenpå ledningerne. I dag kender vi imidlertid også polymerer med intrinsisk elektrisk ledningsevne, og plast er på vej ind i anvendelser, der tidligereudelukkende var baseret på metaller og uorganiske...... halvledere. Hertil kommer, at en del af de ledende polymerer kan stimuleres til at skifte mellem en ledende og en halvledende tilstand, hvorved de ændret både form og farve. I foredraget gives der enrække eksempler på anvendelse af polymerer som elektriske komponenter - rækkende fra polymer elektronik over...

  6. Rapid Detection of miRNA Using Nucleic Acids-templated AgNCs

    DEFF Research Database (Denmark)

    Shah, Pratik

    . In the case of plants, the levels of certain miRNAs can be used as biomarkers to evaluate the physiological status. Specific miRNA levels are influenced by stresses such as drought, salt, cold, heat and pathogenic infestations. In humans, the dysregulation of miRNAs have been highlighted in many diseases...... such as cancer, diabetes, cardiovascular disease and Alzheimer’s disease. MiRNAs, thus, can be useful markers for disease diagnosis, prognosis, and treatment. Because of its attractive optical properties such as brightness, tuneable emission wavelengths and photo-stability, DNA stabilized silver nano......-clusters (AgNCs) has increasingly been used to create nanoscale bio-sensing systems for selective and specific detection of bio-molecules. During the course of my Ph.D., I have focused on developing a novel diagnostic tool for miRNA detection using the fluorescent properties of DNA encapsulated AgNCs (DNA...

  7. An amphipathic alpha-helix controls multiple roles of brome mosaic virus protein 1a in RNA replication complex assembly and function.

    Directory of Open Access Journals (Sweden)

    Ling Liu

    2009-03-01

    Full Text Available Brome mosaic virus (BMV protein 1a has multiple key roles in viral RNA replication. 1a localizes to perinuclear endoplasmic reticulum (ER membranes as a peripheral membrane protein, induces ER membrane invaginations in which RNA replication complexes form, and recruits and stabilizes BMV 2a polymerase (2a(Pol and RNA replication templates at these sites to establish active replication complexes. During replication, 1a provides RNA capping, NTPase and possibly RNA helicase functions. Here we identify in BMV 1a an amphipathic alpha-helix, helix A, and use NMR analysis to define its structure and propensity to insert in hydrophobic membrane-mimicking micelles. We show that helix A is essential for efficient 1a-ER membrane association and normal perinuclear ER localization, and that deletion or mutation of helix A abolishes RNA replication. Strikingly, mutations in helix A give rise to two dramatically opposite 1a function phenotypes, implying that helix A acts as a molecular switch regulating the intricate balance between separable 1a functions. One class of helix A deletions and amino acid substitutions markedly inhibits 1a-membrane association and abolishes ER membrane invagination, viral RNA template recruitment, and replication, but doubles the 1a-mediated increase in 2a(Pol accumulation. The second class of helix A mutations not only maintains efficient 1a-membrane association but also amplifies the number of 1a-induced membrane invaginations 5- to 8-fold and enhances viral RNA template recruitment, while failing to stimulate 2a(Pol accumulation. The results provide new insights into the pathways of RNA replication complex assembly and show that helix A is critical for assembly and function of the viral RNA replication complex, including its central role in targeting replication components and controlling modes of 1a action.

  8. Location of the binding domains for the RNA polymerase L and the ribonucleocapsid template within different halves of the NS phosphoprotein of vesicular stomatitis virus

    International Nuclear Information System (INIS)

    Emerson, S.U.; Schubert, M.

    1987-01-01

    Recombinant DNA techniques were used to delete regions of a cDNA clone of the phosphoprotein NS gene of vesicular stomatitis virus. The complete NS gene and four mutant genes containing internal or terminal deletions were inserted into a modified pGem4 vector under the transcriptional control of the page T7 promoter. Run-off transcripts were synthesized and translated in vitro to provide [ 35 S]methionine-labeled complete NS or deletion mutant NS proteins. Immune coprecipitation assays involving these proteins were developed to map the regions of the NS protein responsible for binding to the structural viral nucleocapsid protein N and the catalytic RNA polymerase protein L. The data indicate the NS protein is a bivalent protein consisting of two discrete functional domains. Contrary to previous suggestions, the negatively charged amino-terminal half of NS protein binds to L protein, while the carboxyl-terminal half of NS protein binds to both soluble recombinant nucleocapsid protein N and viral ribonucleocapsid template

  9. Enrichment of measles virus-like RNA in the nucleocapsid fraction isolated from subacute sclerosing panencephalitis brains

    International Nuclear Information System (INIS)

    Bedows, E.; Payne, F.E.; Kohne, D.E.; Tourtellotte, W.W.

    1982-01-01

    A procedure has been developed which facilitates the detection of measles virus RNA sequences in human brains. The procedure involves isolating subviral components (nucleocapsids) from brain tissues prior to RNA purification, followed by hybridization of these RNAs to cDNA synthesized from measles virus 50 S RNA template. Using these techniques we were able to obtain an RNA fraction which was manyfold enriched in measles virus-specific RNA, relative to unfractionated subacute sclerosing panencephalitis (SSPE) brain RNAs. 70-100% of the measles virus-specific RNA present in these SSPE brain samples were recovered in this enriched fraction. (Auth.)

  10. Enrichment of measles virus-like RNA in the nucleocapsid fraction isolated from subacute sclerosing panencephalitis brains

    Energy Technology Data Exchange (ETDEWEB)

    Bedows, E; Payne, F E [Michigan Univ., Ann Arbor (USA). School of Public Health; Kohne, D E [Center for Neurologic Study, San Diego, CA, USA; Tourtellotte, W W [Neurology Service, V.A. Wadsworth Hospital Center, Los Angeles, CA, USA

    1982-02-01

    A procedure has been developed which facilitates the detection of measles virus RNA sequences in human brains. The procedure involves isolating subviral components (nucleocapsids) from brain tissues prior to RNA purification, followed by hybridization of these RNAs to cDNA synthesized from measles virus 50 S RNA template. Using these techniques we were able to obtain an RNA fraction which was manyfold enriched in measles virus-specific RNA, relative to unfractionated subacute sclerosing panencephalitis (SSPE) brain RNAs. 70-100% of the measles virus-specific RNA present in these SSPE brain samples were recovered in this enriched fraction.

  11. Bio-based alkyds by direct enzymatic bulk polymerization

    DEFF Research Database (Denmark)

    Nguyen, Hiep Dinh

    to a corresponding classical reference. In a further development of the system, it has been found possible to use the esters of pentaerythritol and stearic acid in combination with the penta-aze derivative for the preparation of pseudo alkyds containing only pentaerythritol as polyol with high degree of branching....... Bio-based alkyds prepared from a combination of glycerol, and tall oil fatty acids, and azelaic acid by enzymatic polymerization show improved hydrophobicity and lower glass transition temperatures compared to an alkyd prepared from the same raw materials by a classical boiling method. The enzymatic...... of pentaerythritol derivatized with azelaic acid (or penta-aze) was examined and tested for the production of more branched alkyd systems. A photostability test validated the concept, and the method also resulted in alkyds with improved hydrophobicity and lower glass transition temperatures compared...

  12. Hierarchical templating in deposition of semi-covalently imprinted inverse opal polythiophene film for femtomolar determination of human serum albumin.

    Science.gov (United States)

    Dabrowski, Marcin; Cieplak, Maciej; Sharma, Piyush Sindhu; Borowicz, Pawel; Noworyta, Krzysztof; Lisowski, Wojciech; D'Souza, Francis; Kuhn, Alexander; Kutner, Wlodzimierz

    2017-08-15

    Nanostructured artificial receptor materials with unprecedented hierarchical structure for determination of human serum albumin (HSA) are designed and fabricated. For that purpose a new hierarchical template is prepared. This template allowed for simultaneous structural control of the deposited molecularly imprinted polymer (MIP) film on three length scales. A colloidal crystal templating with optimized electrochemical polymerization of 2,3'-bithiophene enables deposition of an MIP film in the form of an inverse opal. Thickness of the deposited polymer film is precisely controlled with the number of current oscillations during potentiostatic deposition of the imprinted poly(2,3'-bithiophene) film. Prior immobilization of HSA on the colloidal crystal allows formation of molecularly imprinted cavities exclusively on the internal surface of the pores. Furthermore, all binding sites are located on the surface of the imprinted cavities at locations corresponding to positions of functional groups present on the surface of HSA molecules due to prior derivatization of HSA molecules with appropriate functional monomers. This synergistic strategy results in a material with superior recognition performance. Integration of the MIP film as a recognition unit with a sensitive extended-gate field-effect transistor (EG-FET) transducer leads to highly selective HSA determination in the femtomolar concentration range. Copyright © 2017 Elsevier B.V. All rights reserved.

  13. MicroRNA-320a suppresses human colon cancer cell proliferation by directly targeting β-catenin

    International Nuclear Information System (INIS)

    Sun, Jian-Yong; Huang, Yi; Li, Ji-Peng; Zhang, Xiang; Wang, Lei; Meng, Yan-Ling; Yan, Bo; Bian, Yong-Qian; Zhao, Jing; Wang, Wei-Zhong

    2012-01-01

    Highlights: ► miR-320a is downregulated in human colorectal carcinoma. ► Overexpression of miR-320a inhibits colon cancer cell proliferation. ► β-Catenin is a direct target of miR-320a in colon cancer cells. ► miR-320a expression inversely correlates with mRNA expression of β-catenin’s target genes in human colon carcinoma. -- Abstract: Recent profile studies of microRNA (miRNA) expression have documented a deregulation of miRNA (miR-320a) in human colorectal carcinoma. However, its expression pattern and underlying mechanisms in the development and progression of colorectal carcinoma has not been elucidated clearly. Here, we performed real-time PCR to examine the expression levels of miR-320a in colon cancer cell lines and tumor tissues. And then, we investigated its biological functions in colon cancer cells by a gain of functional strategy. Further more, by the combinational approaches of bioinformatics and experimental validation, we confirmed target associations of miR-320a in colorectal carcinoma. Our results showed that miR-320a was frequently downregulated in cancer cell lines and colon cancer tissues. And we demonstrated that miR-320a restoration inhibited colon cancer cell proliferation and β-catenin, a functionally oncogenic molecule was a direct target gene of miR-320a. Finally, the data of real-time PCR showed the reciprocal relationship between miR-320a and β-catenin’s downstream genes in colon cancer tissues. These findings indicate that miR-320a suppresses the growth of colon cancer cells by directly targeting β-catenin, suggesting its application in prognosis prediction and cancer treatment.

  14. MicroRNA-320a suppresses human colon cancer cell proliferation by directly targeting {beta}-catenin

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Jian-Yong [State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 710032 Xi' an (China); State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 710032 Xi' an (China); Huang, Yi [Department of Anesthesiology, Xijing Hospital, Fourth Military Medical University, 710032 Xi' an (China); Li, Ji-Peng [State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 710032 Xi' an (China); Zhang, Xiang; Wang, Lei [State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 710032 Xi' an (China); Meng, Yan-Ling [Department of Immunology, Fourth Military Medical University, 710032 Xi' an (China); Yan, Bo [State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 710032 Xi' an (China); Bian, Yong-Qian [State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 710032 Xi' an (China); Zhao, Jing [State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, 710032 Xi' an (China); Wang, Wei-Zhong, E-mail: weichang@fmmu.edu.cn [State Key Laboratory of Cancer Biology, Xijing Hospital of Digestive Diseases, Fourth Military Medical University, 710032 Xi' an (China); and others

    2012-04-20

    Highlights: Black-Right-Pointing-Pointer miR-320a is downregulated in human colorectal carcinoma. Black-Right-Pointing-Pointer Overexpression of miR-320a inhibits colon cancer cell proliferation. Black-Right-Pointing-Pointer {beta}-Catenin is a direct target of miR-320a in colon cancer cells. Black-Right-Pointing-Pointer miR-320a expression inversely correlates with mRNA expression of {beta}-catenin's target genes in human colon carcinoma. -- Abstract: Recent profile studies of microRNA (miRNA) expression have documented a deregulation of miRNA (miR-320a) in human colorectal carcinoma. However, its expression pattern and underlying mechanisms in the development and progression of colorectal carcinoma has not been elucidated clearly. Here, we performed real-time PCR to examine the expression levels of miR-320a in colon cancer cell lines and tumor tissues. And then, we investigated its biological functions in colon cancer cells by a gain of functional strategy. Further more, by the combinational approaches of bioinformatics and experimental validation, we confirmed target associations of miR-320a in colorectal carcinoma. Our results showed that miR-320a was frequently downregulated in cancer cell lines and colon cancer tissues. And we demonstrated that miR-320a restoration inhibited colon cancer cell proliferation and {beta}-catenin, a functionally oncogenic molecule was a direct target gene of miR-320a. Finally, the data of real-time PCR showed the reciprocal relationship between miR-320a and {beta}-catenin's downstream genes in colon cancer tissues. These findings indicate that miR-320a suppresses the growth of colon cancer cells by directly targeting {beta}-catenin, suggesting its application in prognosis prediction and cancer treatment.

  15. Role of RNA structure and RNA binding activity of foot-and-mouth disease virus 3C protein in VPg uridylylation and virus replication

    DEFF Research Database (Denmark)

    Nayak, A.; Goodfellow, I. G.; Woolaway, K. E.

    2006-01-01

    The uridylylation of the VPg peptide primer is the first stage in the replication of picornavirus RNA. This process can be achieved in vitro using purified components, including 3B (VPg) with the RNA dependent RNA polymerase (3D(pol)), the precursor 3CD, and an RNA template containing the cre....../bus. We show that certain RNA sequences within the foot-and-mouth disease virus (FMDV) 5' untranslated region but outside of the cre/bus can enhance VPg uridylylation activity. Furthermore, we have shown that the FMDV X protein alone can substitute for 3CD, albeit less efficiently. In addition, the VPg...... precursors, 3B(3)3C and 3B(123)3C, can function as substrates for uridylylation in the absence of added 3C or 3CD. Residues within the FMDV 3C protein involved in interaction with the cre/bus RNA have been identified and are located on the face of the protein opposite from the catalytic site. These residues...

  16. Two RNAs or DNAs May Artificially Fuse Together at a Short Homologous Sequence (SHS) during Reverse Transcription or Polymerase Chain Reactions, and Thus Reporting an SHS-Containing Chimeric RNA Requires Extra Caution

    Science.gov (United States)

    Xie, Bingkun; Yang, Wei; Ouyang, Yongchang; Chen, Lichan; Jiang, Hesheng; Liao, Yuying; Liao, D. Joshua

    2016-01-01

    Tens of thousands of chimeric RNAs have been reported. Most of them contain a short homologous sequence (SHS) at the joining site of the two partner genes but are not associated with a fusion gene. We hypothesize that many of these chimeras may be technical artifacts derived from SHS-caused mis-priming in reverse transcription (RT) or polymerase chain reactions (PCR). We cloned six chimeric complementary DNAs (cDNAs) formed by human mitochondrial (mt) 16S rRNA sequences at an SHS, which were similar to several expression sequence tags (ESTs).These chimeras, which could not be detected with cDNA protection assay, were likely formed because some regions of the 16S rRNA are reversely complementary to another region to form an SHS, which allows the downstream sequence to loop back and anneal at the SHS to prime the synthesis of its complementary strand, yielding a palindromic sequence that can form a hairpin-like structure.We identified a 16S rRNA that ended at the 4th nucleotide(nt) of the mt-tRNA-leu was dominant and thus should be the wild type. We also cloned a mouse Bcl2-Nek9 chimeric cDNA that contained a 5-nt unmatchable sequence between the two partners, contained two copies of the reverse primer in the same direction but did not contain the forward primer, making it unclear how this Bcl2-Nek9 was formed and amplified. Moreover, a cDNA was amplified because one primer has 4 nts matched to the template, suggesting that there may be many more artificial cDNAs than we have realized, because the nuclear and mt genomes have many more 4-nt than 5-nt or longer homologues. Altogether, the chimeric cDNAs we cloned are good examples suggesting that many cDNAs may be artifacts due to SHS-caused mis-priming and thus greater caution should be taken when new sequence is obtained from a technique involving DNA polymerization. PMID:27148738

  17. Targeting miRNA-based medicines to cystic fibrosis airway epithelial cells using nanotechnology

    Directory of Open Access Journals (Sweden)

    McKiernan PJ

    2013-10-01

    TOM1 in CFBE41o- cells, with the most significant reduction of 66% in TOM1 expression elicited at an N/P ratio of 1:1 while chitosan-based miR-126 nanomedicines failed to facilitate statistically significant knockdown of TOM1 and both nanoparticles appeared relatively nontoxic. miRNA nanomedicine uptake can be qualitatively and quantitatively assessed rapidly by high content analysis and is highly polymer-dependent but, interestingly, there is not a direct correlation between the levels of miRNA uptake and the downstream gene knockdown. Polymeric nanoparticles can deliver premiRs effectively to CFBEs in order to modulate gene expression but must be tailored specifically for miRNA delivery.Keywords: miR-126, nanotechnology, cystic fibrosis, TOM1, high content analysis, inflammation

  18. Design and Fabrication of a Precision Template for Spine Surgery Using Selective Laser Melting (SLM).

    Science.gov (United States)

    Wang, Di; Wang, Yimeng; Wang, Jianhua; Song, Changhui; Yang, Yongqiang; Zhang, Zimian; Lin, Hui; Zhen, Yongqiang; Liao, Suixiang

    2016-07-22

    In order to meet the clinical requirements of spine surgery, this paper proposes the fabrication of the customized template for spine surgery through computer-aided design. A 3D metal printing-selective laser melting (SLM) technique was employed to directly fabricate the 316L stainless steel template, and the metal template with tiny locating holes was used as an auxiliary tool to insert spinal screws inside the patient's body. To guarantee accurate fabrication of the template for cervical vertebra operation, the contact face was placed upwards to improve the joint quality between the template and the cervical vertebra. The joint surface of the printed template had a roughness of Ra = 13 ± 2 μm. After abrasive blasting, the surface roughness was Ra = 7 ± 0.5 μm. The surgical metal template was bound with the 3D-printed Acrylonitrile Butadiene Styrene (ABS) plastic model. The micro-hardness values determined at the cross-sections of SLM-processed samples varied from HV0.3 250 to HV0.3 280, and the measured tensile strength was in the range of 450 MPa to 560 MPa, which showed that the template had requisite strength. Finally, the metal template was clinically used in the patient's surgical operation, and the screws were inserted precisely as the result of using the auxiliary template. The geometrical parameters of the template hole (e.g., diameter and wall thickness) were optimized, and measures were taken to optimize the key geometrical units (e.g., hole units) in metal 3D printing. Compared to the traditional technology of screw insertion, the use of the surgical metal template enabled the screws to be inserted more easily and accurately during spinal surgery. However, the design of the high-quality template should fully take into account the clinical demands of surgeons, as well as the advice of the designing engineers and operating technicians.

  19. Template-based preparation of free-standing semiconducting polymeric nanorod arrays on conductive substrates.

    Science.gov (United States)

    Haberkorn, Niko; Weber, Stefan A L; Berger, Rüdiger; Theato, Patrick

    2010-06-01

    We describe the synthesis and characterization of a cross-linkable siloxane-derivatized tetraphenylbenzidine (DTMS-TPD), which was used for the fabrication of semiconducting highly ordered nanorod arrays on conductive indium tin oxide or Pt-coated substrates. The stepwise process allow fabricating of macroscopic areas of well-ordered free-standing nanorod arrays, which feature a high resistance against organic solvents, semiconducting properties and a good adhesion to the substrate. Thin films of the TPD derivate with good hole-conducting properties could be prepared by cross-linking and covalently attaching to hydroxylated substrates utilizing an initiator-free thermal curing at 160 degrees C. The nanorod arrays composed of cross-linked DTMS-TPD were fabricated by an anodic aluminum oxide (AAO) template approach. Furthermore, the nanorod arrays were investigated by a recently introduced method allowing to probe local conductivity on fragile structures. It revealed that more than 98% of the nanorods exhibit electrical conductance and consequently feature a good electrical contact to the substrate. The prepared nanorod arrays have the potential to find application in the fabrication of multilayered device architectures for building well-ordered bulk-heterojunction solar cells.

  20. Partial nucleotide sequence analysis of 18S ribosomal RNA gene of the four genotypes of Trypanosoma congolense

    International Nuclear Information System (INIS)

    Osanya, A.; Majiwa, P.A.O.; Kinyanjui, P.W.

    2006-01-01

    Specific oligonucleotide primers based on conserved nucleotide sequences of 18s ribisomal RNA (18s rRNA) gene of Trypanosoma brucei, Leishmania donovani, Triponema aequale and Lagenidium gigantum have been designed and used in the ploymerase chain reaction (PCR) to amplify genomic DNA from four different clones each representing a different genotypic group of T. congolence. PCR products of approximately 1Kb were generated using as template DNA from each of the trypanosomes. The PCR products cross-hybridized with genomic DNA from T.brucei, T. simiae and the four genotypes of T.congolense implying significant sequence homology of 18S rRNA gene among trypanosomes. The nucleotide sequence of a segment of the PCR products were determined by direct sequencing to provide partial nucleotide sequence of the 18s rRNA gene in each T.congolense genotypic group. The sequences obtained together with those that have been published for T.brucei reveals that although most regions show inter and intra species nucleotide identity, there are several sites where deletions, insertions and base changes have occured in nucleotide sequence of of T.brucei and the four genotypes of T.congolense.(author)

  1. Simultaneous measurement of polymerization stress and curing kinetics for photo-polymerized composites with high filler contents.

    Science.gov (United States)

    Wang, Zhengzhi; Landis, Forrest A; Giuseppetti, Anthony A M; Lin-Gibson, Sheng; Chiang, Martin Y M

    2014-12-01

    Photopolymerized composites are used in a broad range of applications with their performance largely directed by reaction kinetics and contraction accompanying polymerization. The present study was to demonstrate an instrument capable of simultaneously collecting multiple kinetics parameters for a wide range of photopolymerizable systems: degree of conversion (DC), reaction exotherm, and polymerization stress (PS). Our system consisted of a cantilever beam-based instrument (tensometer) that has been optimized to capture a large range of stress generated by lightly-filled to highly-filled composites. The sample configuration allows the tensometer to be coupled to a fast near infrared (NIR) spectrometer collecting spectra in transmission mode. Using our instrument design, simultaneous measurements of PS and DC are performed, for the first time, on a commercial composite with ≈80% (by mass) silica particle fillers. The in situ NIR spectrometer collects more than 10 spectra per second, allowing for thorough characterization of reaction kinetics. With increased instrument sensitivity coupled with the ability to collect real time reaction kinetics information, we show that the external constraint imposed by the cantilever beam during polymerization could affect the rate of cure and final degree of polymerization. The present simultaneous measurement technique is expected to provide new insights into kinetics and property relationships for photopolymerized composites with high filler content such as dental restorative composites. Published by Elsevier Ltd.

  2. Spliced RNA of woodchuck hepatitis virus.

    Science.gov (United States)

    Ogston, C W; Razman, D G

    1992-07-01

    Polymerase chain reaction was used to investigate RNA splicing in liver of woodchucks infected with woodchuck hepatitis virus (WHV). Two spliced species were detected, and the splice junctions were sequenced. The larger spliced RNA has an intron of 1300 nucleotides, and the smaller spliced sequence shows an additional downstream intron of 1104 nucleotides. We did not detect singly spliced sequences from which the smaller intron alone was removed. Control experiments showed that spliced sequences are present in both RNA and DNA in infected liver, showing that the viral reverse transcriptase can use spliced RNA as template. Spliced sequences were detected also in virion DNA prepared from serum. The upstream intron produces a reading frame that fuses the core to the polymerase polypeptide, while the downstream intron causes an inframe deletion in the polymerase open reading frame. Whereas the splicing patterns in WHV are superficially similar to those reported recently in hepatitis B virus, we detected no obvious homology in the coding capacity of spliced RNAs from these two viruses.

  3. Segment-specific terminal sequences of Bunyamwera bunyavirus regulate genome replication

    International Nuclear Information System (INIS)

    Barr, John N.; Elliott, Richard M.; Dunn, Ewan F.; Wertz, Gail W.

    2003-01-01

    Bunyamwera virus (BUNV) is the prototype of both the Orthobunyavirus genus and the Bunyaviridae family of segmented negative sense RNA viruses. The tripartite BUNV genome consists of small (S), medium (M), and large (L) segments that are transcribed to give a single mRNA and replicated to generate an antigenome that is the template for synthesis of further genomic RNA strands. We modified an existing cDNA-derived RNA synthesis system to allow identification of BUNV RNA replication and transcription products by direct metabolic labeling. Direct RNA analysis allowed us to distinguish between template activities that affected either RNA replication or mRNA transcription, an ability that was not possible using previous reporter gene expression assays. We generated genome analogs containing the entire nontranslated terminal sequences of the S, M, and L BUNV segments surrounding a common sequence. Analysis of RNAs synthesized from these templates revealed that the relative abilities of BUNV segments to perform RNA replication was M > L > S. Exchange of segment-specific terminal nucleotides identified a 12-nt region located within both the 3' and 5' termini of the M segment that correlated with its high replication ability

  4. Improved carbon nanotube growth inside an anodic aluminum oxide template using microwave radiation

    Science.gov (United States)

    Dadras, Sedigheh; Faraji, Maryam

    2018-05-01

    In this study, we achieved superfast growth of carbon nanotubes (CNTs) in an anodic aluminum oxide (AAO) template by applying microwave (MW) radiation. This is a simple and direct approach for growing CNTs using a MW oven. The CNTs were synthesized using MW radiation at a frequency of 2.45 GHz and power was applied at various levels of 900, 600, and 450 W. We used graphite and ferrocene in equal portions as precursors. The optimum conditions for the growth of CNTs inside a MW oven were a time period of 5 s and power of 450 W. In order to grow uniform CNTs, an AAO template was applied with the CNTs synthesized under optimum conditions. The morphology of the synthesized CNTs was investigated by scanning electron microscopy analysis. The average diameters of the CNTs obtained without the template were 22-27 nm, whereas the diameters of the CNTs prepared inside the AAO template were about 4-6 nm.

  5. Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

    International Nuclear Information System (INIS)

    Wnęk, M; Stockley, P G; Górzny, M Ł; Evans, S D; Ward, M B; Brydson, R; Wälti, C; Davies, A G

    2013-01-01

    The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating. (paper)

  6. Fabrication and characterization of gold nano-wires templated on virus-like arrays of tobacco mosaic virus coat proteins

    Science.gov (United States)

    Wnęk, M.; Górzny, M. Ł.; Ward, M. B.; Wälti, C.; Davies, A. G.; Brydson, R.; Evans, S. D.; Stockley, P. G.

    2013-01-01

    The rod-shaped plant virus tobacco mosaic virus (TMV) is widely used as a nano-fabrication template, and chimeric peptide expression on its major coat protein has extended its potential applications. Here we describe a simple bacterial expression system for production and rapid purification of recombinant chimeric TMV coat protein carrying C-terminal peptide tags. These proteins do not bind TMV RNA or form disks at pH 7. However, they retain the ability to self-assemble into virus-like arrays at acidic pH. C-terminal peptide tags in such arrays are exposed on the protein surface, allowing interaction with target species. We have utilized a C-terminal His-tag to create virus coat protein-templated nano-rods able to bind gold nanoparticles uniformly. These can be transformed into gold nano-wires by deposition of additional gold atoms from solution, followed by thermal annealing. The resistivity of a typical annealed wire created by this approach is significantly less than values reported for other nano-wires made using different bio-templates. This expression construct is therefore a useful additional tool for the creation of chimeric TMV-like nano-rods for bio-templating.

  7. Early Earth Environments for an Emerging RNA World — More Widespread than Previously Thought?

    Science.gov (United States)

    Rogers, K. L.; Burcar, B.; Ackerson, M.; Riggi, V.; Watson, E. B.; McGown, L. B.

    2017-07-01

    Expanding the potential for an RNA World, we show that several mineral catalysts, beyond montmo-rillonite, can catalyze the polymerization of activated 5'-adenosine monophosphate under high pressure conditions.

  8. Vertically aligned nanowires on flexible silicone using a supported alumina template prepared by pulsed anodization

    DEFF Research Database (Denmark)

    Mátéfi-Tempfli, Stefan; Mátéfi-Tempfli, M.

    2009-01-01

    Carpets of vertically aligned nanowires on flexible substrates are successfully realized by a template method. Applying special pulsed anodization conditions, defect-free nanoporous alumina structures supported on polydimethylsiloxane (PDMS), a flexible silicone elastomer, are created. By using...... this template with nanopores ending on a conducting underlayer, a high-density nanowire array can be simply grown by direct DCelectrodeposition on the top of the silicone rubber....

  9. Templating Organosilicate Vitrification Using Unimolecular Self Organizing Polymers: Evolution of Morphology and Nanoporosity Development with Network Formation

    International Nuclear Information System (INIS)

    Kim, H.-C.

    2004-01-01

    Star-shaped polymers with a compatibilizing outer corona were dispersed into a thermosetting organosilicate matrix and used to create a nanoporous material. These environmentally responsive copolymers create nano-sized domains through a matrix-mediated collapse of the interior core of the core-corona polymeric structure. This approach relies on the outer corona of the star to compatibilize the insoluble core with the thermosetting resin and prevent aggregation such that these individual molecules template the crosslinking of the matrix and ultimately generate a single hole. The organic polymer was selectively thermalized leaving behind its latent image in the matrix with a pore size that reflected the size of the polymer molecule, and provided the expected reduction in dielectric constant. The morphology development as a function of arm number, molecular weight and volume fraction in mixtures with organosilicates as a function of cure/network conversion was investigated by SAXS, SANS, DMA, TEM and FE-SEM measurements. Amphiphilic star-shaped polymers of various block lengths and arm number, prepared by tandem controlled ring-opening polymerization (ROP) and atom transfer radical polymerization (ATRP) from dendritic initiators, were further tailored to facilitate contrast enhancement for various measurements by the incorporation of either ferrocenyl units or deuterated monomers. The pore sizes achieved by the star and dendrimer-like star macromolecular architectures range from ∼7 to 40nm, depending on the molecular weight and architecture

  10. Templated Dry Printing of Conductive Metal Nanoparticles

    Science.gov (United States)

    Rolfe, David Alexander

    Printed electronics can lower the cost and increase the ubiquity of electrical components such as batteries, sensors, and telemetry systems. Unfortunately, the advance of printed electronics has been held back by the limited minimum resolution, aspect ratio, and feature fidelity of present printing techniques such as gravure, screen printing and inkjet printing. Templated dry printing offers a solution to these problems by patterning nanoparticle inks into templates before drying. This dissertation shows advancements in two varieties of templated dry nanoprinting. The first, advective micromolding in vapor-permeable templates (AMPT) is a microfluidic approach that uses evaporation-driven mold filling to create submicron features with a 1:1 aspect ratio. We will discuss submicron surface acoustic wave (SAW) resonators made through this process, and the refinement process in the template manufacturing process necessary to make these devices. We also present modeling techniques that can be applied to future AMPT templates. We conclude with a modified templated dry printing that improves throughput and isolated feature patterning by transferring dry-templated features with laser ablation. This method utilizes surface energy-defined templates to pattern features via doctor blade coating. Patterned and dried features can be transferred to a polymer substrate with an Nd:YAG MOPA fiber laser, and printed features can be smaller than the laser beam width.

  11. Gold-Coated M13 Bacteriophage as a Template for Glucose Oxidase Biofuel Cells with Direct Electron Transfer.

    Science.gov (United States)

    Blaik, Rita A; Lan, Esther; Huang, Yu; Dunn, Bruce

    2016-01-26

    Glucose oxidase-based biofuel cells are a promising source of alternative energy for small device applications, but still face the challenge of achieving robust electrical contact between the redox enzymes and the current collector. This paper reports on the design of an electrode consisting of glucose oxidase covalently attached to gold nanoparticles that are assembled onto a genetically engineered M13 bacteriophage using EDC-NHS chemistry. The engineered phage is modified at the pIII protein to attach onto a gold substrate and serves as a high-surface-area template. The resulting "nanomesh" architecture exhibits direct electron transfer (DET) and achieves a higher peak current per unit area of 1.2 mA/cm(2) compared to most other DET attachment schemes. The final enzyme surface coverage on the electrode was calculated to be approximately 4.74 × 10(-8) mol/cm(2), which is a significant improvement over most current glucose oxidase (GOx) DET attachment methods.

  12. microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein

    OpenAIRE

    Pinder, Benjamin D; Smibert, Craig A

    2012-01-01

    Argonaute 1 directly interacts with the RNA binding protein Smaug in Drosophila, is thereby recruited to the Smaug target nanos mRNA and is required for Smaug-mediated translational repression of the nanos mRNA.

  13. Ambient template synthesis of multiferroic MnWO4 nanowires and nanowire arrays

    International Nuclear Information System (INIS)

    Zhou Hongjun; Yiu Yuen; Aronson, M.C.; Wong, Stanislaus S.

    2008-01-01

    The current report describes the systematic synthesis of polycrystalline, multiferroic MnWO 4 nanowires and nanowire arrays with controllable chemical composition and morphology, using a modified template-directed methodology under ambient room-temperature conditions. We were able to synthesize nanowires measuring 55±10, 100±20, and 260±40 nm in diameter, respectively, with lengths ranging in the microns. Extensive characterization of as-prepared samples has been performed using X-ray diffraction, scanning electron microscopy, transmission electron microscopy (TEM), high-resolution TEM, and energy-dispersive X-ray spectroscopy. Magnetic behavior in these systems was also probed. - Graphical abstract: Systematic synthesis of crystalline, multiferroic MnWO4 nanowires and nanowire arrays with controllable chemical composition and morphology, using a modified template-directed methodology under ambient room-temperature conditions

  14. Preparation and study of tramadol imprinted micro-and nanoparticles by precipitation polymerization: microwave irradiation and conventional heating method.

    Science.gov (United States)

    Seifi, Mahmoud; Hassanpour Moghadam, Maryam; Hadizadeh, Farzin; Ali-Asgari, Safa; Aboli, Jafar; Mohajeri, Seyed Ahmad

    2014-08-25

    In the present work a series of tramadole imprinted micro- and nanoparticles were prepared and study their recognition properties. Methacrylic acid (MAA), as a functional monomer, ethylene glycol dimethacrylate (EGDMA) as a cross-linker and different solvents (chloroform, toluene and acetonitrile (ACN)) were used for the preparation of molecularly imprinted polymers (MIPs) and non-imprinted polymers (NIPs). Several factors such as template/monomer molar ratio, volume of polymerization solvent, total monomers/solvent volume ratio, polymerization condition (heating or microwave irradiation) were also investigated. Particle size of the polymers, transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FT-IR), rebinding, selectivity tests and release study were applied for evaluation of the polymers. The optimized polymers with smaller particle size and superior binding properties were obtained in acetonitrile under heating method. MIPA4 with a size of 42.6 nm and a binding factor (BF) of 6.79 was selected for selectivity and release tests. The polymerization was not successful in acetonitrile and toluene under microwave irradiation. The MIPA4 could selectively adsorb tramadol, compared to imipramine, naltrexone and gabapentin. The data showed that tramadol release from MIPA4 was significantly slower than that of its non-imprinted polymer. Therefore, MIP nanoparticles with high selectivity, binding capacity and ability to control tramadol release could be obtained in precipitation polymerization with optimized condition. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Highly efficient reprogramming to pluripotency and directed differentiation of human cells with synthetic modified mRNA.

    Science.gov (United States)

    Warren, Luigi; Manos, Philip D; Ahfeldt, Tim; Loh, Yuin-Han; Li, Hu; Lau, Frank; Ebina, Wataru; Mandal, Pankaj K; Smith, Zachary D; Meissner, Alexander; Daley, George Q; Brack, Andrew S; Collins, James J; Cowan, Chad; Schlaeger, Thorsten M; Rossi, Derrick J

    2010-11-05

    Clinical application of induced pluripotent stem cells (iPSCs) is limited by the low efficiency of iPSC derivation and the fact that most protocols modify the genome to effect cellular reprogramming. Moreover, safe and effective means of directing the fate of patient-specific iPSCs toward clinically useful cell types are lacking. Here we describe a simple, nonintegrating strategy for reprogramming cell fate based on administration of synthetic mRNA modified to overcome innate antiviral responses. We show that this approach can reprogram multiple human cell types to pluripotency with efficiencies that greatly surpass established protocols. We further show that the same technology can be used to efficiently direct the differentiation of RNA-induced pluripotent stem cells (RiPSCs) into terminally differentiated myogenic cells. This technology represents a safe, efficient strategy for somatic cell reprogramming and directing cell fate that has broad applicability for basic research, disease modeling, and regenerative medicine. Copyright © 2010 Elsevier Inc. All rights reserved.

  16. Ciliate telomerase RNA loop IV nucleotides promote hierarchical RNP assembly and holoenzyme stability.

    Science.gov (United States)

    Robart, Aaron R; O'Connor, Catherine M; Collins, Kathleen

    2010-03-01

    Telomerase adds simple-sequence repeats to chromosome 3' ends to compensate for the loss of repeats with each round of genome replication. To accomplish this de novo DNA synthesis, telomerase uses a template within its integral RNA component. In addition to providing the template, the telomerase RNA subunit (TER) also harbors nontemplate motifs that contribute to the specialized telomerase catalytic cycle of reiterative repeat synthesis. Most nontemplate TER motifs function through linkage with the template, but in ciliate and vertebrate telomerases, a stem-loop motif binds telomerase reverse transcriptase (TERT) and reconstitutes full activity of the minimal recombinant TERT+TER RNP, even when physically separated from the template. Here, we resolve the functional requirements for this motif of ciliate TER in physiological RNP context using the Tetrahymena thermophila p65-TER-TERT core RNP reconstituted in vitro and the holoenzyme reconstituted in vivo. Contrary to expectation based on assays of the minimal recombinant RNP, we find that none of a panel of individual loop IV nucleotide substitutions impacts the profile of telomerase product synthesis when reconstituted as physiological core RNP or holoenzyme RNP. However, loop IV nucleotide substitutions do variably reduce assembly of TERT with the p65-TER complex in vitro and reduce the accumulation and stability of telomerase RNP in endogenous holoenzyme context. Our results point to a unifying model of a conformational activation role for this TER motif in the telomerase RNP enzyme.

  17. Direct determination of the rate constant of propagation by pseudo-stationary polymerization technique: screening investigation for the (implicit) penultimate effect

    International Nuclear Information System (INIS)

    Schnoll-Bitai, I.; Friedrich Olaj, O.; Liu Song Yu

    1999-01-01

    The systems styrene-p-methylstyrene, styrene-p-chlorostyrene, methyl methacrylate-p-methylstyrene and methyl methacrylate-p-chlorostyrene were polymerized under pseudo-stationary conditions (rotating sector or pulsed laser) at 25 degree C, 40 degree C and 50 degree C. The respective molecular weight distributions measured by GPC were analysed in order to derive directly the phenomenological rate constant of propagation, κ sub ρ. Copolymer compositions as a function of monomer feed could be described by the terminal model, whereas the kinetic results could only be interpreted in terms of the restricted penultimate model

  18. In vivo polymerization and manufacturing of wires and supercapacitors in plants

    Science.gov (United States)

    Stavrinidou, Eleni; Nilsson, K. Peter R.; Singh, Sandeep Kumar; Franco-Gonzalez, Juan Felipe; Volkov, Anton V.; Jonsson, Magnus P.; Grimoldi, Andrea; Elgland, Mathias; Zozoulenko, Igor V.; Berggren, Magnus

    2017-01-01

    Electronic plants, e-Plants, are an organic bioelectronic platform that allows electronic interfacing with plants. Recently we have demonstrated plants with augmented electronic functionality. Using the vascular system and organs of a plant, we manufactured organic electronic devices and circuits in vivo, leveraging the internal structure and physiology of the plant as the template, and an integral part of the devices. However, this electronic functionality was only achieved in localized regions, whereas new electronic materials that could be distributed to every part of the plant would provide versatility in device and circuit fabrication and create possibilities for new device concepts. Here we report the synthesis of such a conjugated oligomer that can be distributed and form longer oligomers and polymer in every part of the xylem vascular tissue of a Rosa floribunda cutting, forming long-range conducting wires. The plant’s structure acts as a physical template, whereas the plant’s biochemical response mechanism acts as the catalyst for polymerization. In addition, the oligomer can cross through the veins and enter the apoplastic space in the leaves. Finally, using the plant’s natural architecture we manufacture supercapacitors along the stem. Our results are preludes to autonomous energy systems integrated within plants and distribute interconnected sensor–actuator systems for plant control and optimization. PMID:28242683

  19. Biometric template revocation

    Science.gov (United States)

    Arndt, Craig M.

    2004-08-01

    Biometric are a powerful technology for identifying humans both locally and at a distance. In order to perform identification or verification biometric systems capture an image of some biometric of a user or subject. The image is then converted mathematical to representation of the person call a template. Since we know that every human in the world is different each human will have different biometric images (different fingerprints, or faces, etc.). This is what makes biometrics useful for identification. However unlike a credit card number or a password to can be given to a person and later revoked if it is compromised and biometric is with the person for life. The problem then is to develop biometric templates witch can be easily revoked and reissued which are also unique to the user and can be easily used for identification and verification. In this paper we develop and present a method to generate a set of templates which are fully unique to the individual and also revocable. By using bases set compression algorithms in an n-dimensional orthogonal space we can represent a give biometric image in an infinite number of equally valued and unique ways. The verification and biometric matching system would be presented with a given template and revocation code. The code will then representing where in the sequence of n-dimensional vectors to start the recognition.

  20. Development of Total Knee Replacement Digital Templating Software

    Science.gov (United States)

    Yusof, Siti Fairuz; Sulaiman, Riza; Thian Seng, Lee; Mohd. Kassim, Abdul Yazid; Abdullah, Suhail; Yusof, Shahril; Omar, Masbah; Abdul Hamid, Hamzaini

    In this study, by taking full advantage of digital X-ray and computer technology, we have developed a semi-automated procedure to template knee implants, by making use of digital templating method. Using this approach, a software system called OrthoKneeTMhas been designed and developed. The system is to be utilities as a study in the Department of Orthopaedic and Traumatology in medical faculty, UKM (FPUKM). OrthoKneeTMtemplating process employs uses a technique similar to those used by many surgeons, using acetate templates over X-ray films. Using template technique makes it easy to template various implant from every Implant manufacturers who have with a comprehensive database of templates. The templating functionality includes, template (knee) and manufactures templates (Smith & Nephew; and Zimmer). From an image of patient x-ray OrthoKneeTMtemplates help in quickly and easily reads to the approximate template size needed. The visual templating features then allow us quickly review multiple template sizes against the X-ray and thus obtain the nearly precise view of the implant size required. The system can assist by templating on one patient image and will generate reports that can accompany patient notes. The software system was implemented in Visual basic 6.0 Pro using the object-oriented techniques to manage the graphics and objects. The approaches for image scaling will be discussed. Several of measurement in orthopedic diagnosis process have been studied and added in this software as measurement tools features using mathematic theorem and equations. The study compared the results of the semi-automated (using digital templating) method to the conventional method to demonstrate the accuracy of the system.

  1. Template Assembly for Detailed Urban Reconstruction

    KAUST Repository

    Nan, Liangliang

    2015-05-04

    We propose a new framework to reconstruct building details by automatically assembling 3D templates on coarse textured building models. In a preprocessing step, we generate an initial coarse model to approximate a point cloud computed using Structure from Motion and Multi View Stereo, and we model a set of 3D templates of facade details. Next, we optimize the initial coarse model to enforce consistency between geometry and appearance (texture images). Then, building details are reconstructed by assembling templates on the textured faces of the coarse model. The 3D templates are automatically chosen and located by our optimization-based template assembly algorithm that balances image matching and structural regularity. In the results, we demonstrate how our framework can enrich the details of coarse models using various data sets.

  2. Improved annotation of 3' untranslated regions and complex loci by combination of strand-specific direct RNA sequencing, RNA-Seq and ESTs.

    Directory of Open Access Journals (Sweden)

    Nicholas J Schurch

    Full Text Available The reference annotations made for a genome sequence provide the framework for all subsequent analyses of the genome. Correct and complete annotation in addition to the underlying genomic sequence is particularly important when interpreting the results of RNA-seq experiments where short sequence reads are mapped against the genome and assigned to genes according to the annotation. Inconsistencies in annotations between the reference and the experimental system can lead to incorrect interpretation of the effect on RNA expression of an experimental treatment or mutation in the system under study. Until recently, the genome-wide annotation of 3' untranslated regions received less attention than coding regions and the delineation of intron/exon boundaries. In this paper, data produced for samples in Human, Chicken and A. thaliana by the novel single-molecule, strand-specific, Direct RNA Sequencing technology from Helicos Biosciences which locates 3' polyadenylation sites to within +/- 2 nt, were combined with archival EST and RNA-Seq data. Nine examples are illustrated where this combination of data allowed: (1 gene and 3' UTR re-annotation (including extension of one 3' UTR by 5.9 kb; (2 disentangling of gene expression in complex regions; (3 clearer interpretation of small RNA expression and (4 identification of novel genes. While the specific examples displayed here may become obsolete as genome sequences and their annotations are refined, the principles laid out in this paper will be of general use both to those annotating genomes and those seeking to interpret existing publically available annotations in the context of their own experimental data.

  3. REDIdb: an upgraded bioinformatics resource for organellar RNA editing sites.

    Science.gov (United States)

    Picardi, Ernesto; Regina, Teresa M R; Verbitskiy, Daniil; Brennicke, Axel; Quagliariello, Carla

    2011-03-01

    RNA editing is a post-transcriptional molecular process whereby the information in a genetic message is modified from that in the corresponding DNA template by means of nucleotide substitutions, insertions and/or deletions. It occurs mostly in organelles by clade-specific diverse and unrelated biochemical mechanisms. RNA editing events have been annotated in primary databases as GenBank and at more sophisticated level in the specialized databases REDIdb, dbRES and EdRNA. At present, REDIdb is the only freely available database that focuses on the organellar RNA editing process and annotates each editing modification in its biological context. Here we present an updated and upgraded release of REDIdb with a web-interface refurbished with graphical and computational facilities that improve RNA editing investigations. Details of the REDIdb features and novelties are illustrated and compared to other RNA editing databases. REDIdb is freely queried at http://biologia.unical.it/py_script/REDIdb/. Copyright © 2010 Elsevier B.V. and Mitochondria Research Society. All rights reserved.

  4. Template matching for auditing hospital cost and quality.

    Science.gov (United States)

    Silber, Jeffrey H; Rosenbaum, Paul R; Ross, Richard N; Ludwig, Justin M; Wang, Wei; Niknam, Bijan A; Mukherjee, Nabanita; Saynisch, Philip A; Even-Shoshan, Orit; Kelz, Rachel R; Fleisher, Lee A

    2014-10-01

    Develop an improved method for auditing hospital cost and quality. Medicare claims in general, gynecologic and urologic surgery, and orthopedics from Illinois, Texas, and New York between 2004 and 2006. A template of 300 representative patients was constructed and then used to match 300 patients at hospitals that had a minimum of 500 patients over a 3-year study period. From each of 217 hospitals we chose 300 patients most resembling the template using multivariate matching. The matching algorithm found close matches on procedures and patient characteristics, far more balanced than measured covariates would be in a randomized clinical trial. These matched samples displayed little to no differences across hospitals in common patient characteristics yet found large and statistically significant hospital variation in mortality, complications, failure-to-rescue, readmissions, length of stay, ICU days, cost, and surgical procedure length. Similar patients at different hospitals had substantially different outcomes. The template-matched sample can produce fair, directly standardized audits that evaluate hospitals on patients with similar characteristics, thereby making benchmarking more believable. Through examining matched samples of individual patients, administrators can better detect poor performance at their hospitals and better understand why these problems are occurring. © Health Research and Educational Trust.

  5. Site-specifically modified oligodeoxyribonucleotides as templates for Escherichia coli DNA polymerase I

    International Nuclear Information System (INIS)

    O'Connor, D.; Stoehrer, G.

    1985-01-01

    Oligodeoxyribonucleotides with site-specific modifications have been used as substrates for Escherichia coli DNA polymerase I holoenzyme and Klenow fragment. Modifications included the bulky guanine-8-aminofluorene adduct and a guanine oxidation product resembling the product of photosensitized DNA oxidation. By a combination of primers and nick-mers, conditions of single-strand-directed DNA synthesis and nick-translation could be created. The results show that the polymerase can bypass both types of lesions. Bypass occurs on a single-stranded template but is facilitated on a nicked, double-stranded template. Only purines, with guanine more favored than adenine, are incorporated across both lesions. The results indicate that site-specifically modified oligonucleotides can be sensitive probes for the action of polymerases on damaged templates. They also suggest a function for polymerase I, in its nick-translation capacity, during DNA repair and mutagenesis

  6. High-Surface-Area, Emulsion-Templated Carbon Foams by Activation of polyHIPEs Derived from Pickering Emulsions

    Directory of Open Access Journals (Sweden)

    Robert T. Woodward

    2016-09-01

    Full Text Available Carbon foams displaying hierarchical porosity and excellent surface areas of >1400 m2/g can be produced by the activation of macroporous poly(divinylbenzene. Poly(divinylbenzene was synthesized from the polymerization of the continuous, but minority, phase of a simple high internal phase Pickering emulsion. By the addition of KOH, chemical activation of the materials is induced during carbonization, producing Pickering-emulsion-templated carbon foams, or carboHIPEs, with tailorable macropore diameters and surface areas almost triple that of those previously reported. The retention of the customizable, macroporous open-cell structure of the poly(divinylbenzene precursor and the production of a large degree of microporosity during activation leads to tailorable carboHIPEs with excellent surface areas.

  7. Synthesis of RNA segment 1-3 during generation of incomplete influenza A (fowl plague) virus

    International Nuclear Information System (INIS)

    Carter, M.J.; Mahy, B.W.J.

    1982-01-01

    Incomplete influenza A virus (fowl plague Dobson strain) was prepared by undiluted passage in primary chick embryo fibroblast cells. Analysis of released virus RNA revealed a deficiency in RNA segments 1-3, characteristic of incomplete virus formation. The virus yield from a high multiplicity infection with standard virus always showed this deficiency, even when analysed as early as 6 hours post-infection, whereas infection at low multiplicity gave rise to virus indistinghuishable in RNA composition from the parent virus. The relative amounts of intracellular, non-polyadenylated, complementary RNA (template RNA) were found to reflect accurately the eventual RNA composition of released virus, and were altered in phase with PFU:HAU ratio, throughout a von Magnus cycle. (Author)

  8. Purification and DNA-binding properties of RNA polymerase from Bacillus subtilis.

    Science.gov (United States)

    Giacomoni, P U

    1980-05-01

    Four RNA-polymerizing activities having different subunit composition can be purified from uninfected and from SPO1-infected Bacillus subtilis. Lysozyme and sodium deoxycholate are used for lysing the cells. Polymin P is used for precipitating nucleic acids and DEAE-cellulose chromatography allows separation of enzymatic activity from the residual Polymin P. After these common steps, one can purify core + sigma + delta by chromatography on single-stranded DNA-agarose followed by gel filtration while pure core + sigma can be obtained by chromatography on double-stranded DNA cellulose. Core + delta is obtained by high-salt sucrose/glycerol gradient centrifugation. The host enzyme modified by the product of gene 28 of phage SPO1 can be purified from SPO1 infected cells by chromatography on DNA cellulose (or CNA agarose) followed by chromatography on phosphocellulose. The pH and salt dependance of the initial rate of RNA synthesis of core + sigma has been investigated using SPO1 and SPP1 DNA as templates. The optimum pH for the initial rate of transcription is 8.2 at 30 degrees C in 50 mM N,N-bis(2-hydroxyethyl)glycine buffer, and the optimum Na+ concentration is between 0.1 and 0.15 M. The kinetics of formation and of dissociation of non-filterable complexes between SPP1 DNA and core + sigma have been analyzed at different cationic concentrations. The value of the rate constant of dissociation in 0.1 M NaCl at 30 degrees C is kd = 2.16 x 10(-4) S-1. The value of the rate constant of association, under the same conditions, is ka = 5.5 x 10(8) M-1 S-1; this value is compatible with a diffusion-controlled reaction for promoter selection.

  9. High-throughput SHAPE analysis reveals structures in HIV-1 genomic RNA strongly conserved across distinct biological states.

    Directory of Open Access Journals (Sweden)

    Kevin A Wilkinson

    2008-04-01

    Full Text Available Replication and pathogenesis of the human immunodeficiency virus (HIV is tightly linked to the structure of its RNA genome, but genome structure in infectious virions is poorly understood. We invent high-throughput SHAPE (selective 2'-hydroxyl acylation analyzed by primer extension technology, which uses many of the same tools as DNA sequencing, to quantify RNA backbone flexibility at single-nucleotide resolution and from which robust structural information can be immediately derived. We analyze the structure of HIV-1 genomic RNA in four biologically instructive states, including the authentic viral genome inside native particles. Remarkably, given the large number of plausible local structures, the first 10% of the HIV-1 genome exists in a single, predominant conformation in all four states. We also discover that noncoding regions functioning in a regulatory role have significantly lower (p-value < 0.0001 SHAPE reactivities, and hence more structure, than do viral coding regions that function as the template for protein synthesis. By directly monitoring protein binding inside virions, we identify the RNA recognition motif for the viral nucleocapsid protein. Seven structurally homologous binding sites occur in a well-defined domain in the genome, consistent with a role in directing specific packaging of genomic RNA into nascent virions. In addition, we identify two distinct motifs that are targets for the duplex destabilizing activity of this same protein. The nucleocapsid protein destabilizes local HIV-1 RNA structure in ways likely to facilitate initial movement both of the retroviral reverse transcriptase from its tRNA primer and of the ribosome in coding regions. Each of the three nucleocapsid interaction motifs falls in a specific genome domain, indicating that local protein interactions can be organized by the long-range architecture of an RNA. High-throughput SHAPE reveals a comprehensive view of HIV-1 RNA genome structure, and further

  10. 2D vector-cyclic deformable templates

    DEFF Research Database (Denmark)

    Schultz, Nette; Conradsen, Knut

    1998-01-01

    In this paper the theory of deformable templates is a vector cycle in 2D is described. The deformable template model originated in (Grenander, 1983) and was further investigated in (Grenander et al., 1991). A template vector distribution is induced by parameter distribution from transformation...... matrices applied to the vector cycle. An approximation in the parameter distribution is introduced. The main advantage by using the deformable template model is the ability to simulate a wide range of objects trained by e.g. their biological variations, and thereby improve restoration, segmentation...... and probabillity measurement. The case study concerns estimation of meat percent in pork carcasses. Given two cross-sectional images - one at the front and one near the ham of the carcass - the areas of lean and fat and a muscle in the lean area are measured automatically by the deformable templates....

  11. SYNCHROTRON X-RAY OBSERVATIONS OF A MONOLAYER TEMPLATE FOR MINERALIZATION

    International Nuclear Information System (INIS)

    Dimasi, E.; Gower, L.B.

    2000-01-01

    Mineral nucleation at a Langmuir film interface has been studied by synchrotron x-ray scattering. Diluted calcium bicarbonate solutions were used as subphases for arachidic and stearic acid monolayers, compressed in a Langmuir trough. Self-assembly of the monolayer template is observed directly, and subsequent crystal growth monitored in-situ

  12. Extremely improved InP template and GaInAsP system growth on directly-bonded InP/SiO2-Si and InP/glass substrate

    International Nuclear Information System (INIS)

    Matsumoto, Keiichi; Makino, Tatsunori; Kimura, Katsuya; Shimomura, Kazuhiko

    2013-01-01

    We have developed an ultrathin InP template with low defect density on SiO 2 -Si and glass substrate by employing wet etching and wafer direct bonding technique. We have demonstrated epitaxial growth on these substrates and GaInAs/InP multiple quantum well layers were grown by low pressure metal-organic vapor-phase epitaxy. Photoluminescence measurements of the layers show that they are optically active and we have obtained almost the same intensity from these substrates compared to the InP substrate. These results may be attributed to improvement of InP template quality and should provide further improvements in device performance realized on SiO 2 -Si and glass substrate. And, these are promising results in terms of integration of InP-based several functional optical devices on SiO 2 -Si and glass substrate. (copyright 2013 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  13. Design and Fabrication of a Precision Template for Spine Surgery Using Selective Laser Melting (SLM

    Directory of Open Access Journals (Sweden)

    Di Wang

    2016-07-01

    Full Text Available In order to meet the clinical requirements of spine surgery, this paper proposes the fabrication of the customized template for spine surgery through computer-aided design. A 3D metal printing-selective laser melting (SLM technique was employed to directly fabricate the 316L stainless steel template, and the metal template with tiny locating holes was used as an auxiliary tool to insert spinal screws inside the patient’s body. To guarantee accurate fabrication of the template for cervical vertebra operation, the contact face was placed upwards to improve the joint quality between the template and the cervical vertebra. The joint surface of the printed template had a roughness of Ra = 13 ± 2 μm. After abrasive blasting, the surface roughness was Ra = 7 ± 0.5 μm. The surgical metal template was bound with the 3D-printed Acrylonitrile Butadiene Styrene (ABS plastic model. The micro-hardness values determined at the cross-sections of SLM-processed samples varied from HV0.3 250 to HV0.3 280, and the measured tensile strength was in the range of 450 MPa to 560 MPa, which showed that the template had requisite strength. Finally, the metal template was clinically used in the patient’s surgical operation, and the screws were inserted precisely as the result of using the auxiliary template. The geometrical parameters of the template hole (e.g., diameter and wall thickness were optimized, and measures were taken to optimize the key geometrical units (e.g., hole units in metal 3D printing. Compared to the traditional technology of screw insertion, the use of the surgical metal template enabled the screws to be inserted more easily and accurately during spinal surgery. However, the design of the high-quality template should fully take into account the clinical demands of surgeons, as well as the advice of the designing engineers and operating technicians.

  14. Synthesis of Mesoporous α-Fe2O3 Nanoparticles by Non-ionic Soft Template and Their Applications to Heavy Oil Upgrading

    Science.gov (United States)

    Park, Chulwoo; Jung, Jinhwan; Lee, Chul Wee; Cho, Joungmo

    2016-12-01

    This paper reports the synthetic route of 3-D network shape α-Fe2O3 from aqueous solutions of iron precursor using a non-ionic polymeric soft-template, Pluronic P123. During the synthesis of α-Fe2O3, particle sizes, crystal phases and morphologies were significantly influenced by pH, concentrations of precursor and template. The unique shape of worm-like hematite was obtained only when a starting solution was prepared by a weakly basic pH condition and a very specific composition of constituents. The synthesized nanocrystal at this condition had a narrow pore size distribution and high surface area compared to the bulk α-Fe2O3 or the one synthesized from lower pH conditions. The hydrocracking performance was tested over the synthesized iron oxide catalysts with different morphologies. The worm-like shape of iron oxide showed a superior performance, including overall yield of liquid fuel product and coke formation, over the hydrocracking of heavy petroleum oil.

  15. Novel biocompatible hydrogel nanoparticles: generation and size-tuning of nanoparticles by the formation of micelle templates obtained from thermo-responsive monomers mixtures

    Energy Technology Data Exchange (ETDEWEB)

    Khandadash, Raz; Machtey, Victoria [Bar Ilan University, Department of Chemistry (Israel); Shainer, Inbal [Tel-Aviv University, Department of Neurobiology, The George S. Wise Faculty of Life Sciences (Israel); Gottlieb, Hugo E. [Bar Ilan University, Department of Chemistry (Israel); Gothilf, Yoav [Tel-Aviv University, Department of Neurobiology, The George S. Wise Faculty of Life Sciences, and Sagol School of Neuroscience (Israel); Ebenstein, Yuval [Tel Aviv University, Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry (Israel); Weiss, Aryeh [Bar Ilan University, School of Engineering (Israel); Byk, Gerardo, E-mail: gerardo.byk@biu.ac.il [Bar Ilan University, Department of Chemistry (Israel)

    2014-12-15

    Biocompatible hydrogel nanoparticles are prepared by polymerization and cross-linking of N-isopropyl acrylamide in a micelle template formed by block copolymers macro-monomers at high temperature. Different monomer ratios form, at high temperature, well-defined micelles of different sizes which are further polymerized leading to nanoparticles with varied sizes from 20 to 390 nm. Physico-chemical characterization of the nanoparticles demonstrates their composition and homogeneity. The NPs were tested in vitro and in vivo biocompatibility assays, and their lack of toxicity was proven. The NPs can be labeled with fluorescent probes, and their intracellular fate can be visualized and quantified using confocal microscopy. Their uptake by live stem cells and distribution in whole developing animals is reported. On the basis of our results, a mechanism of nanoparticle formation is suggested. The lack of toxicity makes these nanoparticles especially attractive for biological applications such as screening and bio-sensing.

  16. A Structural Overview of RNA-Dependent RNA Polymerases from the Flaviviridae Family

    Directory of Open Access Journals (Sweden)

    Jiqin Wu

    2015-06-01

    Full Text Available RNA-dependent RNA polymerases (RdRPs from the Flaviviridae family are representatives of viral polymerases that carry out RNA synthesis through a de novo initiation mechanism. They share a ≈ 600-residue polymerase core that displays a canonical viral RdRP architecture resembling an encircled right hand with palm, fingers, and thumb domains surrounding the active site. Polymerase catalytic motifs A–E in the palm and motifs F/G in the fingers are shared by all viral RdRPs with sequence and/or structural conservations regardless of the mechanism of initiation. Different from RdRPs carrying out primer-dependent initiation, Flaviviridae and other de novo RdRPs utilize a priming element often integrated in the thumb domain to facilitate primer-independent initiation. Upon the transition to the elongation phase, this priming element needs to undergo currently unresolved conformational rearrangements to accommodate the growth of the template-product RNA duplex. In the genera of Flavivirus and Pestivirus, the polymerase module in the C-terminal part of the RdRP protein may be regulated in cis by the N-terminal region of the same polypeptide. Either being a methyltransferase in Flavivirus or a functionally unclarified module in Pestivirus, this region could play auxiliary roles for the canonical folding and/or the catalysis of the polymerase, through defined intra-molecular interactions.

  17. Accuracy of templating the acetabular cup size in Total Hip Replacement using conventional acetate templates on digital radiographs.

    Science.gov (United States)

    Krishnamoorthy, Vignesh P; Perumal, Rajamani; Daniel, Alfred J; Poonnoose, Pradeep M

    2015-12-01

    Templating of the acetabular cup size in Total Hip Replacement (THR) is normally done using conventional radiographs. As these are being replaced by digital radiographs, it has become essential to create a technique of templating using digital films. We describe a technique that involves templating the digital films using the universally available acetate templates for THR without the use of special software. Preoperative digital radiographs of the pelvis were taken with a 30 mm diameter spherical metal ball strapped over the greater trochanter. Using standard acetate templates provided by the implant company on magnified digital radiographs, the size of the metal ball (X mm) and acetabular cup (Y mm) were determined. The size of the acetabular cup to be implanted was estimated using the formula 30*Y/X. The estimated size was compared with the actual size of the cup used at surgery. Using this technique, it was possible to accurately predict the acetabular cup size in 28/40 (70%) of the hips. When the accuracy to within one size was considered, templating was correct in 90% (36/40). When assessed by two independent observers, there was good intra-observer and inter-observer reliability with intra-class correlation coefficient values greater than 0.8. It was possible to accurately and reliably predict the size of the acetabular cup, using acetate templates on digital films, without any digital templates.

  18. Mapping Optimal Charge Density and Length of ROMP-Based PTDMs for siRNA Internalization.

    Science.gov (United States)

    Caffrey, Leah M; deRonde, Brittany M; Minter, Lisa M; Tew, Gregory N

    2016-10-10

    A fundamental understanding of how polymer structure impacts internalization and delivery of biologically relevant cargoes, particularly small interfering ribonucleic acid (siRNA), is of critical importance to the successful design of improved delivery reagents. Herein we report the use of ring-opening metathesis polymerization (ROMP) methods to synthesize two series of guanidinium-rich protein transduction domain mimics (PTDMs): one based on an imide scaffold that contains one guanidinium moiety per repeat unit, and another based on a diester scaffold that contains two guanidinium moieties per repeat unit. By varying both the degree of polymerization and, in effect, the relative number of cationic charges in each PTDM, the performances of the two ROMP backbones for siRNA internalization were evaluated and compared. Internalization of fluorescently labeled siRNA into Jurkat T cells demonstrated that fluorescein isothiocyanate (FITC)-siRNA internalization had a charge content dependence, with PTDMs containing approximately 40 to 60 cationic charges facilitating the most internalization. Despite this charge content dependence, the imide scaffold yielded much lower viabilities in Jurkat T cells than the corresponding diester PTDMs with similar numbers of cationic charges, suggesting that the diester scaffold is preferred for siRNA internalization and delivery applications. These developments will not only improve our understanding of the structural factors necessary for optimal siRNA internalization, but will also guide the future development of optimized PTDMs for siRNA internalization and delivery.

  19. Radiation chemistry of polymeric system

    International Nuclear Information System (INIS)

    Machi, Sueo; Ishigaki, Isao

    1978-01-01

    Among wide application of radiation in the field of polymer chemistry, practices of polymerization, graft polymerization, bridging, etc. are introduced hereinafter. As for the radiation sources of radiation polymerization, in addition to the 60 Co-γ ray with long permeation distance which has been usually applied, electron beam accelerators with high energy, large current and high reliability have come to be produced, and the liquid phase polymerization by electron beam has attracted attention industrially. Concerning polymerizing reactions, explanations were given to electron beam polymerization under high dose rate, the polymerization in supercooling state or under high pressure, and emulsifying polymerization. As for radiation bridging, radiation is applied for the bridging of hydrogel, acceleration of bridging and improvement of radiation resistance. It is also utilized for reforming membranes by graft polymerization, and synthesis of polymers for medical use. Application of fixed enzymes in the medical field has been investigated by fixing various enzymes by low temperature γ-ray polymerization with glassy monomers such as HEMA. (Kobatake, H.)

  20. A simple method for determining polymeric IgA-containing immune complexes.

    Science.gov (United States)

    Sancho, J; Egido, J; González, E

    1983-06-10

    A simplified assay to measure polymeric IgA-immune complexes in biological fluids is described. The assay is based upon the specific binding of a secretory component for polymeric IgA. In the first step, multimeric IgA (monomeric and polymeric) immune complexes are determined by the standard Raji cell assay. Secondly, labeled secretory component added to the assay is bound to polymeric IgA-immune complexes previously fixed to Raji cells, but not to monomeric IgA immune complexes. To avoid false positives due to possible complement-fixing IgM immune complexes, prior IgM immunoadsorption is performed. Using anti-IgM antiserum coupled to CNBr-activated Sepharose 4B this step is not time-consuming. Polymeric IgA has a low affinity constant and binds weakly to Raji cells, as Scatchard analysis of the data shows. Thus, polymeric IgA immune complexes do not bind to Raji cells directly through Fc receptors, but through complement breakdown products, as with IgG-immune complexes. Using this method, we have been successful in detecting specific polymeric-IgA immune complexes in patients with IgA nephropathy (Berger's disease) and alcoholic liver disease, as well as in normal subjects after meals of high protein content. This new, simple, rapid and reproducible assay might help to study the physiopathological role of polymeric IgA immune complexes in humans and animals.

  1. Preparation of micro/nanostructure TiO2 spheres by controlling pollen as hard template and soft template.

    Science.gov (United States)

    Yang, Xiaohui; Xu, Bin; Zhang, Xuehong; Song, Xiuqin; Chen, Rufen

    2014-09-01

    In this paper, micro/nanostructure TiO2 spheres were synthesized by a sunflower pollen induced and self-assembly mineralization process, in which a titania precursor and pollen reacted in one-pot at normal pressure. In this paper, the bio-template advantage, as hard and soft template is fully demonstrated. The superiority of our synthesis is that we not only can control pollen as hard template, but also can control it as soft template only by changing reactions temperature. Under 80 degrees C of water bath, TiO2 microspheres which replicated the morphology of pollen were prepared by controlling pollen as hard template. Under 100 degrees C, hierarchical TiO2 spheres with complicated morphology, different from pollen template, were synthesized by using pollen as soft template. At the same time, judicious choice of the amount of pollen affords the synthesis of hierarchical structures spheres with adjustable morphology and crystal structure. The morphology can be tuned from microspheres constructed from TiO2 nanorods to nanospheres constructed from TiO2 nanoparticles, and the crystal structure can be tuned from rutile to anatase. More over this anatase phase can be keep better even at high temperature of 1000 degrees C. The as-prepared micro/nano structure photocatalysts not only have high photocatalytic activities, but also have good separability and reuse performance.

  2. Biometric templates selection and update using quality measures

    Science.gov (United States)

    Abboud, Ali J.; Jassim, Sabah A.

    2012-06-01

    To deal with severe variation in recording conditions, most biometric systems acquire multiple biometric samples, at the enrolment stage, for the same person and then extract their individual biometric feature vectors and store them in the gallery in the form of biometric template(s), labelled with the person's identity. The number of samples/templates and the choice of the most appropriate templates influence the performance of the system. The desired biometric template(s) selection technique must aim to control the run time and storage requirements while improving the recognition accuracy of the biometric system. This paper is devoted to elaborating on and discussing a new two stages approach for biometric templates selection and update. This approach uses a quality-based clustering, followed by a special criterion for the selection of an ultimate set of biometric templates from the various clusters. This approach is developed to select adaptively a specific number of templates for each individual. The number of biometric templates depends mainly on the performance of each individual (i.e. gallery size should be optimised to meet the needs of each target individual). These experiments have been conducted on two face image databases and their results will demonstrate the effectiveness of proposed quality-guided approach.

  3. Optimizing preventive maintenance with maintenance templates

    International Nuclear Information System (INIS)

    Dozier, I.J.

    1996-01-01

    Rising operating costs has caused maintenance professionals to rethink their strategy for preventive maintenance (PM) programs. Maintenance Templates are pre-engineered PM task recommendations for a component type based on application of the component. Development of the maintenance template considers the dominant failure cause of the component and the type of preventive maintenance that can predict or prevent the failure from occurring. Maintenance template development also attempts to replace fixed frequency tasks with condition monitoring tasks such as vibration analysis or thermography. For those components that have fixed frequency PM intervals, consideration is given to the maintenance drivers such as criticality, environment and usage. This helps to maximize the PM frequency intervals and maximize the component availability. Maintenance Templates have been used at PECO Energy's Limerick Generating Station during the Reliability Centered Maintenance (RCM) Process to optimize their PM program. This paper describes the development and uses of the maintenance templates

  4. Promoter binding, initiation, and elongation by bacteriophage T7 RNA polymerase. A single-molecule view of the transcription cycle.

    Science.gov (United States)

    Skinner, Gary M; Baumann, Christoph G; Quinn, Diana M; Molloy, Justin E; Hoggett, James G

    2004-01-30

    A single-molecule transcription assay has been developed that allows, for the first time, the direct observation of promoter binding, initiation, and elongation by a single RNA polymerase (RNAP) molecule in real-time. To promote DNA binding and transcription initiation, a DNA molecule tethered between two optically trapped beads was held near a third immobile surface bead sparsely coated with RNAP. By driving the optical trap holding the upstream bead with a triangular oscillation while measuring the position of both trapped beads, we observed the onset of promoter binding, promoter escape (productive initiation), and processive elongation by individual RNAP molecules. After DNA template release, transcription re-initiation on the same DNA template is possible; thus, multiple enzymatic turnovers by an individual RNAP molecule can be observed. Using bacteriophage T7 RNAP, a commonly used RNAP paradigm, we observed the association and dissociation (k(off)= 2.9 s(-1)) of T7 RNAP and promoter DNA, the transition to the elongation mode (k(for) = 0.36 s(-1)), and the processive synthesis (k(pol) = 43 nt s(-1)) and release of a gene-length RNA transcript ( approximately 1200 nt). The transition from initiation to elongation is much longer than the mean lifetime of the binary T7 RNAP-promoter DNA complex (k(off) > k(for)), identifying a rate-limiting step between promoter DNA binding and promoter escape.

  5. Human Enterovirus Nonstructural Protein 2CATPase Functions as Both an RNA Helicase and ATP-Independent RNA Chaperone

    Science.gov (United States)

    Xia, Hongjie; Wang, Peipei; Wang, Guang-Chuan; Yang, Jie; Sun, Xianlin; Wu, Wenzhe; Qiu, Yang; Shu, Ting; Zhao, Xiaolu; Yin, Lei; Qin, Cheng-Feng; Hu, Yuanyang; Zhou, Xi

    2015-01-01

    RNA helicases and chaperones are the two major classes of RNA remodeling proteins, which function to remodel RNA structures and/or RNA-protein interactions, and are required for all aspects of RNA metabolism. Although some virus-encoded RNA helicases/chaperones have been predicted or identified, their RNA remodeling activities in vitro and functions in the viral life cycle remain largely elusive. Enteroviruses are a large group of positive-stranded RNA viruses in the Picornaviridae family, which includes numerous important human pathogens. Herein, we report that the nonstructural protein 2CATPase of enterovirus 71 (EV71), which is the major causative pathogen of hand-foot-and-mouth disease and has been regarded as the most important neurotropic enterovirus after poliovirus eradication, functions not only as an RNA helicase that 3′-to-5′ unwinds RNA helices in an adenosine triphosphate (ATP)-dependent manner, but also as an RNA chaperone that destabilizes helices bidirectionally and facilitates strand annealing and complex RNA structure formation independently of ATP. We also determined that the helicase activity is based on the EV71 2CATPase middle domain, whereas the C-terminus is indispensable for its RNA chaperoning activity. By promoting RNA template recycling, 2CATPase facilitated EV71 RNA synthesis in vitro; when 2CATPase helicase activity was impaired, EV71 RNA replication and virion production were mostly abolished in cells, indicating that 2CATPase-mediated RNA remodeling plays a critical role in the enteroviral life cycle. Furthermore, the RNA helicase and chaperoning activities of 2CATPase are also conserved in coxsackie A virus 16 (CAV16), another important enterovirus. Altogether, our findings are the first to demonstrate the RNA helicase and chaperoning activities associated with enterovirus 2CATPase, and our study provides both in vitro and cellular evidence for their potential roles during viral RNA replication. These findings increase our

  6. RNA polymerase II transcriptional fidelity control and its functional interplay with DNA modifications

    Science.gov (United States)

    Xu, Liang; Wang, Wei; Chong, Jenny; Shin, Ji Hyun; Xu, Jun; Wang, Dong

    2016-01-01

    Accurate genetic information transfer is essential for life. As a key enzyme involved in the first step of gene expression, RNA polymerase II (Pol II) must maintain high transcriptional fidelity while it reads along DNA template and synthesizes RNA transcript in a stepwise manner during transcription elongation. DNA lesions or modifications may lead to significant changes in transcriptional fidelity or transcription elongation dynamics. In this review, we will summarize recent progress towards understanding the molecular basis of RNA Pol II transcriptional fidelity control and impacts of DNA lesions and modifications on Pol II transcription elongation. PMID:26392149

  7. Direct detection of RNA in vitro and in situ by target-primed RCA: The impact of E. coli RNase III on the detection efficiency of RNA sequences distanced far from the 3'-end.

    Science.gov (United States)

    Merkiene, Egle; Gaidamaviciute, Edita; Riauba, Laurynas; Janulaitis, Arvydas; Lagunavicius, Arunas

    2010-08-01

    We improved the target RNA-primed RCA technique for direct detection and analysis of RNA in vitro and in situ. Previously we showed that the 3' --> 5' single-stranded RNA exonucleolytic activity of Phi29 DNA polymerase converts the target RNA into a primer and uses it for RCA initiation. However, in some cases, the single-stranded RNA exoribonucleolytic activity of the polymerase is hindered by strong double-stranded structures at the 3'-end of target RNAs. We demonstrate that in such hampered cases, the double-stranded RNA-specific Escherichia coli RNase III efficiently assists Phi29 DNA polymerase in converting the target RNA into a primer. These observations extend the target RNA-primed RCA possibilities to test RNA sequences distanced far from the 3'-end and customize this technique for the inner RNA sequence analysis.

  8. Studies on the effects of persistent RNA priming on DNA replication and genomic stability

    OpenAIRE

    Stuckey, Ruth

    2014-01-01

    [EN]: DNA replication and transcription take place on the same DNA template, and the correct interplay between these processes ensures faithful genome duplication. DNA replication must be highly coordinated with other cell cycle events, such as segregation of fully replicated DNA in order to maintain genomic integrity. Transcription generates RNA:DNA hybrids, transient intermediate structures that are degraded by the ribonuclease H (RNaseH) class of enzymes. RNA:DNA hybrids can form R-loops, ...

  9. Twin screw extruders as polymerization reactors for a free radical homo polymerization

    NARCIS (Netherlands)

    Ganzeveld, K.J.; Janssen, L.P.B.M.

    The bulk polymerization of n-butylmethacrylate was investigated in a counter-rotating twin screw extruder. It appeared that the gel effect, occurring with bulk polymerizations, affected the polymerization progress very strongly. Due to this effect the conversion of the reaction is independent of the

  10. Caprine Butchery and Bone Modification Templates: A step towards standardisation

    Directory of Open Access Journals (Sweden)

    Peter Popkin

    2005-03-01

    Full Text Available Widely accepted zooarchaeological procedure for recording butchery marks and other types of bone modification involves two processes: Drawing the bone showing the exact location and orientation of the modification and recording all of the information about the bone and its modification into an electronic database. No recording templates have ever been published, however, resulting in individual zooarchaeologists repeating the effort of developing their own templates or drawings for each bone in an assemblage showing a modification. Both of these tasks are time consuming and lead to inconsistencies in recording and quantification methods. To help alleviate this problem a series of caprine (sheep and goat bone templates have been created. These templates show every bone in a goat skeleton, apart from the skull, from six views at life-size when printed on A4 paper. They have intentionally been produced with a minimum of detail (without shading or stippling etc. so that the recorded butchery marks and bone modifications will be clearly visible. Because the skeletal morphology of sheep and goats is so similar these templates may be used interchangeably for either species. They may also be used for many other artiodactyl species such as cattle and deer as no scale has been indicated. The study of butchery marks and bone modification has the potential to provide zooarchaeologists with information about taphonomy, site formation processes, burial/ritual practices, human behaviour, ancient technologies and possibly ethnicity amongst other things, but only if the recording of these bone modifications is undertaken in a standardised fashion across the field. While much effort has been directed towards standardising the recognition and classification of various bone modifications, the recording of these modifications regularly occurs in various ways. Using standardised recording templates will save valuable time and help to alleviate problems of data

  11. [The template principle: paradigm of modern genetics].

    Science.gov (United States)

    Inge-Vechtomov, S G

    2013-01-01

    The idea of continuity in living systems, which was initially developed in mid-19th century, reached its peak in 1928 thanks to N.K. Koltsov, who proposed the template principle in chromosome reproduction. The determination of genetic functions of nucleic acids and the advent of molecular genetics led to F. Crick's statement of the central dogma of molecular biology in 1958. This dogma became a contemporary version of the template principle (templates of the first order). The discovery of "protein inheritance" underlay the notion of steric or conformational templates (second order) for reproducing conformation in a number of proteins. The template principle supplemented by this notion claims to be the main paradigm of modern genetics.

  12. Synthesis of in vitro Co1E1 transcripts with 5'-terminal ribonucleotides that exhibit noncomplementarity with the DNA template

    International Nuclear Information System (INIS)

    Parker, R.C.

    1986-01-01

    A region that forms the S1 nuclease site in Co1E1 DNA is shown to code for an in vitro transcript, called S1 RNA-B, which contains a 5'-terminal GTP residue that exhibits noncomplementarity with the template's DNA sequence. The synthesis of S1 RNA-B initiates four bases upstream from the start point for S1 RNA-C. The initial four bases in S1 RNA-B and S1 RNA-C are identical. The relative synthesis of S1 RNA-B to S1 RNA-C is sensitive to the concentration of GTP, a substrate that is required for elongation past the +4 position in S1 RNA-C. Dinucleotides that are expected to only initiate synthesis of S1 RNA-C yield two transcripts that appear to initiate from the S1 RNA-C and S1 RNA-B start sites. In vitro studies involving other Co1E1 transcripts, RNA-B and RNA-C, provide similar observations concerning the noncomplementary initiation phenomenon. A model involving transcriptional slippage is suggested to explain the noncomplementary initiation phenomenon. The model proposes that the cycling reaction of Escherichia coli RNA polymerase produces tetranucleotides that are transposed to nearby upstream sequences for priming transcription

  13. Ligand design for alkali-metal-templated self-assembly of unique high-nuclearity CuII aggregates with diverse coordination cage units: crystal structures and properties.

    Science.gov (United States)

    Du, Miao; Bu, Xian-He; Guo, Ya-Mei; Ribas, Joan

    2004-03-19

    The construction of two unique, high-nuclearity Cu(II) supramolecular aggregates with tetrahedral or octahedral cage units, [(mu(3)-Cl)[Li subset Cu(4)(mu-L(1))(3)](3)](ClO(4))(8)(H(2)O)(4.5) (1) and [[Na(2) subset Cu(12)(mu-L(2))(8)(mu-Cl)(4)](ClO(4))(8)(H(2)O)(10)(H(3)O(+))(2)](infinity) (2) by alkali-metal-templated (Li(+) or Na(+)) self-assembly, was achieved by the use of two newly designed carboxylic-functionalized diazamesocyclic ligands, N,N'-bis(3-propionyloxy)-1,4-diazacycloheptane (H(2)L(1)) or 1,5-diazacyclooctane-N,N'-diacetate acid (H(2)L(2)). Complex 1 crystallizes in the trigonal R3c space group (a = b = 20.866(3), c = 126.26(4) A and Z = 12), and 2 in the triclinic P1 space group (a = 13.632(4), b = 14.754(4), c = 19.517(6) A, alpha = 99.836(6), beta = 95.793(5), gamma = 116.124(5) degrees and Z = 1). By subtle variation of the ligand structures and the alkali-metal templates, different polymeric motifs were obtained: a dodecanuclear architecture 1 consisting of three Cu(4) tetrahedral cage units with a Li(+) template, and a supramolecular chain 2 consisting of two crystallographically nonequivalent octahedral Cu(6) polyhedra with a Na(+) template. The effects of ligand functionality and alkali metal template ions on the self-assembly processes of both coordination supramolecular aggregates, and their magnetic behaviors are discussed in detail.

  14. Hard template synthesis of metal nanowires

    OpenAIRE

    Kawamura, Go; Muto, Hiroyuki; Matsuda, Atsunori

    2014-01-01

    Metal nanowires (NWs) have attracted much attention because of their high electron conductivity, optical transmittance, and tunable magnetic properties. Metal NWs have been synthesized using soft templates such as surface stabilizing molecules and polymers, and hard templates such as anodic aluminum oxide, mesoporous oxide, carbon nanotubes. NWs prepared from hard templates are composites of metals and the oxide/carbon matrix. Thus, selecting appropriate elements can simplify the production o...

  15. Mechanocatalytic polymerization and cross-linking in a polymeric matrix

    NARCIS (Netherlands)

    Jakobs, R.T.M.; Ma, Shuang; Sijbesma, R.P.

    2013-01-01

    A latent olefin metathesis catalyst, bearing two polymeric NHC ligands, was embedded in a semicrystalline polymer matrix containing cyclic olefins. The catalyst was activated by straining the solid material under compression, resulting in polymerization and cross-linking reactions of the monomers in

  16. Facile Synthesis of Polyaniline Nanotubes with Square Capillary Using Urea as Template

    Directory of Open Access Journals (Sweden)

    Shuhua Pang

    2017-10-01

    Full Text Available Polyaniline nanotubes were successfully synthesized by a facile in situ chemical oxidative polymerization method using urea as soft template. When the urea/aniline molar ratio is 3:1, the as-prepared nanotubular polyaniline (PANI-3 shows regular and uniform square capillaries, which provides a high electrode/electrolyte contact, easy ion diffusion and enhanced electroactive regions during the electrochemical process, leading to weak internal resistance and improved electrochemical performance. The PANI-3 sample exhibits a high specific capacitance of 405 F/g at current density of 0.2 A/g, and PANI only has a specific capacitance of 263 F/g. At current density of 1 A/g, the capacitance of PANI-3 is still 263 F/g (64.9% of the capacitance at 0.2 A/g. Such a PANI-3 nanotube, with regular and uniform capillary, is a promising electrode material for high-performance supercapacitors.

  17. Detection of hepatitis C virus RNA using reverse transcription PCR

    International Nuclear Information System (INIS)

    Yap, S.F.

    1998-01-01

    Detection of the viral genome (HCV RNA) is by a combination of cDNA synthesis and PCR followed by gel analysis and/or hybridization assay. In principle, cDNA is synthesized using the viral RNA as template and the enzyme, reverse transcriptase. The cDNA is then amplified by PCR and the product detected. Agarose gel electrophoresis provides a rapid and simple detection method; however, it is non-quantitative. The assay protocol described in this paper is adapted from that published by Chan et al. Comments on various aspects of the assay are based on experience with the method in our laboratory

  18. MULTIDIRECTIONAL BUILDING DETECTION IN AERIAL IMAGES WITHOUT SHAPE TEMPLATES

    Directory of Open Access Journals (Sweden)

    A. Manno-Kovacs

    2013-05-01

    Full Text Available The aim of this paper is to exploit orientation information of an urban area for extracting building contours without shape templates. Unlike using shape templates, these given contours describe more variability and reveal the fine details of the building outlines, resulting in a more accurate detection process, which is beneficial for many tasks, like map updating and city planning. According to our assumption, orientation of the closely located buildings is coherent, it is related to the road network, therefore adaptation of this information can lead to more efficient building detection results. The introduced method first extracts feature points for representing the urban area. Orientation information in the feature point neighborhoods is analyzed to define main orientations. Based on orientation information, the urban area is classified into different directional clusters. The edges of the classified building groups are then emphasized with shearlet based edge detection method, which is able to detect edges only in the main directions, resulting in an efficient connectivity map. In the last step, with the fusion of the feature points and connectivity map, building contours are detected with a non-parametric active contour method.

  19. Direct RNA-based detection of CTX-M β-lactamases in human blood samples.

    Science.gov (United States)

    Stein, Claudia; Makarewicz, Oliwia; Pfeifer, Yvonne; Brandt, Christian; Pletz, Mathias W

    2015-05-01

    Bloodstream infections with ESBL-producers are associated with increased mortality, which is due to delayed appropriate treatment resulting in clinical failure. Current routine diagnostics for detection of bloodstream infections consists of blood culture followed by species identification and susceptibility testing. In attempts to improve and accelerate diagnostic procedures, PCR-based methods have been developed. These methods focus on species identification covering only a limited number of ESBL coding genes. Therefore, they fail to cover the steadily further evolving genetic diversity of clinically relevant β-lactamases. We have recently designed a fast and novel RNA targeting method to detect and specify CTX-M alleles from bacterial cultures, based on an amplification-pyrosequencing approach. We further developed this assay towards a diagnostic tool for clinical use and evaluated its sensitivity and specificity when applied directly to human blood samples. An optimized protocol for mRNA isolation allows detection of specific CTX-M groups from as little as 100 CFU/mL blood via reverse transcription, amplification, and pyrosequencing directly from human EDTA blood samples as well as from pre-incubated human blood cultures with a turnaround time for test results of <7 h. Copyright © 2015 Elsevier GmbH. All rights reserved.

  20. Thermodynamic Presynthetic Considerations for Ring-Opening Polymerization.

    Science.gov (United States)

    Olsén, Peter; Odelius, Karin; Albertsson, Ann-Christine

    2016-03-14

    The need for polymers for high-end applications, coupled with the desire to mimic nature's macromolecular machinery fuels the development of innovative synthetic strategies every year. The recently acquired macromolecular-synthetic tools increase the precision and enable the synthesis of polymers with high control and low dispersity. However, regardless of the specificity, the polymerization behavior is highly dependent on the monomeric structure. This is particularly true for the ring-opening polymerization of lactones, in which the ring size and degree of substitution highly influence the polymer formation properties. In other words, there are two important factors to contemplate when considering the particular polymerization behavior of a specific monomer: catalytic specificity and thermodynamic equilibrium behavior. This perspective focuses on the latter and undertakes a holistic approach among the different lactones with regard to the equilibrium thermodynamic polymerization behavior and its relation to polymer synthesis. This is summarized in a monomeric overview diagram that acts as a presynthetic directional cursor for synthesizing highly specific macromolecules; the means by which monomer equilibrium conversion relates to starting temperature, concentration, ring size, degree of substitution, and its implications for polymerization behavior are discussed. These discussions emphasize the importance of considering not only the catalytic system but also the monomer size and structure relations to thermodynamic equilibrium behavior. The thermodynamic equilibrium behavior relation with a monomer structure offers an additional layer of complexity to our molecular toolbox and, if it is harnessed accordingly, enables a powerful route to both monomer formation and intentional macromolecular design.

  1. Learning templates for artistic portrait lighting analysis.

    Science.gov (United States)

    Chen, Xiaowu; Jin, Xin; Wu, Hongyu; Zhao, Qinping

    2015-02-01

    Lighting is a key factor in creating impressive artistic portraits. In this paper, we propose to analyze portrait lighting by learning templates of lighting styles. Inspired by the experience of artists, we first define several novel features that describe the local contrasts in various face regions. The most informative features are then selected with a stepwise feature pursuit algorithm to derive the templates of various lighting styles. After that, the matching scores that measure the similarity between a testing portrait and those templates are calculated for lighting style classification. Furthermore, we train a regression model by the subjective scores and the feature responses of a template to predict the score of a portrait lighting quality. Based on the templates, a novel face illumination descriptor is defined to measure the difference between two portrait lightings. Experimental results show that the learned templates can well describe the lighting styles, whereas the proposed approach can assess the lighting quality of artistic portraits as human being does.

  2. Template Generation and Selection Algorithms

    NARCIS (Netherlands)

    Guo, Y.; Smit, Gerardus Johannes Maria; Broersma, Haitze J.; Heysters, P.M.; Badaway, W.; Ismail, Y.

    The availability of high-level design entry tooling is crucial for the viability of any reconfigurable SoC architecture. This paper presents a template generation method to extract functional equivalent structures, i.e. templates, from a control data flow graph. By inspecting the graph the algorithm

  3. Smart Inulin-Based Polycationic Nanodevices for siRNA Delivery.

    Science.gov (United States)

    Cavallaro, G; Sardo, C; Scialabba, C; Licciardi, M; Giammona, G

    2017-01-01

    The advances of short interfering RNA (siRNA) mediated therapy provide a powerful option for the treatment of many diseases by silencing the expression of targeted genes including cancer development and progression. Inulin is a very simple and biocompatible polysaccharide proposed by our groups to produce interesting delivery systems for Nucleic Acid Based Drugs (NABDs), such as siRNA, either as polycations able to give polyplexes and polymeric coatings for nanosystems having a metallic core. In this research field, different functionalizing groups were linked to the inulin backbone with specific aims including oligoamine such as Ethylendiammine (EDA), Diethylediamine (DETA), Spermine, (SPM) etc. In this contribution the main Inulin-based nanodevices for the delivery of siRNA have been reported, analysed and compared with particular reference to their chemical design and structure, biocompatibility, siRNA complexing ability, silencing ability. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

  4. Direct laser writing by two-photon polymerization as a tool for developing microenvironments for evaluation of bacterial growth

    Energy Technology Data Exchange (ETDEWEB)

    Otuka, A.J.G. [Instituto de Física de São Carlos, Universidade de São Paulo, CP.369, 13560-970 São Carlos, SP (Brazil); Corrêa, D.S. [Laboratório Nacional de Nanotecnologia para o Agronegócio (LNNA), Embrapa Instrumentação, Rua XV de Novembro, 1452, CP.741, 13560-970 São Carlos, SP (Brazil); Fontana, C.R. [Department of Clinical Analysis, School of Pharmaceutical Sciences, University of São Paulo State (UNESP), 1621 Expedicionarios do Brasil Street, Araraquara, Sao Paulo 14801-960 (Brazil); Mendonça, C.R., E-mail: crmendon@ifsc.usp.br [Instituto de Física de São Carlos, Universidade de São Paulo, CP.369, 13560-970 São Carlos, SP (Brazil)

    2014-02-01

    Monitoring bacteria growth and motion in environments is fundamental to understand, for instance, how they proliferate and contaminate organism. Therefore, techniques to fabricate microenvironments for in situ and in vivo studies are interesting for that purpose. In this work we used two-photon polymerization to fabricate microenvironments and, as a proof of principle, we demonstrated the development of the bacteria ATCC 25922 Escherichia coli (E. coli) into the microstructure surroundings. Two varieties of polymeric microenvironments are presented: (i) a microenvironment doped at specific site with ciprofloxacin, an antibiotic typically used in the treatment of diseases caused by E. coli and (ii) micro-fences, which serve as traps for bacteria. These microenvironments, fabricated by two-photon polymerization, may be a potential platform for drug delivery system, by promoting or inhibiting the growth of bacteria in specific biological or synthetic sites. - Highlights: • Microenvironments were fabricated by two-photon polymerization. • We demonstrated the development of Escherichia coli into the microstructure surroundings. • Microenvironment doped with the antibiotic ciprofloxacin was fabricated. • Micro-fences, which serve as traps for bacteria, were also produced.

  5. Direct laser writing by two-photon polymerization as a tool for developing microenvironments for evaluation of bacterial growth

    International Nuclear Information System (INIS)

    Otuka, A.J.G.; Corrêa, D.S.; Fontana, C.R.; Mendonça, C.R.

    2014-01-01

    Monitoring bacteria growth and motion in environments is fundamental to understand, for instance, how they proliferate and contaminate organism. Therefore, techniques to fabricate microenvironments for in situ and in vivo studies are interesting for that purpose. In this work we used two-photon polymerization to fabricate microenvironments and, as a proof of principle, we demonstrated the development of the bacteria ATCC 25922 Escherichia coli (E. coli) into the microstructure surroundings. Two varieties of polymeric microenvironments are presented: (i) a microenvironment doped at specific site with ciprofloxacin, an antibiotic typically used in the treatment of diseases caused by E. coli and (ii) micro-fences, which serve as traps for bacteria. These microenvironments, fabricated by two-photon polymerization, may be a potential platform for drug delivery system, by promoting or inhibiting the growth of bacteria in specific biological or synthetic sites. - Highlights: • Microenvironments were fabricated by two-photon polymerization. • We demonstrated the development of Escherichia coli into the microstructure surroundings. • Microenvironment doped with the antibiotic ciprofloxacin was fabricated. • Micro-fences, which serve as traps for bacteria, were also produced

  6. images_template

    Data.gov (United States)

    National Aeronautics and Space Administration — Images for the website template go here. It will not change their names or locations, but will hopefully help to organize them. Oh, but for a directory structure...

  7. Soft-Template Construction of 3D Macroporous Polypyrrole Scaffolds.

    Science.gov (United States)

    Liu, Shaohua; Wang, Faxing; Dong, Renhao; Zhang, Tao; Zhang, Jian; Zheng, Zhikun; Mai, Yiyong; Feng, Xinliang

    2017-04-01

    A bottom-up approach toward 3D hierarchical macroporous polypyrrole aerogels is demonstrated via soft template-directed synthesis and self-assembly of ultrathin polypyrrole nanosheets in solution, which present interconnected macropores, ultrathin walls, and large specific surface areas, thereby exhibiting a high capacity, satisfactory rate capability, and excellent cycling stability for Na-ion storage. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  8. Template-directed synthesis of pillared-porous carbon nanosheet architectures: High-performance electrode materials for supercapacitors

    Energy Technology Data Exchange (ETDEWEB)

    Fan, Zhuangjun; Liu, Yang; Yan, Jun; Wang, Qian; Wei, Tong [Key Laboratory of Superlight Materials and Surface Technology, Ministry of Education College of Material Science and Chemical Engineering, Harbin Engineering University, Harbin (China); Ning, Guoqing [State Key Laboratory of Heavy Oil Processing, China University of Petroleum, Beijing, Changping (China); Zhi, Linjie [National Center for Nanoscience and Technology of China, Zhongguancun, Beijing (China); Wei, Fei [Beijing Key Laboratory of Green Chemical Reaction Engineering and Technology, Department of Chemical Engineering, Tsinghua University, Beijing (China)

    2012-04-15

    3D pillared-porous carbon nanosheets with supporting carbon pillars between the carbon layers is prepared by the carbonization of pitch on porous MgO templates. This unique structure endows the high-rate transportation of electrolyte ions and electrons throughout the electrode matrix, resulting in excellent electrochemical performance. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

  9. Sensitive and selective electrochemical determination of quinoxaline-2-carboxylic acid based on bilayer of novel poly(pyrrole) functional composite using one-step electro-polymerization and molecularly imprinted poly(o-phenylenediamine)

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Yukun; Fang, Guozhen; Wang, Xiaomin; Pan, Mingfei; Qian, Hailong; Liu, Huilin; Wang, Shuo, E-mail: s.wang@tust.edu.cn

    2014-01-02

    Graphical abstract: -- Highlights: •PPY-GO-BiCoPc composite was formed using a simple electrochemical method for the first time. •A novel PoPD-MIP sensor based on PPY-GO-BiCoPc composite had been fabricated. •The PPY-GO-BiCoPc functional composite was introduced to improve performance of the sensor. •Highly sensitive, selective and stable sensor had been achieved. •The established MIP sensor could be promising in food safety analysis. -- Abstract: A facile and efficient molecularly imprinted polymer (MIP) recognition element of electrochemical sensor was fabricated by directly electro-polymerizing monomer o-phenylenediamine (oPD) in the presence of template quinoxaline-2-carboxylic acid (QCA), based on one-step controllable electrochemical modification of poly(pyrrole)-graphene oxide-binuclear phthalocyanine cobalt (II) sulphonate (PPY-GO-BiCoPc) functional composite on glassy carbon electrode (GCE). The MIP film coated on PPY-GO-BiCoPc functional composite decorated GCE (MIP/PPY-GO-BiCoPc/GCE) was presented for the first time. The synergistic effect and electro-catalytic activity toward QCA redox of PPY-GO-BiCoPc functional composite were discussed using various contrast tests. Also, the effect of experimental variables on the current response such as, electro-polymerization cycles, template/monomer ratio, elution condition for template removal, pH of the supporting electrolyte and accumulation time, were investigated in detail. Under the optimized conditions, the proposed MIP sensor possessed a fast rebinding dynamics and an excellent recognition capacity to QCA, while the anodic current response of square wave voltammetry (SWV) was well-proportional to the concentration of QCA in the range of 1.0 × 10{sup −8}–1.0 × 10{sup −4} and 1.0 × 10{sup −4}–5.0 × 10{sup −4} mol L{sup −1} with a low detection limit of 2.1 nmol L{sup −1}. The established sensor was applied successfully to determine QCA in commercial pork and chicken muscle

  10. Sensitive and selective electrochemical determination of quinoxaline-2-carboxylic acid based on bilayer of novel poly(pyrrole) functional composite using one-step electro-polymerization and molecularly imprinted poly(o-phenylenediamine)

    International Nuclear Information System (INIS)

    Yang, Yukun; Fang, Guozhen; Wang, Xiaomin; Pan, Mingfei; Qian, Hailong; Liu, Huilin; Wang, Shuo

    2014-01-01

    Graphical abstract: -- Highlights: •PPY-GO-BiCoPc composite was formed using a simple electrochemical method for the first time. •A novel PoPD-MIP sensor based on PPY-GO-BiCoPc composite had been fabricated. •The PPY-GO-BiCoPc functional composite was introduced to improve performance of the sensor. •Highly sensitive, selective and stable sensor had been achieved. •The established MIP sensor could be promising in food safety analysis. -- Abstract: A facile and efficient molecularly imprinted polymer (MIP) recognition element of electrochemical sensor was fabricated by directly electro-polymerizing monomer o-phenylenediamine (oPD) in the presence of template quinoxaline-2-carboxylic acid (QCA), based on one-step controllable electrochemical modification of poly(pyrrole)-graphene oxide-binuclear phthalocyanine cobalt (II) sulphonate (PPY-GO-BiCoPc) functional composite on glassy carbon electrode (GCE). The MIP film coated on PPY-GO-BiCoPc functional composite decorated GCE (MIP/PPY-GO-BiCoPc/GCE) was presented for the first time. The synergistic effect and electro-catalytic activity toward QCA redox of PPY-GO-BiCoPc functional composite were discussed using various contrast tests. Also, the effect of experimental variables on the current response such as, electro-polymerization cycles, template/monomer ratio, elution condition for template removal, pH of the supporting electrolyte and accumulation time, were investigated in detail. Under the optimized conditions, the proposed MIP sensor possessed a fast rebinding dynamics and an excellent recognition capacity to QCA, while the anodic current response of square wave voltammetry (SWV) was well-proportional to the concentration of QCA in the range of 1.0 × 10 −8 –1.0 × 10 −4 and 1.0 × 10 −4 –5.0 × 10 −4 mol L −1 with a low detection limit of 2.1 nmol L −1 . The established sensor was applied successfully to determine QCA in commercial pork and chicken muscle samples with acceptable

  11. Engineering and Characterizing Light-Matter Interactions in Photonic Crystals

    Science.gov (United States)

    2010-01-01

    SU8 monomer has, on average, eight epoxy groups, that under go a ring-opening polymerization in the presence of an acid catalyst. SU8 falls into...copper oxide [49] into colloidal and SU8 polymer photonic crystal templates, respectively. 1.5.2 Gas-Phase Infilling Gas-phase deposition typically...resist using direct laser writing. 78 Figure 2. Scanning electron micrograph of an over- polymerized woodpile structure fabricated in SU8 photo-resist

  12. Visualization and characterization of interfacial polymerization layer formation

    NARCIS (Netherlands)

    Zhang, Yali; Benes, Nieck Edwin; Lammertink, Rob G.H.

    2015-01-01

    We present a microfluidic platform to visualize the formation of free-standing films by interfacial polymerization. A microfluidic device is fabricated, with an array of micropillars to stabilize an aqueous–organic interface that allows a direct observation of the films formation process via optical

  13. Chelating polymeric membranes

    KAUST Repository

    Peinemann, Klaus-Viktor; Villalobos Vazquez de la Parra, Luis Francisco; Hilke, Roland

    2015-01-01

    microporous chelating polymeric membrane. Embodiments include, but are not limited to, microporous chelating polymeric membranes, device comprising the membranes, and methods of using and making the same.

  14. microRNA-independent recruitment of Argonaute 1 to nanos mRNA through the Smaug RNA-binding protein.

    Science.gov (United States)

    Pinder, Benjamin D; Smibert, Craig A

    2013-01-01

    Argonaute (Ago) proteins are typically recruited to target messenger RNAs via an associated small RNA such as a microRNA (miRNA). Here, we describe a new mechanism of Ago recruitment through the Drosophila Smaug RNA-binding protein. We show that Smaug interacts with the Ago1 protein, and that Ago1 interacts with and is required for the translational repression of the Smaug target, nanos mRNA. The Ago1/nanos mRNA interaction does not require a miRNA, but it does require Smaug. Taken together, our data suggest a model whereby Smaug directly recruits Ago1 to nanos mRNA in a miRNA-independent manner, thereby repressing translation.

  15. SimFuse: A Novel Fusion Simulator for RNA Sequencing (RNA-Seq Data

    Directory of Open Access Journals (Sweden)

    Yuxiang Tan

    2015-01-01

    Full Text Available The performance evaluation of fusion detection algorithms from high-throughput sequencing data crucially relies on the availability of data with known positive and negative cases of gene rearrangements. The use of simulated data circumvents some shortcomings of real data by generation of an unlimited number of true and false positive events, and the consequent robust estimation of accuracy measures, such as precision and recall. Although a few simulated fusion datasets from RNA Sequencing (RNA-Seq are available, they are of limited sample size. This makes it difficult to systematically evaluate the performance of RNA-Seq based fusion-detection algorithms. Here, we present SimFuse to address this problem. SimFuse utilizes real sequencing data as the fusions’ background to closely approximate the distribution of reads from a real sequencing library and uses a reference genome as the template from which to simulate fusions’ supporting reads. To assess the supporting read-specific performance, SimFuse generates multiple datasets with various numbers of fusion supporting reads. Compared to an extant simulated dataset, SimFuse gives users control over the supporting read features and the sample size of the simulated library, based on which the performance metrics needed for the validation and comparison of alternative fusion-detection algorithms can be rigorously estimated.

  16. CoCl2 reinforced polymeric nanocomposites of conjugated polymer ...

    Indian Academy of Sciences (India)

    Administrator

    biological and gas sensors, anti-corrosion protection coat- ings and microwave absorption.1–7 These polymeric mate- ... composite by the wet chemical method for direct current ... other hand, 4 g ammonium persulphate as an oxidant was.

  17. Template-directed synthesis of nets based upon octahemioctahedral cages that encapsulate catalytically active metalloporphyrins

    KAUST Repository

    Zhang, ZhenJie

    2012-01-18

    meso-Tetra(N-methyl-4-pyridyl)porphine tetratosylate (TMPyP) templates the synthesis of six new metal-organic materials by the reaction of benzene-1,3,5-tricarboxylate with transition metals, five of which exhibit HKUST-1 or tbo topology (M = Fe, Mn, Co, Ni, Mg). The resulting materials, porph@MOMs, selectively encapsulate the corresponding metalloporphyrins in octahemioctahedral cages and can serve as size-selective heterogeneous catalysts for oxidation of olefins. © 2011 American Chemical Society.

  18. Template-directed synthesis of nets based upon octahemioctahedral cages that encapsulate catalytically active metalloporphyrins

    KAUST Repository

    Zhang, ZhenJie; Zhang, Linping; Wojtas, Łukasz; Eddaoudi, Mohamed; Zaworotko, Michael J.

    2012-01-01

    meso-Tetra(N-methyl-4-pyridyl)porphine tetratosylate (TMPyP) templates the synthesis of six new metal-organic materials by the reaction of benzene-1,3,5-tricarboxylate with transition metals, five of which exhibit HKUST-1 or tbo topology (M = Fe, Mn, Co, Ni, Mg). The resulting materials, porph@MOMs, selectively encapsulate the corresponding metalloporphyrins in octahemioctahedral cages and can serve as size-selective heterogeneous catalysts for oxidation of olefins. © 2011 American Chemical Society.

  19. Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein

    Directory of Open Access Journals (Sweden)

    Xu Wanhong

    2008-12-01

    proteins. This implies significant evolutionary constraints are placed on dsRNA RdRp molecules, particularly in regions comprising the canonical polymerase motifs and residues thought to interact directly with template and nascent mRNA. This may point the way to improved design of anti-viral agents specifically targeting this enzyme.

  20. RNA-Mediated Gene Duplication and Retroposons: Retrogenes, LINEs, SINEs, and Sequence Specificity

    Science.gov (United States)

    2013-01-01

    A substantial number of “retrogenes” that are derived from the mRNA of various intron-containing genes have been reported. A class of mammalian retroposons, long interspersed element-1 (LINE1, L1), has been shown to be involved in the reverse transcription of retrogenes (or processed pseudogenes) and non-autonomous short interspersed elements (SINEs). The 3′-end sequences of various SINEs originated from a corresponding LINE. As the 3′-untranslated regions of several LINEs are essential for retroposition, these LINEs presumably require “stringent” recognition of the 3′-end sequence of the RNA template. However, the 3′-ends of mammalian L1s do not exhibit any similarity to SINEs, except for the presence of 3′-poly(A) repeats. Since the 3′-poly(A) repeats of L1 and Alu SINE are critical for their retroposition, L1 probably recognizes the poly(A) repeats, thereby mobilizing not only Alu SINE but also cytosolic mRNA. Many flowering plants only harbor L1-clade LINEs and a significant number of SINEs with poly(A) repeats, but no homology to the LINEs. Moreover, processed pseudogenes have also been found in flowering plants. I propose that the ancestral L1-clade LINE in the common ancestor of green plants may have recognized a specific RNA template, with stringent recognition then becoming relaxed during the course of plant evolution. PMID:23984183

  1. Backtracking dynamics of RNA polymerase: pausing and error correction

    International Nuclear Information System (INIS)

    Sahoo, Mamata; Klumpp, Stefan

    2013-01-01

    Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield–Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates. (paper)

  2. Backtracking dynamics of RNA polymerase: pausing and error correction

    Science.gov (United States)

    Sahoo, Mamata; Klumpp, Stefan

    2013-09-01

    Transcription by RNA polymerases is frequently interrupted by pauses. One mechanism of such pauses is backtracking, where the RNA polymerase translocates backward with respect to both the DNA template and the RNA transcript, without shortening the transcript. Backtracked RNA polymerases move in a diffusive fashion and can return to active transcription either by diffusive return to the position where backtracking was initiated or by cleaving the transcript. The latter process also provides a mechanism for proofreading. Here we present some exact results for a kinetic model of backtracking and analyse its impact on the speed and the accuracy of transcription. We show that proofreading through backtracking is different from the classical (Hopfield-Ninio) scheme of kinetic proofreading. Our analysis also suggests that, in addition to contributing to the accuracy of transcription, backtracking may have a second effect: it attenuates the slow down of transcription that arises as a side effect of discriminating between correct and incorrect nucleotides based on the stepping rates.

  3. Fabrication of Surface Protein-Imprinted Nanoparticles Using a Metal Chelating Monomer via Aqueous Precipitation Polymerization.

    Science.gov (United States)

    Li, Wei; Sun, Yan; Yang, Chongchong; Yan, Xianming; Guo, Hao; Fu, Guoqi

    2015-12-16

    Molecular imprinting is a promising way for constructing artificial protein recognition materials, but it has been challenged by difficulties such as restricted biomacromolecule transfer in the cross-linked polymer networks, and reduced template-monomer interactions that are due to the required aqueous media. Herein, we propose a strategy for imprinting of histidine (His)-exposed proteins by combining previous approaches such as surface imprinting over nanostructures, utilization of metal coordination interactions, and adoption of aqueous precipitation polymerization capable of forming reversible physical crosslinks. With lysozyme as a model template bearing His residues, imprinted polymer nanoshells were grafted over vinyl-modified nanoparticles by aqueous precipitation copolymerization of a Cu(2+) chelating monomer with a temperature-responsive monomer carried out at 37 °C, above the volume phase-transition temperature (VPTT) of the final copolymer. The imprinted nanoshells showed significant temperature sensitivity and the template removal could be facilitated by swelling of the imprinted layers at 4 °C, below the VPTT. The resultant core-shell imprinted nanoparticles exhibited strikingly high rebinding selectivity against a variety of nontemplate proteins. An imprinting factor up to 22.7 was achieved, which is among the best values reported for protein imprinting, and a rather high specific binding capacity of 67.3 mg/g was obtained. Moreover, this approach was successfully extended to preliminary imprinting of hemoglobin, another protein with accessible His. Therefore, it may be a versatile method for fabrication of high-performance surface-imprinted nanoparticles toward His-exposed proteins.

  4. Organized mesoporous silica films as templates for the elaboration of organized nanoparticle networks

    International Nuclear Information System (INIS)

    Gacoin, T; Besson, S; Boilot, J P

    2006-01-01

    Tremendous work achieved in the last 20 years on nanoparticle synthesis has allowed us to study many new physical properties that are found in the nanometre size range. New developments are now expected when considering assemblies of nanoparticles such as 2D or 3D organized arrays. These systems are indeed expected to exhibit original physical properties resulting from particle-particle interactions. Studies in this field are clearly dependent on the elaboration of materials with controlled particle size, organization and interparticle distance. This paper presents a strategy of elaboration that is based on the use of organized mesoporous silica films as templates. These films are made by sol-gel polymerization around surfactant assemblies and further elimination of the surfactant. This provides porous matrices with a pore organization that is the almost perfect replica of the initial micellar structure. The use of such films for the elaboration of organized arrays of nanoparticles is detailed in the case of CdS and Ag particles. The formation of particles inside the pores is achieved through impregnation with precursors that are allowed to diffuse inside the pores. This leads to particles with a size and a spatial arrangement that is directly related to the initial pore structure of the films. This process opens a wide range of investigations due to the relative ease of fabrication over large surfaces and the numerous possibilities offered by the elaboration of porous films with different pore sizes and organizations

  5. Tripartite polyionic complex (PIC) micelles as non-viral vectors for mesenchymal stem cell siRNA transfection.

    Science.gov (United States)

    Raisin, Sophie; Morille, Marie; Bony, Claire; Noël, Danièle; Devoisselle, Jean-Marie; Belamie, Emmanuel

    2017-08-22

    In the context of regenerative medicine, the use of RNA interference mechanisms has already proven its efficiency in targeting specific gene expression with the aim of enhancing, accelerating or, more generally, directing stem cell differentiation. However, achievement of good transfection levels requires the use of a gene vector. For in vivo applications, synthetic vectors are an interesting option to avoid possible issues associated with viral vectors (safety, production costs, etc.). Herein, we report on the design of tripartite polyionic complex micelles as original non-viral polymeric vectors suited for mesenchymal stem cell transfection with siRNA. Three micelle formulations were designed to exhibit pH-triggered disassembly in an acidic pH range comparable to that of endosomes. One formulation was selected as the most promising with the highest siRNA loading capacity while clearly maintaining pH-triggered disassembly properties. A thorough investigation of the internalization pathway of micelles into cells with tagged siRNA was made before showing an efficient inhibition of Runx2 expression in primary bone marrow-derived stem cells. This work evidenced PIC micelles as promising synthetic vectors that allow efficient MSC transfection and control over their behavior, from the perspective of their clinical use.

  6. Protein-RNA linkage and posttranslational modifications of feline calicivirus and murine norovirus VPg proteins

    Directory of Open Access Journals (Sweden)

    Allan Olspert

    2016-06-01

    Full Text Available Members of the Caliciviridae family of positive sense RNA viruses cause a wide range of diseases in both humans and animals. The detailed characterization of the calicivirus life cycle had been hampered due to the lack of robust cell culture systems and experimental tools for many of the members of the family. However, a number of caliciviruses replicate efficiently in cell culture and have robust reverse genetics systems available, most notably feline calicivirus (FCV and murine norovirus (MNV. These are therefore widely used as representative members with which to examine the mechanistic details of calicivirus genome translation and replication. The replication of the calicivirus RNA genome occurs via a double-stranded RNA intermediate that is then used as a template for the production of new positive sense viral RNA, which is covalently linked to the virus-encoded protein VPg. The covalent linkage to VPg occurs during genome replication via the nucleotidylylation activity of the viral RNA-dependent RNA polymerase. Using FCV and MNV, we used mass spectrometry-based approach to identify the specific amino acid linked to the 5′ end of the viral nucleic acid. We observed that both VPg proteins are covalently linked to guanosine diphosphate (GDP moieties via tyrosine positions 24 and 26 for FCV and MNV respectively. These data fit with previous observations indicating that mutations introduced into these specific amino acids are deleterious for viral replication and fail to produce infectious virus. In addition, we also detected serine phosphorylation sites within the FCV VPg protein with positions 80 and 107 found consistently phosphorylated on VPg-linked viral RNA isolated from infected cells. This work provides the first direct experimental characterization of the linkage of infectious calicivirus viral RNA to the VPg protein and highlights that post-translational modifications of VPg may also occur during the viral life cycle.

  7. Pyrogallol-imprinted polymers with methyl methacrylate via precipitation polymerization

    Science.gov (United States)

    Mehamod, Faizatul Shimal; Othman, Nor Amira; Bulat, Ku Halim Ku; Suah, Faiz Bukhari Mohd

    2018-06-01

    Molecular simulation techniques are important to study the understanding of chemical and physical properties of any material. Computational modeling is considered as time reducer in finding the best recipes for Molecularly-Imprinted Polymers (MIPs). In this study, Pyrogallol-imprinted polymers (PIP) and non-imprinted polymers (NIPs) were synthesized via precipitation polymerization using Pyrogallol (Py), methyl methacrylate (MMA), divinylbenzene (DVB) as template, functional monomer and cross-linker, respectively. The recipe was according to the results from computational techniques. The synthesized PIP and NIPs were characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy (SEM), Brunauer-Emmett-Teller (BET) and UV-visible spectroscopy (UV-vis). Studies on adsorption isotherm showed that PIP and NIPs follow Scatchard isotherm models. Sorption kinetic study found that PIP and NIPs follow pseudo-second order which indicates the rate-limiting step is the surface adsorption. The imprinting factor of PIP was determined by selectivity study and showed the value of k >1, which proved that PIP was selective toward Pyrogallol compared to NIP.

  8. Hyperbranched polymers from polymerization in solid state

    International Nuclear Information System (INIS)

    Tomaz, Vivian A.; Silva, Rafael; Muniz, Edvani C.; Rubira, Adley F.

    2009-01-01

    The macroscopic properties of polymers are directly related to the chemical characteristics of the monomeric units and also with the geometric arrangement of polymer chains. Thus, polymers were synthesized from two well-known chelators EDTA and EDA. We evaluated the conditions for the polymerization of the precursors in the solid state. The polymerization was carried out varying the proportions of reagents, aiming the polymers with different degrees of chain branching and the materials were characterized by FTIR. The materials obtained from the best condition for synthesis were purified by size-exclusion chromatography of and were subjected to characterization by FTIR and NMR of 1 H and 13 C. The content of end groups in these samples was determined by back titration. (author)

  9. MicroRNA Delivery for Regenerative Medicine

    OpenAIRE

    Peng, Bo; Chen, Yongming; Leong, Kam W.

    2015-01-01

    MicroRNA (miRNA) directs post-transcriptional regulation of a network of genes by targeting mRNA. Although relatively recent in development, many miRNAs direct differentiation of various stem cells including induced pluripotent stem cells (iPSCs), a major player in regenerative medicine. An effective and safe delivery of miRNA holds the key to translating miRNA technologies. Both viral and nonviral delivery systems have seen success in miRNA delivery, and each approach possesses advantages an...

  10. Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

    Directory of Open Access Journals (Sweden)

    Dominik M Meinel

    2013-11-01

    Full Text Available Messenger RNA (mRNA synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5 diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1 phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.

  11. Recruitment of TREX to the transcription machinery by its direct binding to the phospho-CTD of RNA polymerase II.

    Science.gov (United States)

    Meinel, Dominik M; Burkert-Kautzsch, Cornelia; Kieser, Anja; O'Duibhir, Eoghan; Siebert, Matthias; Mayer, Andreas; Cramer, Patrick; Söding, Johannes; Holstege, Frank C P; Sträßer, Katja

    2013-11-01

    Messenger RNA (mRNA) synthesis and export are tightly linked, but the molecular mechanisms of this coupling are largely unknown. In Saccharomyces cerevisiae, the conserved TREX complex couples transcription to mRNA export and mediates mRNP formation. Here, we show that TREX is recruited to the transcription machinery by direct interaction of its subcomplex THO with the serine 2-serine 5 (S2/S5) diphosphorylated CTD of RNA polymerase II. S2 and/or tyrosine 1 (Y1) phosphorylation of the CTD is required for TREX occupancy in vivo, establishing a second interaction platform necessary for TREX recruitment in addition to RNA. Genome-wide analyses show that the occupancy of THO and the TREX components Sub2 and Yra1 increases from the 5' to the 3' end of the gene in accordance with the CTD S2 phosphorylation pattern. Importantly, in a mutant strain, in which TREX is recruited to genes but does not increase towards the 3' end, the expression of long transcripts is specifically impaired. Thus, we show for the first time that a 5'-3' increase of a protein complex is essential for correct expression of the genome. In summary, we provide insight into how the phospho-code of the CTD directs mRNP formation and export through TREX recruitment.

  12. A facile template method to synthesize significantly improved LiNi0.5Mn1.5O4 using corn stalk as a bio-template

    International Nuclear Information System (INIS)

    Liu, Guiyang; Kong, Xin; Sun, Hongyan; Wang, Baosen; Yi, Zhongzhou; Wang, Quanbiao

    2014-01-01

    In order to simplify the template method for the synthesis of cathode materials for lithium ion batteries, a facile template method using plant stalks as bio-templates has been introduced. Based on this method, LiNi 0.5 Mn 1.5 O 4 spinel with a significantly improved electrochemical performance has been synthesized using corn stalk as a template. X-ray diffraction (XRD), Fourier transform infrared pectroscopy (FTIR) and scanning electron microscope (SEM) have been used to investigate the phase composition and micro-morphologies of the products. Charge-discharge measurements in lithium cells, cyclic voltammetry (CV) and Electrochemical impedance spectroscopy (EIS) have been used to study the electrochemical performance of the products. The results indicate that the templated product exhibits higher crystallinity than that of non-templated product. Both of the templated product and the non-templated product are combination of the ordered space group P4 3 32 and the disordered Fd-3 m. The specific BET surface area of the templated product is about twice larger than that of the non-templated product. Moreover, the electrochemical performances of the templated product including specific capacity, cycling stability and rate capability are significantly improved as compared with the non-templated product, due to its higher crystallinity, larger Li + diffusion coefficient and lower charge transfer resistance

  13. Template-controlled piezoactivity of ZnO thin films grown via a bioinspired approach

    Directory of Open Access Journals (Sweden)

    Nina J. Blumenstein

    2017-01-01

    Full Text Available Biomaterials are used as model systems for the deposition of functional inorganic materials under mild reaction conditions where organic templates direct the deposition process. In this study, this principle was adapted for the formation of piezoelectric ZnO thin films. The influence of two different organic templates (namely, a carboxylate-terminated self-assembled monolayer and a sulfonate-terminated polyelectrolyte multilayer on the deposition and therefore on the piezoelectric performance was investigated. While the low negative charge of the COOH-SAM is not able to support oriented attachment of the particles, the strongly negatively charged sulfonated polyelectrolyte leads to texturing of the ZnO film. This texture enables a piezoelectric performance of the material which was measured by piezoresponse force microscopy. This study shows that it is possible to tune the piezoelectric properties of ZnO by applying templates with different functionalities.

  14. The Application of Template Selectophores for the Preparation of Molecularly Imprinted Polymers

    Directory of Open Access Journals (Sweden)

    Basil Danylec

    2015-09-01

    Full Text Available Molecularly imprinted polymers are versatile materials with wide application scope for the detection, capture and separation of specific compounds present in complex feed stocks. A major challenge associated with their preparation has been the need to sacrifice one mole equivalent of the template molecule to generate the complementary polymer cavities that selectively bind the target molecule. Moreover, template molecules can often be difficult to synthesise, expensive or lack stability. In this study, we describe a new approach, directed at the use of synthetic selectophores, chosen as readily prepared and low cost structural analogues with recognition groups in similar three-dimensional arrangements as found in the target molecule. To validate the approach, a comparative study of selectophores related to the polyphenolic compound (E-resveratrol has been undertaken using traditional and green chemical synthetic approaches. These molecular mimic compounds were employed as polymer templates and also as binding analytes to interrogate the recognition sites associated with the molecularly imprinted polymers. Importantly, the study confirms that the use of selectophores has the potential to confer practical advantages, including access to more efficient methods for selection and preparation of suitable template molecules with a broader range of molecular diversity, as well as delivering imprinted polymers capable of recognizing the target compound and structurally related products.

  15. Template occluded SBA-15: An effective dissolution enhancer for poorly water-soluble drug

    International Nuclear Information System (INIS)

    Fu Tingming; Guo Liwei; Le Kang; Wang Tianyao; Lu Jin

    2010-01-01

    The aim of the present work was to improve the dissolution rate of piroxicam by inclusion into template occluded SBA-15. Our strategy involves directly introducing piroxicam into as-prepared SBA-15 occluded with P123 (EO 20 PO 70 EO 20 ) by self assembling method in acetonitrile/methylene chloride mixture solution. Ultraviolet spectrometry experiment and thermogravimetric analysis-differential scanning calorimetry (TG-DSC) profiles show that the piroxicam and P123 contents in the inclusion compound are 12 wt% and 28 wt%, respectively. X-ray powder diffraction and DSC analysis reveal that the included piroxicam is arranged in amorphous form. N 2 adsorption-desorption experiment indicates that the piroxicam has been introduced to the mesopores instead of precipitating at the outside of the silica material. The inclusion compound was submitted to in vitro dissolution tests, the results show that the piroxicam dissolve from template occluded inclusion compound more rapidly, than these from the piroxicam crystalline and template removed samples in all tested conditions. Thus a facile method to improve the dissolution rate of poorly water-soluble drug was established, and this discovery opens a new avenue for the utilization of templates used for the synthesis of mesoporous materials.

  16. Biomimetic synthesis of calcium carbonate bilayers interfaced by a diblock copolymer template

    NARCIS (Netherlands)

    Goos, J.A.C.M.; Vo, C.D.; Dey, A.; Hoogen, van den C.J.; Lousberg, N.J.H.G.M.; Hendrix, M.M.R.M.; Tirelli, N.; With, de G.; Sommerdijk, N.A.J.M.

    2012-01-01

    The synthesis of a new class of hybrid materials with two differently oriented layers of calcite at adjacent sides of an organic template is demonstrated. A Langmuir monolayer of the amphiphilic block copolymer poly(butyl acrylate)-b-poly(hydroxypropyl acrylate) directs the formation of a first

  17. Emulsion polymerization with high energy radiation

    International Nuclear Information System (INIS)

    Stannett, V.T.; Stahel, E.P.

    1992-01-01

    High energy radiation, particularly that of cobalt-60 or caesium-137 gamma-rays, provides in principle an ideal initiator for emulsion polymerization. The high free radical yields from the radiolysis of the aqueous phase combined with the high kinetic chain lengths associated with emulsion polymerization lead to a highly effective utilization of the radiation. There are other important advantages compared with the use of chemical initiators such as potassium persulfate. These are outlined in the chapter, together with some attendant disadvantages. Radiation-induced initiation is temperature independent, and low temperature polymerizations can be conducted with ease. Monomers that mainly terminate their growing chains by chain transfer to monomer give higher molecular weights at lower temperatures. Industrially, vinyl acetate is an important example of such a monomer, and it has been studied using radiation initiation. Both laboratory and pilot plant studies have been carried out and reported. The results are summarized in this chapter. Styrene is the classical example of a material that under a number of conditions closely obeys the so-called ideal Smith-Ewart kinetics. It has been found that under similar conditions but substituting radiation for potassium persulfate as the initiator, ideal kinetics were closely followed. Most of the conventional and some non-standard vinyl and diene monomers have been studied to some extent with radiation-initiated polymerizations in emulsion. To conserve space however, this chapter presents and discusses the results obtained only with styrene and vinyl acetate, both in laboratory and pilot plant investigations. Other monomers and special situations are referenced either directly or to the other available reviews. (orig.)

  18. In situ, Cr K-edge XAS study on the Phillips catalyst : activation and ethylene polymerization

    NARCIS (Netherlands)

    Groppo, E.; Prestipino, C.; Cesano, F.; Bonino, F.; Bordiga, S.; Lamberti, C.; Thuene, P.C.; Niemantsverdriet, J.W.; Zecchina, A.

    2005-01-01

    In this in situ EXAFS and XANES study on the Phillips ethylene-polymerization Cr/SiO2 catalyst, two polymerization routes are investigated and compared. The first mimics that adopted in industrial plants, where ethylene is dosed directly on the oxidized catalyst, while in the second the oxidized

  19. Microporous silica prepared by organic templating: relationship between the molecular template and pore structure

    International Nuclear Information System (INIS)

    Brinker, C. Jeffrey; Cao, Guozhong; Kale, Rahul P.; Lopez, Gabriel P.; Lu, Yunfeng; Prabakar, S.

    1999-01-01

    Microporous silica materials with a controlled pore size and a narrow pore size distribution have been prepared by sol-gel processing using an organic-templating approach. Microporous networks were formed by pyrolytic removal of organic ligands (methacryloxypropyl groups) from organic/inorganic hybrid materials synthesized by copolymerization of 3-methacryloxypropylsilane (MPS) and tetraethoxysilane (TEOS). Molecular simulations and experimental measurements were conducted to examine the relationship between the microstructural characteristics of the porous silica (e.g., pore size, total pore volume, and pore connectivity) and the size and amount of organic template ligands added. Adsorption measurements suggest that the final porosity of the microporous silica is due to both primary pores (those present in the hybrid materials prior to pyrolysis) and secondary pores (those created by pyrolytic removal of organic templates). Primary pores were inaccessible to N(sub 2) at 77 K but accessible to CO(sub 2) at 195 K; secondary pores were accessible to both N(sub 2) (at 77 K) and CO(sub 2) (at 195 K) in adsorption measurements. Primary porosity decreases with the amount of organic ligands added because of the enhanced densification of MPS/TEOS hybrid materials as the mole fraction of trifunctional MPS moieties increases. pore volumes measured by nitrogen adsorption experiments at 77 K suggest that the secondary (template-derived) porosity exhibits a percolation behavior as the template concentration is increased. Gas permeation experiments indicate that the secondary pores are approximately 5(angstrom) in diameter, consistent with predictions based on molecular simulations

  20. Mango core inner shell membrane template-directed synthesis of porous ZnO films and their application for enzymatic glucose biosensor

    Science.gov (United States)

    Zhou, Yu; Wang, Lei; Ye, Zhizhen; Zhao, Minggang; Cai, Hui; Huang, Jingyun

    2013-11-01

    Micro/nano-porous ZnO films were synthesized through a simple biotemplate-directed method using mango core inner shell membranes as templates. The achieved ZnO films with wrinkles on the surface are combined of large holes and small pores in the bulk. High specific surface area, numerous microspaces, and small channels for fluid circulation provided by this unique structure along with the good biocompatibility and electron communication features of ZnO material make the product an ideal platform for the immobilization of enzymes The fabricated glucose biosensor based on the porous ZnO films exhibits good selective detection ability of analyte with good stability, high sensitivity of 50.58 μA cm-2 mM-1 and a wide linear range of 0.2-5.6 mM along with a low detection limit of 10 μM.