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Casamento de padrões em imagens digitais livre de segmentação e invariante sob transformações de similaridade.; Segmentation-free template matching in digital images invariant to similarity transformations.

Araújo, Sidnei Alves de
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 21/10/2009 PT
Relevância na Pesquisa
56.23%
Reconhecimento de padrões em imagens é um problema clássico da área de visão computacional e consiste em detectar um padrão ou objeto de referência (template) em uma imagem digital. A maioria dos métodos para esta finalidade propostos na literatura simplifica as imagens por meio de operações como binarização, segmentação e detecção de bordas ou pontos de contorno, para em seguida extrair um conjunto de atributos descritores. O problema é que esta simplificação pode descartar informações importantes para descrição dos padrões, fazendo diminuir a robustez do processo de detecção. Um método eficiente deve ter a habilidade de identificar um padrão sujeito a algumas transformações geométricas como rotação, escalonamento, translação, cisalhamento e, no caso de métodos para imagens coloridas, deve ainda tratar do problema da constância da cor. Além disso, o conjunto de atributos que descrevem um padrão deve ser pequeno o suficiente para viabilizar o desenvolvimento de aplicações práticas como um sistema de visão robótica ou um sistema de vigilância. Estes são alguns dos motivos que justificam os esforços empreendidos nos inúmeros trabalhos desta natureza encontrados na literatura. Neste trabalho é proposto um método de casamento de padrões em imagens digitais...

Autoxidação de 1,4-dihidronicotinamidas promovida por N,N,N',N'-tetrametil-p-fenilenodiamina: Modelo de síntese de ATP no sítio I da cadeia respiratória; 1,4-Dihidronicotinamidas autoxidation promoted by N, N, N ', N'-tetramethyl-p-phenylenediamine: ATP synthesis template in site I of the respiratory chain

Bechara, Etelvino Jose Henriques
Fonte: Biblioteca Digitais de Teses e Dissertações da USP Publicador: Biblioteca Digitais de Teses e Dissertações da USP
Tipo: Tese de Doutorado Formato: application/pdf
Publicado em 07/03/1972 PT
Relevância na Pesquisa
35.82%
N,N,N',N '-tetrametil-p-fenilenodiamina (TMPD) catalisa a autoxidação de coenzimas piridínicos (NADH, NADPH) e modelos (ClBCH ,ClPCH ) ao cátion piridínico com rendimentos de 80-100%. A velocidade destas reações mostrou dependência de primeira ordem com respeito à concentração da 1,4-dihidronicotinamida e de meia ordem em relação às concentrações de O2 e TMPD. Estes dados cinéticos e testes com captadores de ion superóxido e superóxido dismutase indicam que os radicais HO•2 oriundos da autoxidação lenta do TMPD promovem a oxidação da dihidronicotinamida numa reação em cadeia; no término os radicais HO•2 se aniquilam por dismutação. O mecanismo proposto também é confirmado (1º) pela razão kC-H/kC-D=2,3 quando se substitui um dos hidrogênios do C4 de ClBCH por deutério, (2º) pelas idênticas velocidades iniciais em H2O e D2O, (3º) pelo valor da Ea = 10 kcal/mol na autoxidação do NADH e (4º) pelo aumento da velocidade de pH = 7,8 a pH 6,5. TMPD também promove a autoxidação do derivado 5, 6-hidratado (PHTN) da dihidronicotinamida ao cátion piridínico (ClPC+) apenas de fosfato ou arsenato estão presentes. O ClPC+ nã o se forma a partir do ClPCH em equilíbrio com o PHTN. Muito provavelmente se forma a partir do intermediário fosforilado no C6 por oxidação no C4 seguida de eliminação de fosfato. Quando PHTN e ClPCH foram oxidados pelo sistema O2/TMPD na presença de fosfato de piridínio ou de tetra-n-butilamônio em meio piridínico houve formação de pirofosfato...

Error-free and error-prone lesion bypass by human DNA polymerase κ in vitro

Zhang, Yanbin; Yuan, Fenghua; Wu, Xiaohua; Wang, Mu; Rechkoblit, Olga; Taylor, John-Stephen; Geacintov, Nicholas E.; Wang, Zhigang
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Publicado em 01/11/2000 EN
Relevância na Pesquisa
26.25%
Error-free lesion bypass and error-prone lesion bypass are important cellular responses to DNA damage during replication, both of which require a DNA polymerase (Pol). To identify lesion bypass DNA polymerases, we have purified human Polκ encoded by the DINB1 gene and examined its response to damaged DNA templates. Here, we show that human Polκ is a novel lesion bypass polymerase in vitro. Purified human Polκ efficiently bypassed a template 8-oxoguanine, incorporating mainly A and less frequently C opposite the lesion. Human Polκ most frequently incorporated A opposite a template abasic site. Efficient further extension required T as the next template base, and was mediated mainly by a one-nucleotide deletion mechanism. Human Polκ was able to bypass an acetylaminofluorene-modified G in DNA, incorporating either C or T, and less efficiently A opposite the lesion. Furthermore, human Polκ effectively bypassed a template (–)-trans-anti-benzo[a]pyrene-N2-dG lesion in an error-free manner by incorporating a C opposite the bulky adduct. In contrast, human Polκ was unable to bypass a template TT dimer or a TT (6-4) photoproduct, two of the major UV lesions. These results suggest that Polκ plays an important role in both error-free and error-prone lesion bypass in humans.

Isolation of an active transcription initiation complex from HeLa cell-free extract.

Tolunay, H E; Yang, L; Anderson, W F; Safer, B
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /10/1984 EN
Relevância na Pesquisa
26.18%
A two-step procedure has been developed for the formation of RNA polymerase II transcription initiation and elongation complexes. Initiation complexes are rapidly formed in HeLa cell-free extract supplemented with a DNA template containing the adenovirus 2 major late promoter and ATP. Assembly of transcription components required for correct initiation is absolutely dependent on specific eukaryotic promoter sequences. Sarkosyl-sensitive transcription initiation complexes are rapidly converted to Sarkosyl-resistant elongation complexes when supplemented with the remaining nucleoside triphosphates. The 60S initiation complex can be extensively purified by glycerol gradient centrifugation and is easily separated from free RNA polymerase II and free DNA template. Recovery of this stable complex is greater than 90%. Specific transcription cannot be detected if the DNA template is subsequently added to gradient fractions containing HeLa cell-free extract components alone. This suggests that the DNA templates promote the specific assembly of RNA polymerase II and transcription factors required for accurate initiation. Since conversion of purified initiation complexes to elongation complexes can occur without additional HeLa cell components...

Cell-free cloning using φ29 DNA polymerase

Hutchison, Clyde A.; Smith, Hamilton O.; Pfannkoch, Cynthia; Venter, J. Craig
Fonte: National Academy of Sciences Publicador: National Academy of Sciences
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
26.28%
We describe conditions for rolling-circle amplification (RCA) of individual DNA molecules 5–7 kb in size by >109-fold, using φ29 DNA polymerase. The principal difficulty with amplification of small amounts of template by RCA using φ29 DNA polymerase is “background” DNA synthesis that usually occurs when template is omitted, or at low template concentrations. Reducing the reaction volume while keeping the amount of template fixed increases the template concentration, resulting in a suppression of background synthesis. Cell-free cloning of single circular molecules by using φ29 DNA polymerase was achieved by carrying out the amplification reactions in very small volumes, typically 600 nl. This procedure allows cell-free cloning of individual synthetic DNA molecules that cannot be cloned in Escherichia coli, for example synthetic phage genomes carrying lethal mutations. It also allows cell-free cloning of genomic DNA isolated from bacteria. This DNA can be sequenced directly from the φ29 DNA polymerase reaction without further amplification. In contrast to PCR amplification, RCA using φ29 DNA polymerase does not produce mutant jackpots, and the high processivity of the enzyme eliminates stuttering at homopolymer tracts. Cell-free cloning has many potential applications to both natural and synthetic DNA. These include environmental DNA samples that have proven difficult to clone and synthetic genes encoding toxic products. The method may also speed genome sequencing by eliminating the need for biological cloning.

Heat-resistant DNA tile arrays constructed by template-directed photoligation through 5-carboxyvinyl-2′-deoxyuridine

Tagawa, Miho; Shohda, Koh-ichiroh; Fujimoto, Kenzo; Sugawara, Tadashi; Suyama, Akira
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
35.98%
Template-directed DNA photoligation has been applied to a method to construct heat-resistant two-dimensional (2D) DNA arrays that can work as scaffolds in bottom-up assembly of functional biomolecules and nano-electronic components. DNA double-crossover AB-staggered (DXAB) tiles were covalently connected by enzyme-free template-directed photoligation, which enables a specific ligation reaction in an extremely tight space and under buffer conditions where no enzymes work efficiently. DNA nanostructures created by self-assembly of the DXAB tiles before and after photoligation have been visualized by high-resolution, tapping mode atomic force microscopy in buffer. The improvement of the heat tolerance of 2D DNA arrays was confirmed by heating and visualizing the DNA nanostructures. The heat-resistant DNA arrays may expand the potential of DNA as functional materials in biotechnology and nanotechnology.

Absolute free energy and entropy of a mobile loop of the enzyme AcetylCholineEsterase

Mihailescu, Mihail; Meirovitch, Hagai
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em 04/06/2009 EN
Relevância na Pesquisa
36.35%
The loop 287–290 (Ile, Phe, Arg, and Phe) of the protein AcetylCholineEsterase (AChE) changes its structure upon interaction of AChE with diisopropylphosphorofluoridate (DFP). Reversible dissociation measurements suggest that the free energy (F) penalty for the loop displacement is ΔF=Ffree − Fbound ~ −4 kcal/mol. Therefore, this loop has been the target of two studies by Olson’s group for testing the efficiency of procedures for calculating F. In this paper we test for the first time the performance of our “hypothetical scanning molecular dynamics” (HSMD) method and the validity of the related modeling for a loop with bulky sidechains in explicit water. Thus, we consider only atoms of the protein that are the closest to the loop (they constitute the “template”) where the rest of the atoms are ignored. The template’s atoms are fixed in the x-ray coordinates of the free protein, and the loop is capped with a sphere of TIP3P water molecules; also, the x-ray structure of the bound loop is attached to the free template. We carry out two separate MD simulations starting from the free and bound x-ray structures, where only the atoms of the loop and waters are allowed to move while the template-water and template-loop (AMBER) interactions are considered. The absolute Ffree and Fbound (of the loop and water) are calculated from the corresponding trajectories. A main objective of this paper is to assess the reliability of this model and for that several template sizes are studied capped with 80–220 water molecules. We find that consistent results for the free energy (which also agree with the experimental data above) require a template larger than a minimal size...

Template-based and free modeling by RAPTOR++ in CASP8

Xu, Jinbo; Peng, Jian; Zhao, Feng
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em //2009 EN
Relevância na Pesquisa
26.32%
We developed and tested RAPTOR++ in CASP8 for protein structure prediction. RAPTOR++ contains four modules: threading, model quality assessment, multiple protein alignment and template-free modeling. RAPTOR++ first threads a target protein to all the templates using three methods and then predicts the quality of the 3D model implied by each alignment using a model quality assessment method. Based upon the predicted quality, RAPTOR++ employs different strategies as follows. If multiple alignments have good quality, RAPTOR++ builds a multiple protein alignment between the target and top templates and then generates a 3D model using MODELLER. If all the alignments have very low quality, RAPTOR++ uses template-free modeling. Otherwise, RAPTOR++ submits a threading-generated 3D model with the best quality. RAPTOR++ was not ready for the first 1/3 targets and was under development during the whole CASP8 season. The template-based and template-free modeling modules in RAPTOR++ are not closely integrated. We are using our template-free modeling technique to refine template-based models.

Interaction of Escherichia coli RNA Polymerase σ70 Subunit with Promoter Elements in the Context of Free σ70, RNA Polymerase Holoenzyme, and the β′-σ70 Complex*

Mekler, Vladimir; Pavlova, Olga; Severinov, Konstantin
Fonte: American Society for Biochemistry and Molecular Biology Publicador: American Society for Biochemistry and Molecular Biology
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
26.2%
Promoter recognition by RNA polymerase is a key point in gene expression and a target of regulation. Bacterial RNA polymerase binds promoters in the form of the holoenzyme, with the σ specificity subunit being primarily responsible for promoter recognition. Free σ, however, does not recognize promoter DNA, and it has been proposed that the intrinsic DNA binding ability is masked in free σ but becomes unmasked in the holoenzyme. Here, we use a newly developed fluorescent assay to quantitatively study the interactions of free σ70 from Escherichia coli, the β′-σ complex, and the σ70 RNA polymerase (RNAP) holoenzyme with non-template strand of the open promoter complex transcription bubble in the context of model non-template oligonucleotides and fork junction templates. We show that σ70, free or in the context of the holoenzyme, recognizes the −10 promoter element with the same efficiency and specificity. The result implies that there is no need to invoke a conformational change in σ for recognition of the −10 element in the single-stranded form. In the holoenzyme, weak but specific interactions of σ are increased by contacts with DNA downstream of the −10 element. We further show that region 1 of σ70 is required for stronger interaction with non-template oligonucleotides in the holoenzyme but not in free σ. Finally...

Sliding over the Blocks in Enzyme-Free RNA Copying – One-Pot Primer Extension in Ice

Löffler, Philipp M. G.; Groen, Joost; Dörr, Mark; Monnard, Pierre-Alain
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 18/09/2013 EN
Relevância na Pesquisa
36.13%
Template-directed polymerization of RNA in the absence of enzymes is the basis for an information transfer in the ‘RNA-world’ hypothesis and in novel nucleic acid based technology. Previous investigations established that only cytidine rich strands are efficient templates in bulk aqueous solutions while a few specific sequences completely block the extension of hybridized primers. We show that a eutectic water/ice system can support Pb2+/Mg2+-ion catalyzed extension of a primer across such sequences, i.e. AA, AU and AG, in a one-pot synthesis. Using mixtures of imidazole activated nucleotide 5′-monophosphates, the two first “blocking” residues could be passed during template-directed polymerization, i.e., formation of triply extended products containing a high fraction of faithful copies was demonstrated. Across the AG sequence, a mismatch sequence was formed in similar amounts to the correct product due to U·G wobble pairing. Thus, the template-directed extension occurs both across pyrimidine and purine rich sequences and insertions of pyrimidines did not inhibit the subsequent insertions. Products were mainly formed with 2′-5′-phosphodiester linkages, however, the abundance of 3′–5′-linkages was higher than previously reported for pyrimidine insertions. When enzyme-free...

The Yeast Shu Complex Utilizes Homologous Recombination Machinery for Error-free Lesion Bypass via Physical Interaction with a Rad51 Paralogue

Xu, Xin; Ball, Lindsay; Chen, Wangyang; Tian, Xuelei; Lambrecht, Amanda; Hanna, Michelle; Xiao, Wei
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 05/12/2013 EN
Relevância na Pesquisa
26.18%
DNA-damage tolerance (DDT) is defined as a mechanism by which eukaryotic cells resume DNA synthesis to fill the single-stranded DNA gaps left by replication-blocking lesions. Eukaryotic cells employ two different means of DDT, namely translesion DNA synthesis (TLS) and template switching, both of which are coordinately regulated through sequential ubiquitination of PCNA at the K164 residue. In the budding yeast Saccharomyces cerevisiae, the same PCNA-K164 residue can also be sumoylated, which recruits the Srs2 helicase to prevent undesired homologous recombination (HR). While the mediation of TLS by PCNA monoubiquitination has been extensively characterized, the method by which K63-linked PCNA polyubiquitination leads to template switching remains unclear. We recently identified a yeast heterotetrameric Shu complex that couples error-free DDT to HR as a critical step of template switching. Here we report that the Csm2 subunit of Shu physically interacts with Rad55, an accessory protein involved in HR. Rad55 and Rad57 are Rad51 paralogues and form a heterodimer to promote Rad51-ssDNA filament formation by antagonizing Srs2 activity. Although Rad55-Rad57 and Shu function in the same pathway and both act to inhibit Srs2 activity, Shu appears to be dedicated to error-free DDT while the Rad55-Rad57 complex is also involved in double-strand break repair. This study reveals the detailed steps of error-free lesion bypass and also brings to light an intrinsic interplay between error-free DDT and Srs2-mediated inhibition of HR.

Evaluating template-based and template-free protein–protein complex structure prediction

Vreven, Thom; Hwang, Howook; Pierce, Brian G.; Weng, Zhiping
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
26.24%
We compared the performance of template-free (docking) and template-based methods for the prediction of protein–protein complex structures. We found similar performance for a template-based method based on threading (COTH) and another template-based method based on structural alignment (PRISM). The template-based methods showed similar performance to a docking method (ZDOCK) when the latter was allowed one prediction for each complex, but when the same number of predictions was allowed for each method, the docking approach outperformed template-based approaches. We identified strengths and weaknesses in each method. Template-based approaches were better able to handle complexes that involved conformational changes upon binding. Furthermore, the threading-based and docking methods were better than the structural-alignment-based method for enzyme–inhibitor complex prediction. Finally, we show that the near-native (correct) predictions were generally not shared by the various approaches, suggesting that integrating their results could be the superior strategy.

The strength of the template effect attracting nucleotides to naked DNA

Kervio, Eric; Claasen, Birgit; Steiner, Ulrich E.; Richert, Clemens
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
26.22%
The transmission of genetic information relies on Watson–Crick base pairing between nucleoside phosphates and template bases in template–primer complexes. Enzyme-free primer extension is the purest form of the transmission process, without any chaperon-like effect of polymerases. This simple form of copying of sequences is intimately linked to the origin of life and provides new opportunities for reading genetic information. Here, we report the dissociation constants for complexes between (deoxy)nucleotides and template–primer complexes, as determined by nuclear magnetic resonance and the inhibitory effect of unactivated nucleotides on enzyme-free primer extension. Depending on the sequence context, Kd′s range from 280 mM for thymidine monophosphate binding to a terminal adenine of a hairpin to 2 mM for a deoxyguanosine monophosphate binding in the interior of a sequence with a neighboring strand. Combined with rate constants for the chemical step of extension and hydrolytic inactivation, our quantitative theory explains why some enzyme-free copying reactions are incomplete while others are not. For example, for GMP binding to ribonucleic acid, inhibition is a significant factor in low-yielding reactions, whereas for amino-terminal DNA hydrolysis of monomers is critical. Our results thus provide a quantitative basis for enzyme-free copying.

Modularity of Protein Folds as a Tool for Template-Free Modeling of Structures

Vallat, Brinda; Madrid-Aliste, Carlos; Fiser, Andras
Fonte: Public Library of Science Publicador: Public Library of Science
Tipo: Artigo de Revista Científica
Publicado em 07/08/2015 EN
Relevância na Pesquisa
26.18%
Predicting the three-dimensional structure of proteins from their amino acid sequences remains a challenging problem in molecular biology. While the current structural coverage of proteins is almost exclusively provided by template-based techniques, the modeling of the rest of the protein sequences increasingly require template-free methods. However, template-free modeling methods are much less reliable and are usually applicable for smaller proteins, leaving much space for improvement. We present here a novel computational method that uses a library of supersecondary structure fragments, known as Smotifs, to model protein structures. The library of Smotifs has saturated over time, providing a theoretical foundation for efficient modeling. The method relies on weak sequence signals from remotely related protein structures to create a library of Smotif fragments specific to the target protein sequence. This Smotif library is exploited in a fragment assembly protocol to sample decoys, which are assessed by a composite scoring function. Since the Smotif fragments are larger in size compared to the ones used in other fragment-based methods, the proposed modeling algorithm, SmotifTF, can employ an exhaustive sampling during decoy assembly. SmotifTF successfully predicts the overall fold of the target proteins in about 50% of the test cases and performs competitively when compared to other state of the art prediction methods...

Avaliação da síntese e caracterização de zeólita ZSM-5 ausente de direcionador orgânico estrutural

Caldeira, Vinícius Patrício da Silva
Fonte: Universidade Federal do Rio Grande do Norte; BR; UFRN; Programa de Pós-Graduação em Química; Físico-Química; Química Publicador: Universidade Federal do Rio Grande do Norte; BR; UFRN; Programa de Pós-Graduação em Química; Físico-Química; Química
Tipo: Dissertação Formato: application/pdf
POR
Relevância na Pesquisa
46.22%
The catalytic processes play a vital role in the worldwide economy, a business that handles about US$ 13 billion per year because the value of products depends on the catalytic processes, including petroleum products, chemicals, pharmaceuticals, synthetic rubbers and plastics, among others. The zeolite ZSM-5 is used as catalyst for various reactions in the area petrochemical, petroleum refining and fine chemicals, especially the reactions of cracking, isomerization, alkylation, aromatization of olefins, among others. Many researchers have studied the hydrothermal synthesis of zeolite ZSM-5 free template and they obtained satisfactory results, so this study aims to evaluate the hydrothermal synthesis and the physicochemical properties of ZSM-5 with the presence and absence of template compared with commercial ZSM-5. The methods for hydrothermal synthesis of zeolite ZSM-5 are of scientific knowledge, providing the chemical composition required for the formation of zeolitic structure in the presence and absence of template. Samples of both zeolites ZSM-5 in protonic form were obtained by heat treatment and ion exchange, according to procedures reported in the literature. The sample of commercial ZSM-5 was acquired by the company Sentex Industrial Ltda. All samples were characterized by XRD...

A new method of reconstructing VHE γ -ray spectra: the Template Background Spectrum; A new method of reconstructing VHE gamma -ray spectra: the Template Background Spectrum

Fernandes, M.V.; Horns, D.; Kosack, K.; Raue, M.; Rowell, G.
Fonte: EDP Sciences Publicador: EDP Sciences
Tipo: Artigo de Revista Científica
Publicado em //2014 EN
Relevância na Pesquisa
26.18%
Context. Very-high-energy (VHE, E > 0.1 TeV) γ-ray emission regions with angular extents comparable to the field-of-view of current imaging air-Cherenkov telescopes (IACT) require additional observations of source-free regions to estimate the background contribution to the energy spectrum. This reduces the effective observation time and deteriorates the sensitivity. Aims. A new method of reconstructing spectra from IACT data without the need of additional observations of source-free regions is developed. Its application is not restricted to any specific IACT or data format. Methods. On the basis of the template background method, which defines the background in air-shower parameter space, a new spectral reconstruction method from IACT data is developed and studied, the Template Background Spectrum (TBS); TBS is tested on published H.E.S.S.  data and H.E.S.S.  results. Results. Good agreement is found between VHE γ-ray spectra reported by the H.E.S.S. collaboration and those re-analysed with TBS. This includes analyses of point-like sources, sources in crowded regions, and of very extended sources down to sources with fluxes of a few percent of the Crab nebula flux and excess-to-background ratios around 0.1. However, the TBS background normalisation introduces new statistical and systematic errors which are accounted for...

Electromechanical properties of engineered lead free potassium sodium niobate based materials; Propriedades electromecânicas de materiais à base de niobato de potássio e sódio

Rafiq, Muhammad Asif
Fonte: Universidade de Aveiro Publicador: Universidade de Aveiro
Tipo: Tese de Doutorado
ENG
Relevância na Pesquisa
35.9%
K0.5Na0.5NbO3 (KNN), is the most promising lead free material for substituting lead zirconate titanate (PZT) which is still the market leader used for sensors and actuators. To make KNN a real competitor, it is necessary to understand and to improve its properties. This goal is pursued in the present work via different approaches aiming to study KNN intrinsic properties and then to identify appropriate strategies like doping and texturing for designing better KNN materials for an intended application. Hence, polycrystalline KNN ceramics (undoped, non-stoichiometric; NST and doped), high-quality KNN single crystals and textured KNN based ceramics were successfully synthesized and characterized in this work. Polycrystalline undoped, non-stoichiometric (NST) and Mn doped KNN ceramics were prepared by conventional ceramic processing. Structure, microstructure and electrical properties were measured. It was observed that the window for mono-phasic compositions was very narrow for both NST ceramics and Mn doped ceramics. For NST ceramics the variation of A/B ratio influenced the polarization (P-E) hysteresis loop and better piezoelectric and dielectric responses could be found for small stoichiometry deviations (A/B = 0.97). Regarding Mn doping...

Interaction of herpes simplex virus type 1 DNA polymerase and the UL42 accessory protein with a model primer template.

Gottlieb, J; Challberg, M D
Fonte: PubMed Publicador: PubMed
Tipo: Artigo de Revista Científica
Publicado em /08/1994 EN
Relevância na Pesquisa
26.2%
Genetic and biochemical studies have shown that the products of the herpes simplex virus type 1 (HSV-1) DNA polymerase (UL30) and UL42 genes are both required for viral DNA replication. A number of studies have previously suggested that these two proteins specifically interact, and more recent studies have confirmed that the viral DNA polymerase from HSV-1-infected cells consists of a heterodimer of the UL30 (Pol; the catalytic subunit) and UL42 polypeptides. A comparison of the catalytic properties of the Pol-UL42 complex with those of the isolated subunits of the enzyme purified from recombinant baculovirus-infected insect cells indicated that the Pol-UL42 complex is more highly processive than Pol alone on singly primed M13 single-stranded substrates. The results of these studies are consistent with the idea that the UL42 polypeptide is an accessory subunit of the HSV-1 DNA polymerase that acts to increase the processivity of polymerization. Preliminary experiments suggested that the increase in processivity was accompanied by an increase in the affinity of the polymerase for the ends of linear duplex DNA. We have further characterized the effect of the UL42 polypeptide on a defined hairpin primer template substrate. Gel shift and filter binding studies show that the affinity of the Pol catalytic subunit for the 3' terminus of the primer template increases 10-fold in the presence of UL42. DNase I footprinting experiments indicate that the Pol catalytic subunit binds to the primer template at a position that protects 14 bp of the 3' duplex region and an adjacent 18 bases of the single-stranded template. The presence of the UL42 polypeptide results in the additional protection of a contiguous 5 to 14 bp in the duplex region but does not affect the 5' position of the Pol subunit. Free UL42 protects the entire duplex region of the substrate but does not bind to the single-stranded region. Taken together...

Towards a free-free template for CMB foregrounds

Dickinson, C.; Davies, R. D.; Davis, R. J.
Fonte: Universidade Cornell Publicador: Universidade Cornell
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.33%
A full-sky template map of the Galactic free-free foreground emission component is increasingly important for high sensitivity CMB experiments. We use the recently published \ha data of both the northern and southern skies as the basis for such a template. The first step is to correct the \ha maps for dust absorption using the 100 $\mu$m dust maps of Schlegel, Finkbeiner & Davis (1998). We show that for a range of longitudes, the Galactic latitude distribution of absorption suggests that it is 33 per cent of the full extragalactic absorption. A reliable absorption-corrected \ha map can be produced for $\sim 95$ per cent of the sky; the area for which a template cannot be recovered is the Galactic plane area $|b| < 5^{\circ}$, $l=260^{\circ}-0^{\circ}-160^{\circ}$ and some isolated dense dust clouds at intermediate latitudes. The second step is to convert the dust-corrected \ha data into a predicted radio surface brightness. The free-free emission formula is revised to give an accurate expression (1 per cent) for the radio emission covering the frequency range 100 MHz to 100 GHz and the electron temperature range 3000 to 20000 K. The main uncertainty when applying this expression is the variation of electron temperature across the sky. The emission formula is verified in several extended H{\sc ii} regions using data in the range 408 to 2326 MHz. A full-sky free-free template map is presented at 30 GHz; the scaling to other frequencies is given. The Haslam et al. all-sky 408 MHz map of the sky can be corrected for this free-free component...

Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation

Qian, Bin; Ortiz, Ángel R.; Baker, David
Fonte: National Academy of Sciences (U.S.) Publicador: National Academy of Sciences (U.S.)
Tipo: Artículo Formato: 586968 bytes; application/pdf
ENG
Relevância na Pesquisa
26.25%
Accurate high-resolution refinement of protein structure models is a formidable challenge because of the delicate balance of forces in the native state, the difficulty in sampling the very large number of alternative tightly packed conformations, and the inaccuracies in current force fields. Indeed, energy-based refinement of comparative models generally leads to degradation rather than improvement in model quality, and, hence, most current comparative modeling procedures omit physically based refinement. However, despite their inaccuracies, current force fields do contain information that is orthogonal to the evolutionary information on which comparative models are based, and, hence, refinement might be able to improve comparative models if the space that is sampled is restricted sufficiently so that false attractors are avoided. Here, we use the principal components of the variation of backbone structures within a homologous family to define a small number of evolutionarily favored sampling directions and show that model quality can be improved by energy-based optimization along these directions. With the progression of structural genomics initiatives (1–3), comparative modeling has become an increasingly important method for building protein structure models (4...