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Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species Nature Precedings
I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn –algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata. Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics & Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012 URL: http://precedings.nature.com/documents/7083/version/1
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An approach able to escape the most common problem during protein Crystallization i.e. formation of salt crystal Nature Precedings
K. Awaneesh Singh; Patrick Celie; G. R. K. Rao; M. V. Jagannatham.
Formation and differentiation of salt crystal is a most common as well as challenging problem during protein crystallography. Although there are some methods used for their differentiation i.e. physical manipulation, birefringence, dye absorption and run a gel but all of them are totally depends on own perception and expertise as well as also require a good crystal (final stage crystal). To escape this problem the screening was done with PACT, JCSG and other automated screens as everyone do. But during optimization the additives/salts were ignored at first and optimization screen was made just based on different buffers and precipitant. After selecting suitable buffer, the type and percentage of precipitant was optimized. We got some ugly crystals and with...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4725/version/1
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Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for Composition Improvements Nature Precedings
I. C. Baianu; Valentin Prisecaru.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions. Conventional “wet chemistry” analytical methods are time-consuming and costly. As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry. Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Genetics & Genomics; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6231/version/1
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Extending the semi-empirical PM6 method for carbon oxyacid pKa prediction to sulfonic acids: Application towards congener-specific estimates for the environmentally and toxicologically relevant C1 through C8 perfluoroalkyl derivatives Nature Precedings
Sierra Rayne; Kaya Forest; Ken J. Friesen.
A positive bias in the semi-empirical PM6 method for estimating pKa values of sulfonic acids was corrected by a correlation developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl, and halogen substituted sulfonic acids. Application of this correction to PM6 values allows for extension of this computational method to a new acid functional group.
Tipo: Manuscript Palavras-chave: Chemistry; Earth & Environment.
Ano: 2009 URL: http://precedings.nature.com/documents/2922/version/1
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Direct fluorophore conjugation to genomic DNA for microarray-based epigenomic profiling Nature Precedings
Vineet Gupta.
A methodology for microarray based epigenomic profiling is presented. The method relies on platinum-based fluorescence labeling reagents for direct (non-enzymatic) labeling of DNA and RNA. This is a work in progress and only preliminary data is presented here.
Tipo: Presentation Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2007 URL: http://precedings.nature.com/documents/444/version/1
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Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods Nature Precedings
Sierra Rayne; Kaya Forest; Ken J. Friesen.
Perfluorinated acids (PFAs) are contaminants detected worldwide in a range of abiotic and biotic environmental matrices. The two major classes of PFAs include the perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), both of which are considered persistent and potentially bioaccumulative. Current research and regulatory efforts are focussed on the straight-chain members of each PFA class and homologue group, primarily because these congeners are the major components of technical mixtures and are also available as pure standards. However, the numerous potential branched congeners in each PFA class represent a poorly understood family of environmental contaminants whose environmental and toxicological properties may be more...
Tipo: Poster Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/1956/version/1
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Dielectric Constant of Water Discovered to be Simple Function of Density over Extreme Ranges from – 35 to + 600^o^C and to 1200 MPa (12000 Atm.), Believed Universal Nature Precedings
William L. Marshall.
The experimental static dielectric constants (_[epsilon]_) of water formulated by Fernández, et al., (1997-International Association for the Properties of Water and Steam, IAPWS), –35 to 600^o^C; 0.1 to 1200 MPa, are discovered to be closely described throughout by a simple equation of density (_[rho]_), presented here, and agreeing with their reported calculated (extrapolated) values to 923^o^C. Eight limiting boundary conditions are observed. Values of _[epsilon]_ follow isothermal straight-line slopes of log (_[epsilon]_ – 1) vs log _[rho]_ down to densities of 0.25 g cm^-3^ water, even in dioxane-water solutions. At lower densities, all slopes curve asymptotically in approaching unity, while becoming unity throughout...
Tipo: Manuscript Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2472/version/1
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Quantification of growth hormone in serum by isotope dilution mass spectrometry Nature Precedings
Cristian Arsene; André Henrion; Nina Diekmann; Jenny Manolopoulou; Martin Bidlingmaier.
Inter-assay variation of antibody based routine tests is hampering comparability of measurement results for growth hormone (GH) between different laboratories and decision making in clinical practice. Here it is demonstrated, that quantification of GH by isotope dilution mass spectrometry (IDMS) constitutes a way to precise and reliable results which can be referred to in evaluation of performance of commercial test kits. With the IDMS method developed, tryptic cleavage products YSFLQNPQTSLCFSESIPTPSNR (T6) and LEDGSPR (T12) of GH are quantified by LC/MS-MS using the isotopically labeled forms of the peptides as internal standards. The GH cleavage fragments are obtained by whole-serum tryptic proteolysis and then extracted from the resulting mixture by...
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2009 URL: http://precedings.nature.com/documents/4050/version/1
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Determination of Isoflavone Contents for Selected Soybean Lines and Soy Foods by Fourier Transform Near Infrared Reflectance Spectroscopy Nature Precedings
I. C. Baianu; Tiefeng You; Randall L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. Rapid and economical determination of soybean isoflavone contents is essential for breeding and selection of soybean seeds with optimal isoflavone levels for food applications. Fourier Transform Near Infrared Spectroscopy (FT-NIR) calibrations were developed for rapid and reliable analysis of soybean isoflavone content. Our isoflavone calibrations are characterized by low standard errors (<0.02%) and high degrees of correlation (>99%).
Tipo: Presentation Palavras-chave: Biotechnology; Chemistry; Genetics & Genomics; Immunology; Plant Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6194/version/1
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Detection systems cross reacting with peptides - Analysis at the amino acid level Nature Precedings
Carsten C. Mahrenholz; Victor Tapia; Rolf Stigler; Rudolf Volkmer.
There are several methods commonly used to measure protein-protein interactions and binding affinities. Quite contrary to most of these methods, protein- and peptide arrays on cellulose membranes or glass slides are suitable for high-throughput measurement, as they provide a higher density of probes and a multitude of peptide-protein interactions can be measured in parallel [1]. The most important application of the SPOT synthesis technique is to simultaneously detect a high number of peptides that have a strong binding affinity to defined targets. The validity of the results, however, depends on the ability of the detection system to indicate binding events whilst not interfering with the experiment itself through cross reaction. We tested three common...
Tipo: Poster Palavras-chave: Biotechnology; Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4448/version/1
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A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics Nature Precedings
I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012 URL: http://precedings.nature.com/documents/7052/version/1
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Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents Nature Precedings
Jean-Claude Bradley; Cameron Neylon; Rajarshi Guha; Antony J. Williams; Bill Hooker; Andrew S. I. D. Lang; Brent Friesen; Tim Bohinski; David Bulger; Matthew Federici; Jenny Hale; Jenna Mancinelli; Khalid B. Mirza; Marshall J. Moritz; Daniel Rein; Cedric Tchakounte; Hai T. Truong.
This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference. The Challenge was sponsored by Submeta, Nature and Sigma-Aldrich.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/4243/version/1
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Preservation of C Hexagons in C Allotrope Transformations Nature Precedings
Michael J. Bucknum; Eduardo A. Castro.
In this Letter is described the analogous hexagon preserving C allotrope transformations of graphite to diamond, as a packing of C spheres on the one hand, and alternatively C nanotubes to the C allotrope hexagonite, as a packing of C cylinders on the other hand.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/6481/version/1
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Cellular delivery of antibodies: effective targeted subcellular imaging and new therapeutic tool Nature Precedings
Marzia Massignani; Irene Canton; Nisa Patikarnmonthon; Nicholas J. Warren; Steven P. Armes; Andrew L. Lewis; Giuseppe Battaglia.
It is already more than a century since the pioneering work of the Nobel Laureate Ehrlich gave birth to the side chain theory1, which helped to define antibodies and their ability to target specific biological sites. However, the use of antibodies is still restricted to the extracellular space due to the lack of a suitable delivery vehicle for the efficient transport of antibodies into live cells without inducing toxicity. In this work, we report the efficient encapsulation and delivery of antibodies into live cells with no significant loss of cell viability or any deleterious affect on the cell metabolic activity. This delivery system is based on poly(2-(methacryloyloxy)ethyl phosphorylcholine)-block-(2-(diisopropylamino)ethyl methacrylate), (PMPC-PDPA),...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Immunology; Pharmacology.
Ano: 2010 URL: http://precedings.nature.com/documents/4427/version/1
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A Bacterial Enzyme Catalyzing Double Reduction of a β,δ-Diketo Ester with Unprecedented Stereoselectivity Nature Precedings
Xuri Wu; Nan Liu; Yunmian He; Yijun Chen.
Various ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in _Escherichia coli_ and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A...
Tipo: Manuscript Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2010 URL: http://precedings.nature.com/documents/1697/version/2
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Ionization effects on the partitioning behavior of food and beverage aroma compounds between aqueous phases and air and organic matrices Nature Precedings
Sierra Rayne; Kaya Forest.
Aroma compounds in the Flavornet database were screened for ionizable functional groups such as carboxylic acids, aliphatic and aromatic amines, phenols, alcohols, and thiols. Of the 738 aroma compounds listed in this database, 101 molecules have ionizable moieties with estimated monomeric aqueous pK~a~ values ranging between 1.75 and 10.97. pH dependent effective air/water partitioning coefficients (K~aw,eff~) and n-octanol/water partitioning coefficients (D~ow~) were estimated for all ionizable aroma compounds over the pH range from 0 to 14. The ionizable aroma compounds display a broad range of K~aw,eff~ (1.8×10^-23^ to 6.1 atm M^-1^) and log D~ow~ (-6.2 to +7.2 units) values. For many aroma compounds, pH dependent ionization will have a...
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2011 URL: http://precedings.nature.com/documents/6269/version/1
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Phytochemical Approach and Bioanalytical Strategy to Develop Chaperone-Based Medications Nature Precedings
Bernd Kastenholz.
Currently, no pharmaceuticals for the etiological treatment of degenerative protein-misfolding diseases (e.g., ALS, Alzheimer’s or prion diseases) are commercially available. Therefore, in this technical note theoretical considerations and practical approaches concerning the development of chaperone-based medications from medicinal plants (e.g., Ginkgo biloba) are reviewed and discussed in detail. Phytochaperones and other agents isolated from medicinal plants are proposed to serve as the general basis of drug development in protein-misfolding diseases.
Tipo: Manuscript Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1431/version/2
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Geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes: A comparative density functional theory study Nature Precedings
Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes were calculated using the B3LYP, B97D, M062X, and PBE0 density functionals with the 6-311++G(d,p) basis set. For both halogen classes and at all levels of theory, the C~3~ compounds adopt a trans conformation analogous to that of perfluoropropane. Similar to their perfluorinated counterparts, the perchlorinated and perbrominated C~4~ through C~6~ n-alkanes are predicted to have helical geometries. In contrast to perfluoroalkyl chains, the central CCCC dihedral angles of the perchlorinated and perbrominated derivatives are expected to decline with increasing chain length.
Tipo: Manuscript Palavras-chave: Chemistry.
Ano: 2010 URL: http://precedings.nature.com/documents/5157/version/1
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Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models Nature Precedings
I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. Łukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable 'next-state functions' is extended to a Łukasiewicz Topos with an n-valued Łukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics & Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6206/version/1
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Determination of adsorptive and diffusive properties of carbon dioxide - methane - water in coal-like structures using molecular simulations Nature Precedings
Alaaeldin Salih; Erich A. Müller.
This work employs molecular modeling to simulate both the equilibrium and kinetic behavior pertaining adsorption/desorption and permeation of carbon dioxide within the enhanced coal bed methane (ECBM) process and the corresponding CO~2~ sequestration processes in deep coal mines. The coal structure is modeled on the basis of a carbon, nanotubes, slit pores and more realistic “virtual” carbons. (from bottom up in the figure) The grand canonical Monte Carlo method is used to simulate the adsorption isotherms and isosteric heats of adsorption of the methane-carbon dioxide-water ternary mixture into the carbon structure, while Molecular Dynamics is applied to the same systems to study the competitive diffusion properties of these fluids...
Tipo: Presentation Palavras-chave: Chemistry; Earth & Environment.
Ano: 2008 URL: http://precedings.nature.com/documents/2625/version/1
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