DNA Antenna Tile‐Associated Deoxyribozyme Sensor with Improved Sensitivity

Some natural enzymes increase the rate of diffusion‐limited reactions by facilitating substrate flow to their active sites. Inspired by this natural phenomenon, we developed a strategy for efficient substrate delivery to a deoxyribozyme (DZ) catalytic sensor. This resulted in a three‐ to fourfold increase in sensitivity and up to a ninefold improvement in the detection limit. The reported strategy can be used to enhance catalytic efficiency of diffusion‐limited enzymes and to improve sensitivity of enzyme‐based biosensors.     

Conductivity and intermolecular interactions in proton‐conducting gel electrolytes

Proton‐conducting gel electrolytes based on poly(methyl methacrylate) (PMMA), poly(vinylidene fluoride) (PVdF), and mixtures of PMMA with PVdF or poly(vinyl chloride) doped by acid solutions in aprotic solvents were synthesized and are discussed in this article. The gel conductivity as a function of the concentrations of acid and polymer and the polymeric matrix composition has been analyzed. Extreme dependence of the conductivity on acid and polymer concentrations was found. It was revealed that within the acid concentration range studied, the gel conductivity was higher than the conductivity of the corresponding liquid electrolytes used for the synthesis. The increase in the electrical conductivity with the growth of the systems viscosity is discussed as an indication of a certain involvement of the polymer matrix in the increase of the charge carrier mobility within the frame of a Grotthuss mechanism. © 2014 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2014 , 131, 40674.     

天然和热变性乳铁蛋白与α-乳白蛋白聚集体的超分子结构表征

本文在pH6.5磷酸盐缓冲溶液中研究了热变性前后牛乳铁蛋白(bovine lactoferrin,LF)和α-乳白蛋白(α-lactalbumin,ALA)之间的自组装行为。采用ζ-电位、浊度法、动态光散射、光学显微镜、荧光光谱和红外色谱等方法进行表征。结果表明,与天然LF和ALA自组装复合物相比,热变性LF和ALA自组装复合物的ζ-电位较低。天然LF与ALA可以自组装可形成纳米颗粒,粒径最大为(35.24±0.82) nm;经过热变性的LF与ALA自组装形成超分子结构,通过调整ALA浓度,可以得到亚微米和微米颗粒,颗粒粒径最大为(4.11±0.14) μm。天然LF与ALA的复合物均为球状聚集体,分布均一;而热变性LF与ALA的复合物则为网状聚集体,分布不均一。ALA的添加增强了LF中色氨酸残基的疏水性。LF中的C=O和C-N基团均参与了与ALA_{25 ℃}的相互作用。本研究为构建新型双蛋白自组装体及理解双蛋白组装机制提供了理论依据。     

The UCSC Kestrel parallel processor

The architectural landscape of high-performance computing stretches from superscalar uniprocessor to explicitly parallel systems, to dedicated hardware implementations of algorithms. Single-purpose hardware can achieve the highest performance and uniprocessors can be the most programmable. Between these extremes, programmable and reconfigurable architectures provide a wide range of choice in flexibility, programmability, computational density, and performance. The UCSC Kestrel parallel processor strives to attain single-purpose performance while maintaining user programmability. Kestrel is a single-instruction stream, multiple-data stream (SIMD) parallel processor with a 512-element linear array of 8-bit processing elements. The system design focuses on efficient high-throughput DNA and protein sequence analysis, but its programmability enables high performance on computational chemistry, image processing, machine learning, and other applications. The Kestrel system has had unexpected longevity in its utility due to a careful design and analysis process. Experience with the system leads to the conclusion that programmable SIMD architectures can excel in both programmability and performance. This work presents the architecture, implementation, applications, and observations of the Kestrel project at the University of California at Santa Cruz.     

Systolic self-organizing lists under transpose

Systolic array architectures for self-organizing linear lists under the transpose update heuristic are presented. The first model has linear delay and restricts input on every other system cycle. The second system combines a systolic array with trees to provide logarithmic delay and input on every clock cycle. These preliminary designs can be the basis of hardware used to achieve high-speed lossless data compression for data communication and storage. On large files (greater than 40 kilobytes), our designs provide better compression than other systolic list compression schemes     

Severe accidents in the energy sector: comparative perspective

This paper addresses one of the controversial issues in the current comparative studies of the environmental and health impacts of energy systems, i.e. the treatment of severe accidents. The work covers technical aspects of severe accidents and thus primarily reflects an engineering perspective on the energy-related risk issues, though some social implications are also touched upon. The assessment concerns fossil energy sources (coal, oil and gas), nuclear power and hydro power. The scope is not limited to the power production (conversion) step of these energy chains but, whenever applicable, also includes exploration, extraction, transports, processing, storage and waste disposal. With the exception of the nuclear chain the focus of the work has been on the evaluation of the historical experience of accidents. The basis used for this evaluation is a comprehensive database ENSAD (Energy-related Severe Accident Database), established by the Paul Scherrer Institut (PSI). For hypothetical nuclear accidents the probabilistic technique has also been employed and extended to cover the assessment of economic consequences of such accidents. The broader picture obtained by coverage of full energy chains leads on the world-wide basis to aggregated immediate fatality rates being much higher for the fossil chains than what one would expect if only power plants were considered. Generally, the immediate fatality rates are for all considered energy carriers significantly higher for the non-OECD countries than for OECD countries. In the case of hydro and nuclear the difference is in fact dramatic. The presentation of results is not limited to the aggregated values specific for each energy chain. Also frequency-consequence curves are provided. They reflect implicitly the ranking based on the aggregated values but include also such information as the observed or predicted chain-specific maximum extents of damages. This perspective on severe accidents may lead to different system rankings, depending on the individual risk aversion.     

Electropolymerized flavin adenine dinucleotide as an advanced NADH transducer

Electropolymerizing the prosthetic group (flavin adenine dinucleotide, FAD) responsible in the active sites of dehydrogenases for NAD(+)|NADH regeneration, we succeeded in mimicking enzyme activity. Poly(FAD) characterized by an additional polymer-type redox reaction has been discovered as a highly effective electrocatalyst for NADH oxidation: operating at the lowest potentials reported for NADH transducers (0.00 V, pH 7.4), poly(FAD) is characterized by the electrochemical rate constant of 1.8 +/- 0.6 x 10(-3) cm s(-1), which is at the level of the NADH mass-transfer constant. Flow injection analysis of NADH with the poly(FAD)-modified wall-jet electrode as a detector has been characterized by a linear calibration range prolonged down to 5 x 10(-7) M and a sensitivity of 0.08 A M(-1) cm(-2), which taking into account the dispersion coefficient ( approximately 3), is at the diffusion-limiting value. In contrast to the low molecular weight mediators able to exhibit similar electrocatalytic properties, poly(FAD)-modified electrodes are characterized by the dramatically improved stability and, thus, can be considered as the most advantageous NADH transducers for analytical chemistry.     

Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology

A compact disk (CD)-based microfluidic method for selective detection of phosphopeptides by mass spectrometry is described. It combines immobilized metal affinity chromatography (IMAC) and enzymatic dephosphorylation. Phosphoproteins are digested with trypsin and processed on the CD using nanoliter scale IMAC with and without subsequent in situ alkaline phosphatase treatment. This is followed by on-CD matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Dephosphorylation of the IMAC-enriched peptides allows selective phosphopeptide detection based on the differential mass maps generated (mass shifts of 80 Da or multiples of 80 Da). The CD contains 96 microstructures, each with a 16 nL IMAC microfluidic column. Movement of liquid is controlled by differential spinning of the disk. Up to 48 samples are distributed onto the CD in two equal sets. One set is for phosphopeptide enrichment only, the other for identical phosphopeptide enrichment but combined with in situ dephosphorylation. Peptides are eluted from the columns directly into MALDI target areas, still on the CD, using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into a MALDI mass spectrometer for analysis down to the femtomole level. The average success rate in phosphopeptide detection is over 90%. Applied to noncharacterized samples, the method identified two novel phosphorylation sites, Thr 735 and Ser 737, in the ligand-binding domain of the human mineralocorticoid receptor.     

Synthetic Peroxides Promote Apoptosis of Cancer Cells by Inhibiting P-Glycoprotein ABCB5

This article discloses a new horizon for the application of peroxides in medical chemistry. Stable cyclic peroxides are demonstrated to have cytotoxic activity against cancer cells; in addition a mechanism of cytotoxic action is proposed. Synthetic bridged 1,2,4,5-tetraoxanes and ozonides were effective against HepG2 cancer cells and some ozonides selectively targeted liver cancer cells (the selectivity indexes for compounds 11 b and 12 a are 8 and 5, respectively). In some cases, tetraoxanes and ozonides were more selective than paclitaxel, artemisinin, and artesunic acid. Annexin V flow-cytometry analysis revealed that the active ozonides 22 a and 23 a induced cell death of HepG2 by apoptosis. Further study showed that compounds 22 a and 23 a exhibited a strong inhibitory effect on P-glycoprotein (P-gp/ABCB5)-overexpressing HepG2 cancer cells. ABCB5 is a key player in the multidrug-resistant phenotype of liver cancer. Peroxides failed to demonstrate a direct correlation between oxidative potential and their biological activity. To our knowledge this is the first time that peroxide diastereoisomers have been found to show stereospecific antimalarial action against the chloroquine-sensitive 3D7 strain of Plasmodium falciparum. Stereoisomeric ozonide 12 b is 11 times more active than stereoisomeric ozonide 12 a (IC₅₀=5.81 vs 65.18 μm ). Current findings mean that ozonides merit further investigation as potential therapeutic agents for drug-resistant hepatocellular carcinoma.     

New Octopus-like Phthalocyanines as Fullerene Receptors: Synthesis and Photophysical Investigation

Octopus-like zinc and magnesium phthalocyaninates bearing eight flexible benzylated diethylene glycol chains were synthesized and their interaction with fullerenes C₆₀ and C₇₀ was investigated by UV-Vis spectrophotometric titration, as well as by steady-state and time-resolved fluorescence spectroscopy in chloroform and toluene media. These measurements revealed a high affinity of receptors for C₆₀ and C₇₀, with selectivity to C₇₀: binding constants for C₇₀ are almost two times higher than for C₆₀. These results are interpreted by means of quantum-chemical calculations using the PM6-DH2 Hamiltonian. The binding constants also depend on both the nature of the metal ion in the receptor and the solvent. It is expected that the obtained molecules and supramolecular complexes can be used for further elaboration of optoelectronic donor-acceptor materials.